gebhart/patrepeval huggingface dataset:
A Novel Homozygous p.R1105X Mutation of the AP4E1 Gene in Twins with Hereditary Spastic Paraplegia and Mycobacterial Disease (2013)

We report identical twins with intellectual disability, progressive spastic paraplegia and short stature, born to a consanguineous family. Intriguingly, both children presented with lymphadenitis caused by the live Bacillus Calmette-Guérin (BCG) vaccine. Two syndromes - hereditary spastic paraplegia (HSP) and mycobacterial disease - thus occurred simultaneously. Whole-exome sequencing (WES) revealed a homozygous nonsense mutation (p.R1105X) of the AP4E1 gene, which was confirmed by Sanger sequencing. The p.R1105X mutation has no effect on AP4E1 mRNA levels, but results in lower levels of AP-4ε protein and of the other components of the AP-4 complex, as shown by western blotting, immunoprecipitation and immunofluorescence. Thus, the C-terminal part of the AP-4ε subunit plays an important role in maintaining the integrity of the AP-4 complex. No abnormalities of the IL-12/IFN-γ axis or oxidative burst pathways were identified. In conclusion, we identified twins with autosomal recessive AP-4 deficiency associated with HSP and mycobacterial disease, suggesting that AP-4 may play important role in the neurological and immunological systems.
Polymyxin Induces Significant Transcriptomic Perturbations of Cellular Signalling Networks in Human Lung Epithelial Cells (2022)

Inhaled polymyxins are increasingly used to treat pulmonary infections caused by multidrug-resistant Gram-negative pathogens. We have previously shown that apoptotic pathways, autophagy and oxidative stress are involved in polymyxin-induced toxicity in human lung epithelial cells. In the present study, we employed human lung epithelial cells A549 treated with polymyxin B as a model to elucidate the complex interplay of multiple signalling networks underpinning cellular responses to polymyxin toxicity. Polymyxin B induced toxicity (1.0 mM, 24 h) in A549 cells was assessed by flow cytometry and transcriptomics was performed using microarray. Polymyxin B induced cell death was 19.0 ± 4.2% at 24 h. Differentially expressed genes (DEGs) between the control and polymyxin B treated cells were identified with Student’s t-test. Pathway analysis was conducted with KEGG and Reactome and key hub genes related to polymyxin B induced toxicity were examined using the STRING database. In total we identified 899 DEGs (FDR < 0.01), KEGG and Reactome pathway analyses revealed significantly up-regulated genes related to cell cycle, DNA repair and DNA replication. NF-κB and nucleotide-binding oligomerization domain-like receptor (NOD) signalling pathways were identified as markedly down-regulated genes. Network analysis revealed the top 5 hub genes (i.e., degree) affected by polymyxin B treatment were PLK1(48), CDK20 (46), CCNA2 (42), BUB1 (40) and BUB1B (37). Overall, perturbations of cell cycle, DNA damage and pro-inflammatory NF-κB and NOD-like receptor signalling pathways play key roles in polymyxin-induced toxicity in human lung epithelial cells. Noting that NOD-like receptor signalling represents a group of key sensors for microorganisms and damage in the lung, understanding the mechanism of polymyxin-induced pulmonary toxicity will facilitate the optimisation of polymyxin inhalation therapy in patients.
Open Nested Transactions: Semantics and Support (2006)

We describe semantics for serializable (safe) open nested transactions. Given these semantics, we then suggest hardware necessary to support them directly. We further consider some useful, but not serializable, applications for open nesting, and their hardware implications. We focus primarily on linear nesting, which we previously argued to be more amenable to hardware support than the general case.
Constraint Effects on Energy Absorption in Unidirectional PMC Tubes (1999)

