gebhart/patrepeval huggingface dataset:
c-Abl is required for development and optimal cell proliferation in the context of p53 deficiency (2000)

The c-Abl tyrosine kinase and the p53 tumor suppressor protein interact functionally and biochemically in cellular genotoxic stress response pathways and are implicated as downstream mediators of ATM (ataxia-telangiectasia mutated). This fact led us to study genetic interactions in vivo between c-Abl and p53 by examining the phenotype of mice and cells deficient in both proteins. c-Abl-null mice show high neonatal mortality and decreased B lymphocytes, whereas p53-null mice are prone to tumor development. Surprisingly, mice doubly deficient in both c-Abl and p53 are not viable, suggesting that c-Abl and p53 together contribute to an essential function required for normal development. Fibroblasts lacking both c-Abl and p53 were similar to fibroblasts deficient in p53 alone, showing loss of the G(1)/S cell-cycle checkpoint and similar clonogenic survival after ionizing radiation. Fibroblasts deficient in both c-Abl and p53 show reduced growth in culture, as manifested by reduction in the rate of proliferation, saturation density, and colony formation, compared with fibroblasts lacking p53 alone. This defect could be restored by reconstitution of c-Abl expression. Taken together, these results indicate that the ATM phenotype cannot be explained solely by loss of c-Abl and p53 and that c-Abl contributes to enhanced proliferation of p53-deficient cells. Inhibition of c-Abl function may be a therapeutic strategy to target p53-deficient cells selectively.
Cases (2018)

Chapter 3 introduces the use of mathematical models and modeling practices in contemporary biological and cognitive sciences. The familiar Lotka–Volterra model of predator–prey relations is used to explain these practices and show how they promote the extensions of predicates, including psychological predicates, into new and often unexpected domains. It presents two models of cognitive capacities that were developed to explain human behavioral data: Ratcliff’s drift-diffusion model of decision-making and Sutton and Barto’s temporal difference model of reinforcement learning. These are now used for fruit flies and neural populations. It also discusses contemporary and ongoing attempts to revise psychological concepts in response to empirical discovery.
Method of producing synthetic pitch (2023)

Embodiments of a method are described for modifying pitches, oils, tars, and binders by using these materials as solvents to extract organic chemicals from coal.
Pirottaea trichostoma (Helotiales), une espèce remarquable et rarement découverte (2012)

Pirottaea trichostoma is described and illustrated after a collection on stems of Knautia dipsacifolia. A taxonomic discussion compares the close genera Pirottaea and Pyrenopeziza
Hydrothermal refining of biomass - an overview and future perspectives (2015)

Biomass is a promising alternative for the production of energy, novel materials, chemicals, and other valuable products. A certain degree of processing is required to achieve those results. Hydrothermal processes offer a unique way to obtain a wide range of biorefinery products. They can be considered as environmentally friendly processes, using solely water at different temperatures as a process medium to convert abundant and inexpensive biomass into products. We provide a short overview on hydrothermal processes that use water in its liquid state, including hot water extraction, pressurized hot water extraction, liquid hot water pretreatment, hydrothermal carbonization, and hydrothermal liquefaction. We also provide examples of current research and realworld findings. We then present a novel hydrothermal biorefinery concept for sequencing these single processes, giving concrete examples of possible raw materials and products. Sequencing gives new possibilities for biorefineries to exploit all the biomass components as valuable products with zero losses. The added value comes from the increased efficiency of the bio-based products’ value chain, by reducing losses and generating higher-value products and services.
The Case for Robotic Wireless Networks (2016)

This paper explores the possibility of injecting mobility into wireless network infrastructure. We envision WiFi access points on wheels that move to optimize user performance. Movements need not be all around the floor, neither do they have to operate on batteries. As a first step, WiFi APs at home could remain tethered to power and Ethernet outlets while moving in small areas (perhaps under the couch). If such systems prove successful, perhaps future buildings and cities could offer explicit support for network infrastructure mobility. This paper begins with a higher level discussion of robotic wireless networks -- the opportunities and the hurdles -- and then pivots by developing a smaller slice of the vision through a system called iMob. With iMob, a WiFi AP is mounted on a Roomba robot and made to periodically move within a 2x2 sqft region. The core research questions pertain to finding the best location to move to, such that the SNRs from its clients are strong, and the interferences from other APs are weak. Our measurements show that the richness of wireless multipath offers significant opportunities -- even within a 2x2 sqft region, locations exist that are 1.7x better than the average location in terms of throughput. When multiple APs in a neighborhood coordinate, the gains can be even higher. In sum, although infrastructure mobility has been discussed in the context of Google Balloons, ad hoc networks, and delay tolerant networks, we believe that the possibility of moving our personal devices in homes and offices is relatively unexplored, and could open doors to new kinds of innovation.
Ultrasonic wave propagation in powders (2018)

