gebhart/patrepeval huggingface dataset:
New insights in wound response and repair of epithelium (2012)

Epithelial wounds usually heal relatively quickly, but repair may be impaired by environmental stressors, such as hypoxic or diabetic states, rendering patients vulnerable to a number of corneal pathologies. Though this response appears simple, at first, years of research have uncovered the complicated biochemical pathways coordinating the wound healing response. Here, we investigate signaling cascades and individual proteins involved in the corneal epithelium's self-repair. We will explore how an epithelial cell migrates across the wound bed and attaches itself to its new post-injury surroundings, including its neighboring cells and the basement membrane, through focal adhesions and hemidesmosomes. We will also discuss how the cell coordinates this motion physiologically, through calcium signaling and protein phosphorylation, focusing on the communication through purinergic, glutamatergic, and growth factor receptors. Many of these aspects reflect and can be extended to similar epithelial surfaces, and can be used to facilitate wound healing in patients with various underlying pathologies. The collective library of laboratory and clinical research done around the world has demonstrated how important precise regulation of these processes is in order for the injured corneal epithelium to properly heal.
Ruxolitinib and Tofacitinib Are Potent and Selective Inhibitors of HIV-1 Replication and Virus Reactivation <i>In Vitro</i> (2014)

The JAK-STAT pathway is activated in both macrophages and lymphocytes upon human immunodeficiency virus type 1 (HIV-1) infection and thus represents an attractive cellular target to achieve HIV suppression and reduced inflammation, which may impact virus sanctuaries. Ruxolitinib and tofacitinib are JAK1/2 inhibitors that are FDA approved for rheumatoid arthritis and myelofibrosis, respectively, but their therapeutic application for treatment of HIV infection was unexplored. Both drugs demonstrated submicromolar inhibition of infection with HIV-1, HIV-2, and a simian-human immunodeficiency virus, RT-SHIV, across primary human or rhesus macaque lymphocytes and macrophages, with no apparent significant cytotoxicity at 2 to 3 logs above the median effective antiviral concentration. Combination of tofacitinib and ruxolitinib increased the efficacy by 53- to 161-fold versus that observed for monotherapy, respectively, and each drug applied alone to primary human lymphocytes displayed similar efficacy against HIV-1 containing various polymerase substitutions. Both drugs inhibited virus replication in lymphocytes stimulated with phytohemagglutinin (PHA) plus interleukin-2 (IL-2), but not PHA alone, and inhibited reactivation of latent HIV-1 at low-micromolar concentrations across the J-Lat T cell latency model and in primary human central memory lymphocytes. Thus, targeted inhibition of JAK provided a selective, potent, and novel mechanism to inhibit HIV-1 replication in lymphocytes and macrophages, replication of drug-resistant HIV-1, and reactivation of latent HIV-1 and has the potential to reset the immunologic milieu in HIV-infected individuals.
Preparation of Bi<sub>2</sub>Sr<sub>2</sub>CaCu<sub>2</sub>O<sub>8-<i>x</i></sub>tracks and thick films by jet printing (2000)

The formation of the 2212 phase material on both silver and magnesium oxide (100) substrates was successfully achieved by the dropwise deposition of solutions of 2212 dissolved in nitric acid or organic acids such as acetic acid or propionic acid using commercial ink-jet printing head using so-called technique `droplet-on-request'. Precursor solutions were prepared by dissolving either a mixture of metal nitrates (Bi(NO3)3·5H2O, Sr(NO3)2, Ca(NO3)2·4H2O and Cu(NO3)2·3H2O) or 2212 superconducting powder in acid solutions. From this initial study using simple solutions on conventional substrates such as polycrystalline silver and large MgO single crystals, the preparation of the textured thick 2212 film for superconducting circuits and interconnections by the ink-jet printing process appears quite promising. The critical temperatures of the selected superconducting coatings were in range of 82-92 K.
A Two-Sided Optimization for Theater Ballistic Missile Defense (2005)