An investigation was carried out to understand the effect of an external constraint on the failure modes and energy absorption capability of unidirectional polymeric composite (PMG) tubes. The constraint was a steel ring that was tightened on the outside of the tube. This ring could slide during tube crushing. The tightness of the ring was determined using a strain gage positioned on the ring. The effect of the constraint was shown to depend on the initial position of the ring along the tube. The study was performed on fiberglass/polyester tubes and the results showed that the external constraint not only can improve the specific energy absorption of the tubes, but also can reduce significantly the undesired high initial peak loads. A nonlinear finite element approach was used to model the fundamental failure modes that dominate the energy absorption of the tubes with an external constraint. These modes including delamination and longitudinal crack propagation (splitting), were modeled using the finite element code ABAQUS. A user friendly FOR-TRAN subroutine was implemented to the code to incorporate the material failure model for predicting the fiber/matrix failures that occur as crushing is experienced by the tube. The predicted model results compared well with the experimental data for the various crushing stages of the polyester tubes.
New findings regarding the epidemic history and population dynamics of Japan‐indigenous genotype 3 hepatitis E virus inferred by molecular evolution (2011)

Population dynamics of the three lineages shared some common characteristics, but had distinguishing features. The appearance of 3a and 3e lineages coincides with the increase of large-race pig importation from Europe and the USA after 1960. The epidemic phase of 3a and 3b strains from 1960 to 1980 could be related to increased opportunity for HEV infection arising from large-scale pig breeding since 1960. Our observations revealed new findings concerning the close relationship between the epidemic history of Japan-indigenous genotype 3 HEV and the improvement of the Japanese pig industry. Infection control in pig farms should be an effective method of preventing HEV infection in humans.
Speech as a Feedback Modality for Smart Objects. (2009)

Abstract—One part of the vision of ubiquitous computing is the integration of sensing and actuation nodes into everyday objects, clothes worn on the body, and in large numbers into the environment. These augmented environments require novel types of interfaces that provide for naturalistic and adaptive interaction depending on user context. In this paper, we investigate the use of speech synthesis on sensor nodes that may be integrated into smart objects. We evaluate the so-called Wireless Voice Node, a small, wireless sensor node with the ability to generate voice output as a novel feedback modality for applications for ambient intelligence. As an example, we present the design and implementation of a speaking doll integrating this node. Using voice output from the doll we aim at using speech synthesis to improve the playing experience of children. I.
Rare and Emerging Opportunistic Fungal Pathogens: Concern for Resistance beyondCandida albicansandAspergillus fumigatus (2004)

The frequency of invasive mycoses due to opportunistic fungal pathogens has increased significantly over the past two decades ([35][1], [74][2], [83][3], [88][4], [89][5], [101][6], [106][7]). This increase in infections is associated with excessive morbidity and mortality ([33][8], [50][9], [108][
Multiple reaction monitoring profiling as an analytical strategy to investigate lipids in extracellular vesicles (2020)

Extracellular vesicles (EVs) convey information used in cell-to-cell interactions. Lipid analysis of EVs remains challenging because of small sample amounts available. Lipid discovery using traditional mass spectrometry platforms based on liquid chromatography and high mass resolution typically employs milligram sample amounts. We report a simple workflow for lipid profiling of EVs based on multiple reaction monitoring (MRM) profiling that uses microgram amounts of sample. After liquid-liquid extraction, individual EV samples were injected directly into the electrospray ionization (ESI) ion source at low flow rates (10 μl/min) and screened for 197 MRM transitions chosen to be a characteristic of several classes of lipids. This choice was based on a discovery experiment, which applied 1,419 MRMs associated with multiple lipid classes to a representative pooled sample. EVs isolated from 12 samples of human lymphocytes and 16 replicates from six different rat cells lines contained an estimated amount of total lipids of 326 to 805 μg. Samples showed profiles that included phosphatidylcholine (PC), sphingomyelin (SM), cholesteryl ester (CE), and ceramide (Cer) lipids, as well as acylcarnitines. The lipid profiles of human lymphocyte EVs were distinguishable using principal component and cluster analysis in terms of prior antibody and drug exposure. Lipid profiles of rat cell lines EV's were distinguishable by their tissue of origin.
Arctic chemical ozone depletion during the 1994–1995 winter deduced from POAM II satellite observations and the REPROBUS three‐dimensional model (1998)