Powder clumps (cakes) has a significant effect on the flowability and stability of powders. Powder caking is mainly caused by moisture migration due to wetting and environmental (temperature and humidity) changes. The process of moisture migration caking involves creating liquid bridges between the particles during condensation which subsequently harden to form solid bridges. Therefore, an effective and reliable technique is required to quantitatively and non-invasively monitor caking kinetics and effective stiffness. This paper describes two ultrasonic instruments (ultrasonic velocity pulse and airborne ultrasound systems) that have been used to monitor the caking phenomenon. Also, it discusses the relationship between the ultrasonic velocity and attenuation measurements and tracking caking kinetics and the effective stiffness of powders.
White-light solitons (2003)

Optical spatial solitons made from incoherent white light were experimentally observed in 1997 by Mitchell and Segev [Nature (London) 387, 880 (1997)]. We present what is believed to be the first theory describing these solitons and find the characteristic features of their spatiotemporal coherence properties and their temporal power spectrum.
Non-cell autonomous OTX2 transcription factor regulates anxiety-related behavior in the mouse (2019)

SUMMARY The Otx2 homeoprotein transcription factor is expressed in the dopaminergic neurons of the ventral tegmental area, a mesencephalic nucleus involved in the control of complex behaviors through its projections to limbic structures, including the ventral hippocampus, amygdala, nucleus accumbens and medial prefrontal cortex. We find adult mice heterozygous for Otx2 show anxiolysis-like phenotype in light-dark box and elevated plus maze paradigms. However, the number of dopaminergic neurons, the integrity of their axons, their projection patterns in target structures, and the amounts of dopamine and dopamine metabolites in targets structures were not modified. Because OTX2 is expressed by the choroid plexus, secreted into cerebrospinal fluid and transferred to parvalbumin interneurons of the cortex, hippocampus, and amygdala, we investigated if this phenotype could result from the decreased synthesis of OTX2 in the choroid plexus. Indeed, the anxiolysis-like phenotype was partially recapitulated in the Otx2 +/ AA and scFvOtx2 tg/0 choroid-plexus dependent non-cell-autonomous OTX2 loss of function mouse models. Furthermore, the phenotype was reversed by the overexpression of Otx2 specifically in choroid plexus of adult Otx2 heterozygous mice. Taken together, OTX2 synthesis by the choroid plexus followed by its secretion into the cerebrospinal fluid is an important regulator of the anxiety phenotype in the mouse.
On generalized adaptive neural filters with application to enhancing EKG signals (2002)

A class of nonlinear adaptive filters called generalized adaptive neural filters (GANFs) developed to generalize stack filters to a larger class of nonlinear filters and to outperform stack filters is discussed. They are based on the theory of stack filters and neural networks. It is shown that GANFs have better noise suppression performance than stack filters. The implementation of GANFs is discussed, and the theoretical analysis in regards to the performance of GANFs on EKG signal processing is also presented. >
Monte Carlo Simulations of Diblock Copolymer Thin Films Confined between Chemically Heterogeneous Hard Surfaces (2000)

Thin films of symmetric diblock copolymers confined between two hard, flat and parallel surfaces have been investigated by means of Monte Carlo simulations on a simple cubic lattice. The upper surface is homogeneous, either neutral or preferential to one of the two blocks, and the lower surface is stripe-patterned, with all the stripes having the same width Ls/2 and alternatively preferring A and B blocks with the same strength of preference. We studied the effects of surface configuration (including surface type, surface pattern period, and surface separation) on the morphology of confined diblock copolymer thin films. Our results show that two conditions are essential for obtaining macroscopically ordered (over micrometers) perpendicular lamellae in the confined films (with film thickness no less than the bulk lamellar period L0): a stripe-patterned substrate with pattern period Ls comparable to L0, which directs the ordering of perpendicular lamellae over a macroscopic scale, and a neutral or weakly preferential hard surface on the top of the confined films, which stabilizes the perpendicular lamellae. When the perpendicular lamellae complying with the lower surface pattern form throughout the entire film, undulations of the A−B interfaces in the perpendicular lamellae are observed if the upper surface is not truly neutral, which could have adverse effects for nanolithography.
The Impact of Repeat Biopsies on Infectious Complications in Men with Prostate Cancer on Active Surveillance (2013)

