gebhart/patrepeval huggingface dataset:
Perspectives for Clinical Translation (2018)

Cells are the basis of life and the foundational elements of disease and pathology. The ability to cure chronic disease is the goal of regenerative medicine and cellular therapy. To this end, it is necessary to identify cells that can grow and replace damaged tissue, as well as alter the tissue environment, for effective cellular therapy. The lack of cell survival and differentiation after transplantation in a damaged and inhospitable environment is a major obstacle facing successful translation of cell therapy to the clinic. Improved delivery and survival of stem cells post-transplantation is of utmost importance in order to translate cell therapies into preclinical and clinical therapies. Biomaterials afford protection and directed guidance for the differentiation of transplanted stem cells through physical protection from an inhospitable tissue environment. Moreover, biomaterials can provide biological and pharmaceutical compounds that support cell survival, growth, and differentiation. This chapter discusses the current use of different stem cell types in preclinical and clinical research, with a particular focus on the use of stem cell–biomaterial mixed therapies, which are being explored clinically to enhance vascularization and innervation in damaged tissue.
Induction of Interleukin‐2 Production in CD4+ and CD8+ T‐Cell Subsets after Activation via CD3 and CD2 (1988)

The activation signals necessary for interleukin-2 (IL-2) receptor induction, IL-2 production, and DNA synthesis in resting T cells were investigated. IL-2 receptors were induced after activation via CD2 or CD3 alone, while IL-2 production in both CD4+ and CD8+ T cells required activation via both CD3 and CD2. The sequence of activation signals via CD3 and CD2 was shown to be important since DNA synthesis was induced when the primary activation signal was delivered via CD3, and the CD2 signal within 8 h. In contrast, no DNA synthesis was demonstrated when the primary activation signal was delivered via CD2 and the CD3 signal later. Ciclosporin A (CyA) inhibited T-cell DNA synthesis after activation via CD2 and CD3. The inhibition seemed to be due to the prevention of IL-2 synthesis.
Centralized Multicell Scheduling with Interference Mitigation (2012)

This chapter formulates the network sum-rate maximization problem as a pricing game that is played between base stations (BSs), and presents an iterative solution for the problem based on utility maximization within each cell. The solution obtained by the pricing game is enhanced when a central control unit (CCU) is in charge of resource allocation in the network. The chapter presents a suboptimal scheduling scheme based on pricing and collaboration between the BSs and an interference avoidance scheme combined with uplink scheduling in orthogonal frequency division multiple access (OFDMA) systems. It shows a comparison of results of the pricing games with and without CCU to the results of the suboptimal scheduling schemes with and without BS cooperation. Controlled Vocabulary Terms base stations; frequency division multiaccess; scheduling
Regulation of kynurenine biosynthesis during influenza virus infection (2017)

Influenza A viruses (IAVs) remain serious threats to public health because of the shortage of effective means of control. Developing more effective virus control modalities requires better understanding of virus-host interactions. It has previously been shown that IAV induces the production of kynurenine, which suppresses T-cell responses, enhances pain hypersensitivity and disturbs behaviour in infected animals. However, the regulation of kynurenine biosynthesis during IAV infection remains elusive. Here we showed that IAV infection induced expression of interferons (IFNs), which upregulated production of indoleamine-2,3-dioxygenase (IDO1), which catalysed the kynurenine biosynthesis. Furthermore, IAV attenuated the IDO1 expression and the production of kynurenine through its NS1 protein. Interestingly, inhibition of viral replication prior to IFN induction limited IDO1 expression, while inhibition after did not. Finally, we showed that kynurenine biosynthesis was activated in macrophages in response to other stimuli, such as influenza B virus, herpes simplex virus 1 and 2 as well as bacterial lipopolysaccharides. Thus, the tight regulation of the kynurenine biosynthesis by host cell and, perhaps, pathogen might be a basic signature of a wide range of host-pathogen interactions, which should be taken into account during development of novel antiviral and antibacterial drugs.
In Operando XRD and TXM Study on the Metastable Structure Change of NaNi1/3Fe1/3Mn1/3O2 under Electrochemical Sodium‐Ion Intercalation (2016)