Chemical ozone depletion during the unusually cold 1994–1995 Arctic winter is quantified using ozone profile measurements from the space‐based Polar Ozone and Aerosol Measurement (POAM II) instrument and the REPROBUS three‐dimensional chemistry transport model. The model is first used to determine the dynamical component of the observed variations, allowing the chemical component to be quantified from the observations. This technique has been previously used to estimate ozone loss from ground‐based total column measurements. In the present study, it has been adapted to the POAM II vertical profile measurements in order to document the vertical evolution of ozone chemical loss throughout the winter both inside and outside the polar vortex. The cumulative ozone loss thus obtained inside the vortex at the end of the winter is found to reach a maximum of 51% (with respect to the REPROBUS dynamics‐only prediction) at the 430 K potential temperature level. The largest ozone depletion rates were observed in late January when record low temperatures were reported, and the vortex was largely displaced towards midlatitudes. The maximum depletion rate was 1.4%/d occurring at the 470 K potential temperature level. Smaller but significant chemical ozone depletion was also found outside the vortex, where cumulative ozone losses of 19% were observed in the lower stratosphere. Finally, comparison of chemical ozone loss inferred from the POAM measurements with that obtained from the REPROBUS model indicates that the model underestimates cumulative ozone loss inside the vortex (by ∼30% in the lower stratosphere).
Effect of Molecular Noise in Diffusion-Based Molecular Communication (2014)

In this paper, we consider the Langevin model for Brownian motion in a fluid medium. As a molecule travels through a fluid medium, its continuous collision with the molecules of the fluid can be considered as a continuous random force acting on the molecule. This force is the source of uncertainty in the position of the molecule and can be treated as a noise. The mathematical model for such noise is proposed in this work. The role of finite life expectancy of molecules and inter-symbol interference is also considered. Closed form expressions for the probability of error and the channel capacity are derived considering a binary communication scheme. Furthermore, our results illustrate the impact of these parameters on the performance of molecular communication techniques.
Collective atomic scattering and motional effects in a dense coherent medium (2016)

We investigate collective emission from coherently driven ultracold (88)Sr atoms. We perform two sets of experiments using a strong and weak transition that are insensitive and sensitive, respectively, to atomic motion at 1 μK. We observe highly directional forward emission with a peak intensity that is enhanced, for the strong transition, by >10(3) compared with that in the transverse direction. This is accompanied by substantial broadening of spectral lines. For the weak transition, the forward enhancement is substantially reduced due to motion. Meanwhile, a density-dependent frequency shift of the weak transition (∼10% of the natural linewidth) is observed. In contrast, this shift is suppressed to <1% of the natural linewidth for the strong transition. Along the transverse direction, we observe strong polarization dependences of the fluorescence intensity and line broadening for both transitions. The measurements are reproduced with a theoretical model treating the atoms as coherent, interacting radiating dipoles.
Small Molecule Inhibition of Ligand-Stimulated RAGE-DIAPH1 Signal Transduction (2016)

The receptor for advanced glycation endproducts (RAGE) binds diverse ligands linked to chronic inflammation and disease. NMR spectroscopy and x-ray crystallization studies of the extracellular domains of RAGE indicate that RAGE ligands bind by distinct charge- and hydrophobicity-dependent mechanisms. The cytoplasmic tail (ct) of RAGE is essential for RAGE ligand-mediated signal transduction and consequent modulation of gene expression and cellular properties. RAGE signaling requires interaction of ctRAGE with the intracellular effector, mammalian diaphanous 1 or DIAPH1. We screened a library of 58,000 small molecules and identified 13 small molecule competitive inhibitors of ctRAGE interaction with DIAPH1. These compounds, which exhibit in vitro and in vivo inhibition of RAGE-dependent molecular processes, present attractive molecular scaffolds for the development of therapeutics against RAGE-mediated diseases, such as those linked to diabetic complications, Alzheimer's disease, and chronic inflammation, and provide support for the feasibility of inhibition of protein-protein interaction (PPI).
Prospects for high fidelity imaging in nonlinear EIT using high performance computing (1999)