In men with prostate cancer on active surveillance the number of previous prostate biopsies is associated with a significant risk of infectious complications and every previous biopsy increases the risk of infectious complication. Fluoroquinolone resistant and extended spectrum beta-lactamase producing isolates represent the most commonly identified organisms. Men with prostate cancer on active surveillance should be informed of the risks associated with serial repeat prostate biopsies.
Search on the Replay Buffer: Bridging Planning and Reinforcement Learning (2019)

The history of learning for control has been an exciting back and forth between two broad classes of algorithms: planning and reinforcement learning. Planning algorithms effectively reason over long horizons, but assume access to a local policy and distance metric over collision-free paths. Reinforcement learning excels at learning policies and the relative values of states, but fails to plan over long horizons. Despite the successes of each method in various domains, tasks that require reasoning over long horizons with limited feedback and high-dimensional observations remain exceedingly challenging for both planning and reinforcement learning algorithms. Frustratingly, these sorts of tasks are potentially the most useful, as they are simple to design (a human only need to provide an example goal state) and avoid reward shaping, which can bias the agent towards finding a sub-optimal solution. We introduce a general control algorithm that combines the strengths of planning and reinforcement learning to effectively solve these tasks. Our aim is to decompose the task of reaching a distant goal state into a sequence of easier tasks, each of which corresponds to reaching a subgoal. Planning algorithms can automatically find these waypoints, but only if provided with suitable abstractions of the environment -- namely, a graph consisting of nodes and edges. Our main insight is that this graph can be constructed via reinforcement learning, where a goal-conditioned value function provides edge weights, and nodes are taken to be previously seen observations in a replay buffer. Using graph search over our replay buffer, we can automatically generate this sequence of subgoals, even in image-based environments. Our algorithm, search on the replay buffer (SoRB), enables agents to solve sparse reward tasks over one hundred steps, and generalizes substantially better than standard RL algorithms.
Terahertz-frequency mode-locking of monolithic compound-cavity laser diodes (2003)

We present harmonic modelocked operation of a novel design of monolithic compound-cavity semiconductor laser. Modelocking is achieved at a harmonic of the fundamental round-trip frequency with pulse repetition rates from 131 GHz to 2.1 THz.
Targeting and tracing of specific DNA sequences with dTALEs in living cells (2013)

Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.
Self-assembly at metal surfaces (1998)

The recent development of temperature controlled scanning tunneling microscopy opened the door to a fascinating new world on the nanometer scale. The atomic scale information obtained provides unprecedented insight into the kinetics of surface phenomena such as epitaxial growth or chemisorption. In particular, a rich variety of surface structures could be observed, whose morphologies are determined by the self-assembly of the adsorbed particles. Temperature control allows for detailed investigations of the microscopic processes which are at the origin of the self-assembly. Some illustrative examples are discussed, particularly the initial stages in heteroepitaxial growth of metals (Ag, Cu) On fcc Single crystal metal substrates with different symmetry (Pd(110), Pt(111), Ni(100)) with emphasis on the island shapes as well as a novel pattern formation in dissociative adsorption of molecular oxygen on Pt(111).
Response of Plasma Histaminase Activity to Heparin in Normal Subjects and in Patients With Small Cell Carcinoma of the Lung 2 3 (1978)

Plasma histaminase (PH) activity only partially reflected the consistently high activity of histaminase in tumor tissue of patients with small cell carcinoma of the lung (SCC). To determine whether heparin might release histaminase from tumor tissue into the circulation as it does from some normal tissues, we studied the response of PH activity to small doses of heparin in 41 patients with SCC and in 57 normal subjects. In patients with SCC, the initial mean PH activity (2.0 U/m) was not different from that in normal subjects (1.7 U/ml). After heparin administration, the mean PH activity was no different between the 2 groups (patients with SCC, 3.1 U/ml; normal subjects, 3.5 U/ml). In both groups, the higher the initial PH activity, the greater the magnitude of the PH activity response to heparin. This relationship was linear (normal subjects, r = 0.88; patients with SCC, r = 0.91). However, in patients with SCC, the increase in post-heparin PH activity, as related to the basal levels, was significantly less than that in normal subjects (P less than 0.001 by analysis of covariance). The data suggested that heparin did not affect the release of histaminase from tumor tissue into plasma to the same degree as it promoted the enzyme's entry from normal tissue sources. The differences between the groups may enable us to differentiate between selected patients with SCC and normal subjects with borderline high PH activity values.
Basis set dependence of the structure and properties of liquid hydrogen fluoride (1979)