In operando XRD and TXM-XANES approaches demonstrate that structure evolution in NaNi1/3Fe1/3Mn1/3O2 during cycling follows a continuous change, and the formation of a nonequilibrium solid solution phase in the existence of two phases. An O3′ and P3′ monoclinic phase occur, and redox couples of Ni3+/Ni4+ and Fe3+/Fe4+ are mainly responsible in the charge voltage range from 4.0 to 4.3 V. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Tractography-Pathology Correlations in Traumatic Brain Injury: A TRACK-TBI Study (2020)

Abstract Diffusion tractography MRI can infer changes in network connectivity in patients with traumatic brain injury (TBI), but pathological substrates of disconnected tracts have not been well-defined due to a lack of high-resolution imaging with histopathological validation. We developed an ex vivo MRI protocol to analyze tract terminations at 750 μm resolution, followed by histopathologic evaluation of white matter pathology, and applied these methods to a 60-year-old man who died 26 days after TBI. Analysis of 74 cerebral hemispheric white matter regions revealed a heterogeneous distribution of tract disruptions. Associated histopathology identified variable white matter injury with patchy deposition of amyloid precursor protein and loss of neurofilament-positive axonal processes, myelin dissolution, astrogliosis, microgliosis, and perivascular hemosiderin-laden macrophages. Multiple linear regression revealed that tract disruption strongly correlated with neurofilament loss. Ex vivo diffusion MRI can detect tract disruptions in the human brain that reflect axonal injury.
Rheological and thermogravimetric studies of the crosslinking process of functionalized acrylic latexes (2005)

Abstract Acrylic latexes are among one of the most widely used binders in the chemical bonding of textile nonwovens. This article investigates the crosslinking process of functionalized acrylic latices to understand the binder behavior during the processing of nonwovens and in the final product. Two techniques are used: rheology, to follow the structural development within the latex polymer, and thermogravimetry, to investigate the reaction through the weight loss resulting from the formation of evolving side products. The work has been carried out on latices functionalized by two crosslinking agents: N ‐methylol acrylamide (NMA) and N ‐methylol methacrylamide (NMMA). The results highlight the importance of the nature of the crosslinking agent, especially, its hydrophilic character, and the influence of the pH of the latex dispersions on the crosslinking mechanism, as well as on the final mechanical properties of the latex films. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1117–1123, 2006
Fluorescence Microscopy of Nanochannel-Confined DNA (2011)

Stretching of DNA in nanoscale confinement allows for direct visualization of the genetic contents of the DNA on the single DNA molecule level. DNA stretched in nanoscale confinement also allows for studies of DNA-protein interactions and DNA polymer physics in confined environments. This chapter describes the basic steps to fabricate the nanostructures, to perform the experiments, and to analyze the data.
Control of mammalian brain aging by the unfolded protein response (UPR) (2020)

Abstract Aging is the major risk factor for the development of dementia and neurodegenerative disorders, and the aging brain manifests severe deficits in buffering capacity by the proteostasis network. Accordingly, we investigated the significance of the unfolded protein response (UPR), a major signaling pathway that copes with endoplasmic reticulum (ER) stress, to normal mammalian brain aging. Genetic disruption of ER stress sensor IRE1α accelerated cognitive and motor dysfunction during aging. Exogenous bolstering of the UPR by overexpressing an active form of the transcription factor XBP1 restored synaptic and cognitive function in addition to reducing cell senescence. Remarkably, proteomic profiling of hippocampal tissue indicated that XBP1s expression corrected age-related alterations in synaptic function. Collectively, our data demonstrate that strategies to manipulate the UPR sustain healthy brain aging. One Sentence Summary The IRE1/XBP1 pathway dictates when and how brain function declines during aging.
HAL3D: Hierarchical Active Learning for Fine-Grained 3D Part Labeling (2023)