Linear image reconstruction in EIT has been widely used in medical and process applications, and nearly all of these have been based on approximately uniform distributions of the electrical conductivity in the object under study. Successful applications in medicine have been reported although the markedly non-uniform conductivity distribution in the human body, which is not known a priori, means that artefacts produced by the linear imaging approximation are difficult to exclude. It is important therefore to pursue the full nonlinear problem in order to provide a firm basis for subsequent linear treatments; we have already shown that effective nonlinear EIT can be achieved when appropriate choices are made to constrain the form of the images sought [Blott et al 1998]. In this paper we explore the image resolutions potentially achievable with the availability of improved signal-to-noise in the data. The advent of modern high performance computing allows the production of accurate reference images in practicable time scales, and these can then be used as the basis of high fidelity linear imaging systems in real-time applications. In addition, it becomes feasible to tackle the full 3-d problem.
Use of Ground Penetrating Radar for Accurate Concrete Thickness Measurements (2008)

Ground Penetrating Radar (GPR) is commonly used for locating abnormalities or as a means of quality control in buildings and infrastructures. The objective of this project is to accurately detect the thickness of concrete pavement sections and to minimize the need for core samples using GPR. The project is sponsored by the Nebraska Department of Roads and several project sites in Nebraska are utilized for case studies. Through the use of the SIR-3000 GPR equipment and a 1500 MHz antenna, several pavement sections are scanned, validation cores are taken, and accuracy is evaluated. Laboratory and field experiments are also utilized to develop practical and inexpensive means to increase the accuracy of the GPR scans and further the confidence in the use of the system by professionals. Through the use of a strong reflection material placed at the bottom of the pavement, the thickness of the pavement may be determined accurately. With fewer core samples and a strong ground reflection at the bottom of the concrete, the GPR data can be calibrated for variances in concrete mixture, water content, and ground conditions. The study is still ongoing; however, the preliminary results show that with the use of inexpensive construction adjustments, such as use of a high reflection metal at the bottom of a concrete section, an accurate thickness measurement can be gathered without as many destructive core samples.
Creating Decoherence-Free Subspaces Using Strong and Fast Pulses (2002)

A decoherence-free subspace (DFS) isolates quantum information from deleterious environmental interactions. We give explicit sequences of strong and fast ["bang-bang" (BB)] pulses that create the conditions allowing for the existence of DFSs that support scalable, universal quantum computation. One such example is the creation of the conditions for collective decoherence, wherein all system particles are coupled in an identical manner to their environment. The BB pulses needed for this are generated using only the Heisenberg exchange interaction. In conjunction with previous results, this shows that Heisenberg exchange is by itself an enabler of universal fault-tolerant quantum computation on DFSs.
Avalanche Behavior in the Dynamics of Chemical Reactions (2001)

Sudden bursts of chemical activity, displaying avalanche-like behavior, have been observed in reactions between metals and liquid electrolytes by measuring the time-dependent chemomagnetic fields with a high-T(c) SQUID. The observed intermittent chemomagnetic field pulses exhibit power-law behavior in the distributions of peak sizes, noise spectra, and return-time distributions. Such power-law behavior provides evidence for self-organized criticality occurring in the form of "chemical avalanches" over a wide range of size and time scales.
Demonstration of minute continuous-wave triggered supercontinuum generation at 1 μm for high-speed biophotonic applications (2012)

Ultra-broadband supercontinuum (SC) at 1-&mu;m wavelength is regarded as diagnostics window in bio-photonics due to its large penetration depth in tissues and less Rayleigh scattering. Dispersive Fourier transform (DFT) is an important technique to realize the high-speed, ultra-fast and high-throughput spectroscopy. Thus, a stable light source with good temporal stability plays an important role in the bio-imaging and spectroscopy applications. We here demonstrate stabilized and enhanced SC generation at 1 &mu;m by a minute continuous-wave (CW) triggering scheme. By introducing a weak CW (~200,000 times weaker than the pump), a significant broadening in the SC bandwidth and an improvement in the temporal stability can be obtained. Over 8 dB gain is achieved in both blue and red edges and the SC spectrum can span from 900 nm to over 1300 nm with the CW trigger. We present the CW-triggered SC capability of enabling highspeed spectroscopy based on DFT at 1 &mu;m. In regards to the performance of DFT, the wavelength-time mapping fluctuation reduced by 50% which is an indication of the improvement of the temporal stability. This triggering scheme allows, for the first time, 1-&mu;m DFT at a spectral acquisition rate of 20 MHz with good temporal stability - paving the way toward realizing practical real-time, ultrafast biomedical spectroscopy and imaging.
Usefulness of the Twinkling Artifact in Identifying Implanted Mesh After Inguinal Hernia Repair (2011)