An intermolecular potential function for the hydrogen fluoride dimer has been obtained from ab initio molecular orbital calculations with a minimal basis set (STO-3G). Dimerization energies for 285 orientations of (HF)2 selected using the enery distributed random geometries method were fit to a 12–6–3–1 potential with standard deviations of ∼0.3 kcal/mol. The function was used in a Monte Carlo simulation of liquid hydrogen fluoride at 0 °C. Structural and thermodynamic results are compared with those based on an earlier potential derived from double zeta basis set (6-31G) calculations. The structural predictions are affected by the local density which is too high from the 6-31G potential. Significant improvement is obtained with the STO-3G function. A detailed analysis of the structure of liquid HF is presented including coordination number and energy distribution functions. Each HF monomer has an average of two hydrogen bonded neighbors with an additional five peripheral contacts within 3.6 Å. The hydrogen bonded monomers form winding chains with significantly bent hydrogens bonds in contrast to the linear hydrogen bonds found in the solid and in the gas phase dimer. As in the case for water, it is apparent that reasonable intermolecular potential functions for hydrogen bonded dimers can be obtained from minimal basis set calculations. In the absence of CI level calculations, this appears to be the method of choice.
Rapid 3D in vivo 1H human lung respiratory imaging at 1.5 T using ultra‐fast balanced steady‐state free precession (2016)

Respiratory α-mapping derived from multivolumetric ufSSFP provides insights into functional lung impairment and may serve as a reproducible and normative measure for clinical studies. Magn Reson Med 78:1059-1069, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Factored Semi-Tied Covariance Matrices (2000)

A new form of covariance modelling for Gaussian mixture models and hidden Markov models is presented. This is an extension to an efficient form of covariance modelling used in speech recognition, semi-tied covariance matrices. In the standard form of semi-tied covariance matrices the covariance matrix is decomposed into a highly shared decorrelating transform and a component-specific diagonal covariance matrix. The use of a factored decorrelating transform is presented in this paper. This factoring effectively increases the number of possible transforms without increasing the number of free parameters. Maximum likelihood estimation schemes for all the model parameters are presented including the component /transform assignment, transform and component parameters. This new model form is evaluated on a large vocabulary speech recognition task. It is shown that using this factored form of covariance modelling reduces the word error rate. 1
Reconfigurable-order bandpass filter for frequency agile systems (2010)

This paper presents a tunable bandpass filter with a reconfigurable filter order. The proposed filter consists of an array of tunable resonators with variable inter-resonator coupling structures between adjacent cavities. This allows the frequency selectivity of the filter to be adjusted for the given spectral environment without any geometrical modifications to the filter structure. To demonstrate the concept a 2 × 2 resonator array is fabricated using substrate integrated evanescent-mode cavity resonators at 3.2 GHz. Each resonator has an adjustable frequency response and can be tuned from 2.77 to 3.55 GHz. The filter has two separate signal paths, either through two or four resonators. The reconfigurable inter-resonator coupling is implemented with floating vias inside a coupling iris. The vias are connected using variable capacitors and can be included or excluded from the iris by adjusting the capacitance.
MALDI-TOF mass spectrometry analysis of small molecular weight compounds (under 10 KDa) as biomarkers of rat hearts undergoing arecoline challenge (2013)

This study successfully reports a mass-based method for investigating biomarker candidates with small molecular weight in different types of sample (including serum and tissue). In addition, this reported method is more time-efficient (1 working day) than gel-based proteomics approach (5~7 working days).
Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire (2018)

Abstract Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability of the hexaploid wheat cultivar Chinese Spring reference genome now allows a detailed study of its NLR complement. However, low NLR expression as well as high intra-family sequence homology hinders their accurate gene annotation. Here we developed NLR-Annotator for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. Applying our tool to wheat and combining it with a transcript-validated subset of genes from the reference gene annotation, we characterized the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,540 were confirmed as complete genes. NLRs with integrated domains mostly group in specific sub-clades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts), which may be tissue-specific and/or induced by biotic stress. As a case study for applying our tool to the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease resistant varieties.