We describe JOINT DEFENDER, a new two-sided optimization model for planning the pre-positioning of defensive missile interceptors to counter an attack threat. In our basic model, a defender pre-positions ballistic missile defense platforms to minimize the worst-case damage an attacker can achieve; we assume that the attacker will be aware of defensive pre-positioning decisions, and that both sides have complete information as to target values, attacking-missile launch sites, weapon system capabilities, etc. Other model variants investigate the value of secrecy by restricting the attacker’s and/or defender’s access to information. For a realistic scenario, we can evaluate a completely transparent exchange in a few minutes on a laptop computer, and can plan near-optimal secret defenses in seconds. JOINT DEFENDER’s mathematical foundation and its computational efficiency complement current missile-defense planning tools that use heuristics or supercomputing. The model can also provide unique insight into the value of secrecy and deception to either side. We demonstrate with two hypothetical North Korean scenarios.
Interactions of deuterium with ion-irradiated SiO2 on Si (1990)

The interactions of deuterium with ion-irradiated SiO2 on Si were investigated during annealing in D2 gas and vacuum over the temperature range 373–1273 K. The uptake and release of D by the oxide layer were monitored using the ion-induced nuclear reaction D(3He,p)4He. Results were analyzed in terms of a new mathematical model which describes the diffusion of atomic D and molecular D2 in conjunction with trapping at irradiation defects via SiD and OD bonding. The combined body of experimental data on release is quantitatively described by the model using fitted binding enthalpies of 2.8 eV for the Si-D interaction and 3.2 eV for the O-D coupling. The model predicts a relationship between the activation barriers for trapping and detrapping which is in semiquantitative agreement with the experimental data on uptake. The same relationship is obeyed by independently reported results on the hydrogen passivation and reactivation of Si-dangling-bond defects at the SiO2-Si interface.
Age-related changes in the content of the C-terminal region of aggrecan in human articular cartilage (1996)

The content of the C-terminal region of aggrecan was investigated in samples of articular cartilage from individuals ranging in age from newborn to 65 years. This region contains the globular G3 domain which is known to be removed from aggrecan in mature cartilage, probably by proteolytic cleavage, but the age-related changes in its abundance in human cartilage have not been described previously. The analysis was performed by immunosorbant assay using an antiserum (JD5) against recombinant amino acid residues of human aggrecan, on crude extracts of cartilage without further purification of aggrecan. The results showed that the content of the C-terminal region decreased with age relative to the G1 domain content (correlation coefficient = 0.463). This represented a 92% fall in the content of this region of the molecule from newborn to 65 years of age. furthermore, when the G1 content of the cartilage extracts was corrected to only include the G1 attached to aggrecan and to exclude the G1 fragments which accumulate as a by-product of normal aggrecan turnover (free G1), the age-related decrease in the C-terminal region remained very pronounced. Analysis by composite agarose/PAGE showed that the number of subpopulations of aggrecan resolved increased from one in newborn to three in adult cartilage. All of these reacted with an antiserum to the human G1 domain, but only the slowest migrating species reacted with the C-terminal region antiserum (JD5). Similar analysis by SDS/PAGE confirmed the presence of high-molecular-mass (200 kDa) proteins reactive with JD5, but no reactive fragments of lower electrophoretic mobility were detected. In contrast, when probed with the antiserum to the human G1 domain, the immunoblots showed protein species corresponding to the free G1 and G1-G2 fragments, which were present at high concentrations in adult cartilage. The results suggest that the loss of the C-terminal region is not directly part of the process of aggrecan turnover, but it is a slow independent matrix process that occurs more extensively with aging as turnover rates become slower. Young cartilage with the fastest turnover contains least molecules lacking the C-terminal region, whereas in old tissue with slow turnover few molecules retain this region. An increase in the cleavage of this region with age may also contribute to this change. The content of the C-terminal region may thus give a measure of the abundance of newly synthesized aggrecan.
Electron-impact ionization time-of-flight mass spectrometer for molecular beams (1987)

A method is described for performing electron-impact ionization time-of-flight mass spectrometry in a molecular beam apparatus. It provides a convenient means for optimizing the performance of pulsed or continuous nozzle sources and can be used in conjunction with laser excitation. Mass spectra are produced either as analog waveforms or in a high repetition rate ion counting mode. The device can also be operated as a fast ionization gauge for time-resolved detection of pulsed beams.
Deacetylation of PS-5, a new .BETA.-lactam compound. II. Separation and purification of L- and D-amino acid acylases from Pseudomonas sp. 1158. (1980)