We present the first active learning tool for fine-grained 3D part labeling, a problem which challenges even the most advanced deep learning (DL) methods due to the significant structural variations among the small and intricate parts. For the same reason, the necessary data annotation effort is tremendous, motivating approaches to minimize human involvement. Our labeling tool iteratively verifies or modifies part labels predicted by a deep neural network, with human feedback continually improving the network prediction. To effectively reduce human efforts, we develop two novel features in our tool, hierarchical and symmetry-aware active labeling. Our human-in-the-loop approach, coined HAL3D, achieves 100% accuracy (barring human errors) on any test set with pre-defined hierarchical part labels, with 80% time-saving over manual effort.
Molecular assessment of salt-tolerant, perchlorate- and nitrate-reducing microbial cultures (2009)

The microbial ecology of enrichment cultures adapted to the removal of perchlorate and nitrate from high salt solutions and ion-exchange brines was examined over a period of four years using denaturing gradient gel electrophoresis and total DNA extraction with cloning and in each case partial sequencing of the 16S rDNA genes. The cultures studied were a result of enrichment from marine sediment inoculum initiated in 2001. The resulting enrichment cultures were fed perchlorate, or perchlorate and nitrate, in a 3% (w/v) NaCl defined medium or ion-exchange brines (5.6% NaCl) containing perchlorate and nitrate with acetate as the electron donor. All of the sequences' closest matches in the NCBI GenBank database were to marine or salt-tolerant organisms. Strains belonging to the genera Halomonas or Marinobacter were found to dominate in cultures that were fed nitrate in addition to perchlorate, but were effectively absent from cultures fed perchlorate alone. The cultures fed perchlorate as the sole electron acceptor were relatively diverse with the dominant sequences belonging to the genera Dechloromarinus and Denitromonas. A study examining the effects of growing the cultures on different electron acceptors to the cultures revealed that Denitromonas may be more dominant than Dechloromarinus as the salt-tolerant, perchlorate-reducing organism.
Processing and modeling optimization for grayscale lithography (2008)

Grayscale lithography is an extension of the conventional binary lithographic process for realization of arbitrary three-dimensional features in photoresist materials, with applications especially in micro-optics fabrication. The grayscale photomask possesses a spatially varying transmission that modulates the exposure dose received in the photoresist. By using a low contrast photoresist, such as those based on diazonaphthoquinone (DNQ), the material is only partially removed during development in proportion to the local exposure dose received. In this way, an arbitrary surface topography can be sculpted in the photoresist material. It is common practice in grayscale lithography to encode the transmission levels of the photomask by using the photoresist contrast curve to determine the exposure dose required for a given photoresist thickness at each lateral point in the pattern. This technique is adequate when the surface topography is slowly varying and the photoresist film is thin. However, it is inaccurate when these conditions are not met, because the technique essentially represents a one-dimensional approximation to the lithographic process where the isotropy of the development and the diffractive imaging of the photomask are neglected. Currently we are applying grayscale lithography to the fabrication of a fiber-to-waveguide coupler based on the parabolic reflector, where the efficiency of the device is quite sensitive to fabrication errors in the coupler geometry. In this case the thin photoresist and slowly varying topography conditions are not met, and we turn to more comprehensive process models to determine the appropriate transmission levels to encode in the photomask. We demonstrate that the photomask can be optimized, based on simulation of the lithography process, to produce the required three-dimensional photoresist pattern.
An Efficient Minimum-Time Robot Path Planning under Realistic Conditions (1984)

In this paper, we have developed a method for minimum-time path planning in joint space subject to realistic constraints. This method differs from others in that: (i) an absolute path deviation at each corner point of the path can be specified, (ii) local upper bounds on joint accelerations are derived from the arm dynamics so as to nearly fully utilize robot's capabilities, and (iii) a set of Local optimization problems--one at every local corner point--are employed to replace the global minimum-time problem, thus making the minimum-time path planning problem simpler. As a demonstrative example, we have applied the method to the path planning of the first three joints of the Unimation PUMA 600 series manipulator. The example has indeed shown significant improvements in the total traveling time in addition to the computational simplicity obtained from the decomposition of the global problem into a set of local problems.
Construction of the temporal invariants of the time-reversal operator (2009)