Standard gray scale imaging alone is not reliable when identifying inguinal mesh. The twinkling artifact was present in 79% of inguinal regions with mesh when evaluated with a low-frequency curvilinear array transducer.
Pancreatic β-Cell Failure and Diabetes in Mice With a Deletion Mutation of the Endoplasmic Reticulum Molecular Chaperone Gene P58IPK (2005)

The endoplasmic reticulum (ER) transmits apoptotic signals in the pancreas during ER stress, implicating ER stress-mediated apoptosis in the development of diabetes. P58(IPK) (DNAJC3) is induced during ER stress and functions as a negative feedback component to inhibit eIF-2alpha signaling and attenuate the later phases of the ER stress response. To gain insight into a more comprehensive role of P58(IPK) function, we generated deletion mutant mice that showed a gradual onset of glucosuria and hyperglycemia associated with increasing apoptosis of pancreatic islet cells. Lack of P58(IPK) had no apparent effect on the functional integrity of viable beta-cells. A set of genes associated with apoptosis showed altered expression in pancreatic islets from P58(IPK)-null mice, further substantiating the apoptosis phenotype. The data provide in vivo evidence to support the concept that P58(IPK) functions as a signal for the downregulation of ER-associated proteins involved in the initial ER stress response, thus preventing excessive cell loss by degradation pathways. Insulin deficiency associated with the absence of P58(IPK) mimics beta-cell failure associated with type 1 and late-stage type 2 diabetes. P58(IPK) function and activity may therefore provide a novel area of investigation into ER-mediated mechanistic and therapeutic approaches for diabetes.
Significance of the non-oxidative route of the pentose phosphate pathway for supplying carbon to the purine-nucleotide pathway in Corynebacterium ammoniagenes (2003)

To evaluate the strategy of supplying ribose 5-phosphate to the purine-nucleotide pathway exclusively via the nonoxidative route, the glucose 6-phosphate dehydrogenase gene zwf was disrupted in inosine- and 5'-xanthylic acid-producers of Corynebacterium ammoniagenes. In both producers, interruption of the oxidative route caused a decrease in production yields of about 50%. Attempts to increase the capacity of the nonoxidative route through overexpression of the transketolase or transaldolase gene in the zwf mutants led to no discernable effects on production, indicating that, in C. ammoniagenes, the nonoxidative route alone cannot provide sufficient ribose 5-phosphate for high-level production, although nonoxidative synthesis of the precursor is possible.
Immobilized cellulose nanospheres in lateral flow immunoassay enable rapid nucleocapsid antigen-based diagnosis of SARS-CoV-2 from salivary samples (2021)

Rapid and efficient diagnostic systems are essential in controlling the spread of viral pathogens and efficient patient management. The available technologies for low-cost viral antigen testing have several limitations, including lack of accuracy and sensitivity. Here, we develop sensitive antigen tests based on recently introduced, oppositely charged cellulose II nanoparticles (NPan and NPcat) that are effective in controlling surface protein interactions. Passivation against non-specific adsorption and augmented immobilization of sensing antibodies are achieved by adjusting the electrostatic charge of the nanoparticles. The interactions affecting the performance of the system are investigated by microgravimetry and confocal imaging. We further demonstrate SARS-CoV-2 nucleocapsid rapid sensing by saliva-wicking channels stencil-printed on flexible paper supports. Therein, NPcat inkjet printed on the channels elicit distinctive optical signals, visible after only a few minutes, allowing faster diagnosis compared to current microfluidic devices designed for saliva sampling.
The association between serum sex steroid hormone concentrations and intraprostatic inflammation in men without prostate cancer and irrespective of clinical indication for biopsy in the placebo arm of the Prostate Cancer Prevention Trial (2020)

In this first study in men without prostate cancer and irrespective of clinical indication for biopsy, contrary to the hypothesis, circulating estrogens appeared to be inversely associated, especially in heavy men, whereas androgens appeared to be positively associated with intraprostatic inflammation.