L-Amino acid acylase and D-amino acid acylase of Pseudomonas sp. 1158 which converted PS-5 to NS-5 (deacetylated PS-5) were separated and purified by sonication, streptomycin and ammonium sulfate fractionations, DEAE-Sephacel column chromatography and gel filtration. Molecular weight and the isoelectric point were estimated to be 75,000 and pI 5.45 for L-amino acid acylase and 100,000 and pI 4.95 for D-amino acid acylase.
REAL-TIME MONITORING OF CYTOMEGALOVIRUS INFECTIONS AFTER STEM CELL TRANSPLANTATION USING THE TaqMan POLYMERASE CHAIN REACTION ASSAYS1 (2000)

The TaqMan assays may potentially serve as a useful tool for rapid quantification of CMV infections in stem cell transplant patients.
Performance Characteristics of Seven Automated CA 125 Assays (2005)

Cancer antigen 125 (CA 125) is a high-molecular-mass glycoprotein that is used as a tumor marker to monitor disease progression and response to therapy and in early detection of recurrence after treatment for ovarian cancer. The Access 2 (Beckman Coulter, Brea, CA), ADVIA Centaur (Bayer Diagnostics, Tarrytown, NY), ARCHITECT i2000 (Abbott Diagnostics, Abbott Park, IL), AxSYM (Abbott Diagnostics), Elecsys 2010 (Roche Diagnostics, Indianapolis, IN), IMMULITE 2000 (Diagnostic Products, Los Angeles, CA), and VITROS ECi (Ortho Clinical Diagnostics, Raritan, NJ) assays for CA 125 were evaluated for detection limit, dilution linearity, imprecision, correlation, and reference intervals. The maximum average deviation from target recoveries for dilution linearity studies ranged from 3.7% for the ADVIA Centaur to 18.2% for the IMMULITE 2000. Imprecision studies yielded total coefficients of variation of 2.0% to 8.3% at CA 125 concentrations of 35 and 114 U/mL (35 and 114 kU/L). Method comparison studies revealed good agreement with the VITROS ECi comparison method, with slopes ranging between 0.88 to 1.19 and correlation coefficients of more than 0.95. All methods show acceptable performance characteristics and generally compare well. However, for some samples, substantial differences exist between methods, necessitating parallel testing when introducing a new method.
Correlation between visual acuity and interface reflectivity measured by pentacam following DSAEK (2013)

We present a measurable correlate for reduced visual outcome following DSAEK despite a clear graft. Inverse correlation between interface reflectivity and best spectacle-corrected visual acuity (BSCVA) indicates that irregularities or scarring in the interface region may influence the optical quality following DSAEK.
MIMO-capacities for COST 259 scenarios (2003)

The capacity of multiple input multiple output (MIMO) communication systems depends on the spatial properties of the MIMO channel. This work shows how in particular partial correlation of channel coefficients affects the capacity of the system. For partially correlated channel coefficients the performance of such systems can be further be enhanced by the use of channel knowledge at the transmitter. Resulting capacity gains are presented for complete and only statistical knowledge of the channel at the transmitter.
Asymptotic Methods in the Theory of Nonlinear Oscillations (1961)

Abstract : This book is devoted to the approximate asymptotic methods of solving the problems in the theory of nonlinear oscillations met in many fields of physics and engineering. It is intended for the wide circle of engineering-technical and scientific workers who are concerned with oscillatory processes. Contents include the following: Natural oscillations in quasi-linear systems; The method of the phase plane; The influence of external periodic forces; The method of the mean; Justification of the asymptotic methods.
A Fully-Integrated 16-Element Phased-Array Receiver in SiGe BiCMOS for 60-GHz Communications (2011)