This paper proposes a method to construct the temporal Green's function from a scatterer to an array of transducers in a waveguide using free-space back propagation of the eigenvectors of the time-reversal operator (TRO). The monostatic Green's function is obtained as an eigenvector of the TRO which is known with an arbitrary phase; thus the impulse response cannot be obtained by a simple inverse Fourier transform. Assuming that the monochromatic fields obtained by the back propagation of the eigenvectors are in phase at the focal point, the phase correction is determined. Simulations and laboratory experiments are presented.
Using Preformed Meisenheimer Complexes as Dopants for n‐Type Organic Thermoelectrics with High Seebeck Coefficients and Power Factors (2021)

Abstract A pre‐formed Meisenheimer complex of a naphthalenediimide (NDI) with tetrabutylammonium fluoride (TBAF) is obtained in a simple way by mixing dibrominated 4,9‐dibromo‐2,7‐bis(2‐octyldodecyl)benzo[lmn][3,8]phenanthroline‐1,3,6,8(2H,7H)‐tetraone and TBAF in solution and used as a dopant for n‐type organic thermoelectrics. Two n‐type polymers PNDIClTVT and PBDOPVTT are synthesized, n‐doped, and characterized as conductive and thermoelectric materials. PNDIClTVT doped with NDI‐TBAF presents a high σ value of 0.20 S cm –1 , a Seebeck coefficient ( S ) of −1854 µV K –1 , and a power factor (PF) of 67 µW m –1 K –2 , among the highest reported PF in solution‐processed conjugated n‐type polymer thermoelectrics. Using 4‐(1,3‐dimethyl‐2,3‐dihydro‐1H‐benzoimidazol‐2‐yl)phenyl)dimethylamine and NDI‐TBAF as co‐dopants, PNDIClTVT has a PF &gt; 35 µW m –1 K –2 ; while for PBDOPVTT σ = 0.75 S cm –1 and PF = 58 µW m –1 K –2 . In this study it is found that an ionic adduct together with a neutral dopant improves the performance of n‐type organic thermoelectrics leading to an enhanced power factor, and more generally, the role of such an adduct in polymer doping is also elucidated.
Electricity unplugged (2009)

The judge was driving back late one cold winter night. Entering the garage, the battery-charging indicator in his wirelessly powered electric car came on. "Home at last," crossed his mind. He swiped his personal smartcard on the front-door detector to be let in. He heard a "charging" beep from his mobile phone. The blinking cursor on the half-finished e-mail on the laptop had been waiting all day on the side table. He picked the computer up and walked towards his desk. "Good evening, your honour. Your wirelessly heated robe," said the butler-robot as it approached from the kitchen. Putting on the electric garment, he sat on the medical desk chair. His artificial heart was now beating faster.
Antiguiding index profiles in broad strip semiconductor lasers for high-power, single-mode operation (1988)

Solutions to the wave equations for a one-dimensional quadratic variation in the complex refractive index profile are used to calculate gain and field distributions for the lateral modes of broad-stripe semiconductor lasers. It is found that a large difference in gain between the fundamental mode and higher-order modes is obtained in profiles with strong real-index antiguiding and weak imaginary-index guiding. The effect of truncating the quadratic profile is explored. A criterion for comparing the tendency for single-mode operation in different index profiles is introduced and applied to quadratic, step, and array profiles. Based on the analysis, device structures for achieving high-power, single-mode operation are proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Threshold Voltage Shift Due to Charge Trapping in Dielectric-Gated AlGaN/GaN High Electron Mobility Transistors Examined in Au-Free Technology (2013)

We report on the investigation of the charge trapping characteristics of dielectric-gated AlGaN/GaN high electron mobility transistors (HEMTs) with atomic layer deposited HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (Tetrakis-(ethylmethylamino)hafnium and H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O precursors). The impact of process development and tool contamination in an Au-free 200-mm silicon CMOS line is discussed. The interfacial GaO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> layer is proposed to be the primary location of long time constant traps. We examine the impact of these trap states on threshold voltage engineering of the gate stack. Enhancement mode operation of HEMTs is demonstrated, and the stability of enhancement mode is discussed.
Children Experience Cognitive Decline Despite Reversal of Brain Atrophy One Year After Resolution of Cushing Syndrome (2005)