A fully-integrated 16-element 60-GHz phased-array receiver is implemented in IBM 0.12-μm SiGe BiCMOS technology. The receiver employs RF-path phase-shifting and is designed for multi-Gb/s non-line of sight links in the 60-GHz ISM band (IEEE 802.15.3c and 802.11ad). Each RF front-end includes variable-gain LNAs and phase shifters with each front-end capable of 360° variable phase shift (11.25° phase resolution) from 57 GHz to 66 GHz with coarse/fine gain steps. A detailed analysis of the noise trade-offs in the receiver array design is presented to motivate architectural choices. The hybrid active and passive signal-combining network in the receiver uses a differential cross-coupled Gysel power combiner that reduces combiner loss and area. Each array front-end has 6.8-dB noise figure (at 22°C ) and the array has -10 dB to 58 dB programmable gain from single-input to output. Sixteen 60-GHz aperture-coupled patch-antennas and the RX IC are packaged together in multi-layer organic and LTCC packages. The packaged RX IC is capable of operating in all four IEEE 802.15.3c channels (58.32 to 64.8 GHz). Beam-forming and beam-steering measurements show good performance with 50-ns beam switching time. 5.3-Gb/s OFDM 16-QAM and 4.5 Gb/s SC 16-QAM links are demonstrated using the packaged RX ICs. Both line-of-sight links (~7.8 m spacing) and non-line-of-sight links using reflections (~9 m total path length) have been demonstrated with better than -18 dB EVM. The 16-element receiver consumes 1.8 W and occupies 37.7 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of die area.
A mimetic algorithm for simultaneous multileaf collimator aperture shape and dosimetric optimization in CyberKnife robotic radiosurgery (2015)

A mimetic algorithm for the optimization of multileaf collimator aperture shape and beam weighting is proposed for the CyberKnife M6 delivery platform (Accuray Inc., Sunnyvale, CA). The problem of optimizing a patient-specific treatment plan necessarily requires the determination of the beam geometry, beam-defining aperture shape, and beam weighting. The robotic arm of the CyberKnife moves the linear accelerator through approximately half the solid angle, the multileaf collimator in the head of the accelerator provides for conformal aperture shaping of the radiation, and the linear accelerator generates megavoltage x-rays to irradiate the target. The multileaf collimator leaf positions are optimized, as well as beam weights, by an algorithm consisting of an EA combined with a CMA-ES intense local search. The generation of apertures uses a rule-based approach, based upon dosimetric feedback regarding the radiation dose distribution acquired during each iteration. The purpose of the optimization is to find a Pareto-optimal solution which takes into account the clinical decision-making calculus of the radiation oncologist. The algorithm was tested on CT data set for a patient with carcinoma of the prostate. Twenty algorithm runs were performed; the mean fitness value was 2.48 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> , and the standard deviation was 9.40 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> . In all instances, the algorithm produced clinically acceptable treatment plans, meeting the user-specified dose-volume objectives for the target and critical structures. Note that there is no commercial algorithm currently available for generating these types of treatment plans, so the present work demonstrates feasibility of a novel treatment planning approach.
Review of Multipass Slab Laser Systems (2007)

The multipass slab (MPS) solid-state laser design is a diode-laser, side-pumped configuration that combines high efficiency with high beam quality. Because of a relatively low volumetric thermal loading, the MPS configuration can be used with a wide variety of laser crystals to operate at relatively high powers, and in this paper, we review the MPS lasers based on the materials Nd:YLF, Nd:YVO, Tm:YLF, Er:YLF, Yb:S-FAP, and Cr:LiSAF.
A Computational Drug Repositioning Approach for Targeting Oncogenic Transcription Factors (2016)

Mutations in transcription factor (TF) genes are frequently observed in tumors, often leading to aberrant transcriptional activity. Unfortunately, TFs are often considered undruggable due to the absence of targetable enzymatic activity. To address this problem, we developed CRAFTT, a computational drug-repositioning approach for targeting TF activity. CRAFTT combines ChIP-seq with drug-induced expression profiling to identify small molecules that can specifically perturb TF activity. Application to ENCODE ChIP-seq datasets revealed known drug-TF interactions, and a global drug-protein network analysis supported these predictions. Application of CRAFTT to ERG, a pro-invasive, frequently overexpressed oncogenic TF, predicted that dexamethasone would inhibit ERG activity. Dexamethasone significantly decreased cell invasion and migration in an ERG-dependent manner. Furthermore, analysis of electronic medical record data indicates a protective role for dexamethasone against prostate cancer. Altogether, our method provides a broadly applicable strategy for identifying drugs that specifically modulate TF activity.
Non-operative arterial embolisation in primary liver tumours. (1979)