Adults with Cushing syndrome frequently develop brain atrophy, memory impairment, and depression, with partial to complete resolution after cure. The effect of excess glucocorticoid exposure on the brain of children has not been systematically studied. Eleven children (six girls, five boys; ages, 8–16 yr) with endogenous Cushing syndrome seen at the National Institutes of Health Clinical Center from 1999–2000 and 10 healthy age- and sex-matched control subjects were studied. Cognitive and psychological evaluations and magnetic resonance imaging of the brain were done before and 1 yr after cure for patients with Cushing syndrome and once for controls. The estimated duration of Cushing syndrome was 4.4 ± 1.2 yr. When compared with control subjects, children with Cushing syndrome had significantly smaller cerebral volumes (P < 0.001), larger ventricles (P = 0.02), and smaller amygdala (P = 0.004). At baseline, there were no significant differences in IQ between the two groups, and no psychopathology was identified. Despite reversal of cerebral atrophy 1 yr after surgical cure (total cerebral volume, 947 ± 94 vs.1050 ± 74 ml, P < 0.001; ventricular volume, 21.4 ± 12.5 vs. 14.5 ± 11.6 ml, P < 0.001), children with Cushing syndrome experienced a significant (P < 0.05) decline in Wechsler IQ scores (Full Scale, 112 ± 19 vs. 98 ± 14) and a decline in school performance, without any associated psychopathology. The effect of glucocorticoid excess on the brain of children appears to be different from adults. Despite rapid reversibility of cerebral atrophy, children experience a significant decline in cognitive function 1 yr after correction of hypercortisolism.
100 Gb/s challenges and solutions (2008)

The article consists of a Powerpoint presentation on 100 Gb/s optical transport network. The areas discussed include: 100 Gb/s transport formats; transmission system design and trade-offs; IP traffic; parallel wavelength approach; serial transport approach; serial modulation; ETDM OOK transmitter; optical duobinary filtering and modulation; optical equalization; BER performance; polarization-multiplexed DQPSK; coherent optical receiver; optical signal-to-noise ratio; chromatic dispersion tolerance; polarization mode dispersion; nonlinear interactions; electronic and opto-electronic components; WDM NRZ transmission; VSB transmission; Ethernet; and spectral efficiency etc. etc.
Correction: Synthesis, structural characterization, electrochemical behavior and anticancer activity of gold(iii) complexes of meso-1,2-di(1-naphthyl)-1,2-diaminoethane and tetraphenylporphyrin (2020)

Correction for ‘Synthesis, structural characterization, electrochemical behavior and anticancer activity of gold(<sc>iii</sc>) complexes of <italic>meso</italic>-1,2-di(1-naphthyl)-1,2-diaminoethane and tetraphenylporphyrin’ by Muhammad Altaf <italic>et al.</italic>, <italic>New J. Chem.</italic>, 2016, <bold>40</bold>, 8288–8295, DOI: 10.1039/C6NJ00692B.
Neurotrophic factors switch between two signaling pathways that trigger axonal growth (2007)

Integration of multiple inputs from the extracellular environment, such as extracellular matrix molecules and growth factors, is a crucial process for cell function and information processing in multicellular organisms. Here we demonstrate that co-stimulation of dorsal root ganglion neurons with neurotrophic factors (NTFs) - glial-cell-line-derived neurotrophic factor, neurturin or nerve growth factor - and laminin leads to axonal growth that requires activation of Src family kinases (SFKs). A different, SFK-independent signaling pathway evokes axonal growth on laminin in the absence of the NTFs. By contrast, axonal branching is regulated by SFKs both in the presence and in the absence of NGF. We propose and experimentally verify a Boolean model of the signaling network triggered by NTFs and laminin. Our results demonstrate that NTFs provide an environmental cue that triggers a switch between separate pathways in the cell signaling network.