Three patients with primary hepatic tumours were treated by selective arterial embolisation with gelatin-foam fragments to induce necrosis. In the two with histologically proved hepatocellular carcinoma ultrasonography suggested that necrosis had been induced, as did the rapid initial falls in serum alpha-fetoprotein concentration by 95 and 81% of the original values respectively. Treatment was continued with a course of adriamycin, and both patients remained well and symptom free at 10 and 12 months. In the third patient, who had an expanding and highly vascular benign hepatic adenoma associated with use of a contraceptive pill, embolisation obliterated the tumour mass. Tumour embolisation should be regarded as only the first step in managing hepatocellular carcinoma and as a means of reducing appreciably the viable tumour mass before chemotherapy. It may be used as the primary and definitive treatment in patients with benign liver tumours.
Multiple pathways of capillary permeability. (1977)

Morphological and physiological studies indicate multiple routes for transport across capillary endothelium. However, the identification of the morphological counterparts of specific transport processes (or the assignment of specific transport roles to morphologically identifiable pathways) has been only partly achieved: the contribution of endothelial cell membranes to transport of water and small, lipid-insoluble molecules needs to be evaluated. The identification of the "small pore" pathway for water and lipid-insoluble molecules with the intercellular junctions still remains questionable. The contributions to total macromolecular transport of junctions, single vesicles (pinocytosis, cytopempsis), chains of vesicles, and fenestrae are not yet known.
THE EFFECTS OF LIPID-LOWERING AGENTS ON ACUTE RENAL ALLOGRAFT REJECTION1, 2 (2001)

Lipid-lowering agents may not reduce the incidence of acute renal allograft rejection. However, additional studies are needed to confirm this observation. In the mean time, many if not most renal transplant recipients should be treated with HMG-CoA reductase inhibitors starting early posttransplant to prevent cardiovascular disease complications. The results of this study suggest that starting lipid-lowering therapy immediately after renal transplantation is both safe and effective in lowering total and low density lipoprotein cholesterol.
A critical appraisal of the prevalence and metabolic significance of brown adipose tissue in adult humans (2010)

Brown adipose tissue (BAT) plays a major role in energy homeostasis in animals. Detection of BAT using positron emission tomography (PET)-CT in humans has challenged the view that BAT disappears after infancy. Several recent studies, based on analysis of single scans, have reported a low prevalence of only 5-10% in humans, casting doubt on its significance. We undertook a critical analysis of the sensitivity, reproducibility, and accuracy of PET-CT to deduce the prevalence of BAT and factors associated with its detection in adult humans. In a retrospective evaluation of PET-CT, using [18F]fluorodeoxyglucose, performed in 2,934 patients, BAT was identified in 250 patients, yielding an apparent prevalence of 8.5%. Among those patients with BAT, 145 were scanned more than once. The frequency of another scan being positive increased from 8 to 65% for one to more than four additional studies. The average probability of obtaining another positive scan among patients with BAT is 13%, from which the prevalence of BAT is estimated at 64%. BAT was more commonly detected in women, in younger (36 ± 1 vs. 52 ± 1 years, P < 0.001) and leaner (20.1 ± 0.9 vs. 24.9 ± 0.9 kg/m2, P < 0.01) individuals. Fasting glucose was lower in those with BAT than those without (4.9 ± 0.1 vs. 5.5 ± 0.1 mmol/l, P < 0.01). Among patients scanned more than once, BAT was detected when body weight and fasting glucose were lower (54.9 ± 0.5 vs. 58.2 ± 0.8 kg, P < 0.001 and 4.9 ± 0.3 vs. 5.5 ± 0.3 mmol/l, P = 0.03). We conclude that BAT is present in the majority of adult humans. Presence of BAT correlates negatively with body mass index and glucose concentration. BAT may play an important role in energy homeostasis in adults.
Multi-Word Expressions and Morphology (2019)

Multi-word expressions are linguistic objects formed by two or more words that behave like a ‘unit’ by displaying formal and/or functional idiosyncratic properties with respect to free word combinations. They include an extremely varied set of items (from idioms to collocations, from formulae to sayings) which have been the privileged subject matter of fields such as phraseology, lexicology, lexicography, and computational linguistics. Far from being a marginal phenomenon, multi-word expressions are ubiquitous and pervasive: some estimate that they are as numerous as words in some languages, which makes them as central an issue as words for the understanding of human language. However, their relation with words, and morphology, is by far less explored, not to say neglected, especially in terms of demarcation, competition, and cross-linguistic variation.