gebhart/patrepeval huggingface dataset:
A biomarker‐based mathematical model to predict bone‐forming potency of human synovial and periosteal mesenchymal stem cells (2007)

Our findings indicate that our quality-control mathematical model estimates the bone-forming potency of MSC preparations for bone repair.
Ocean acoustic tomography: Travel time biases (1985)

The travel times of acoustic rays traced through a climatological sound-speed profile are compared with travel times computed through the same profile containing an eddy field. The exact travel time difference is compared with its constituent terms, one of which is linearly related to the deviation of the sound speed (referenced to the climatological profile) and the others which are nonlinearly related to the deviation. At ranges that are much greater than the eddy scale and for eddy fields whose range-averaged temperature anomaly is small, the numerical results are: (1) the values of the nonlinear terms are insensitive to changes in the positions of the eddies and (2) the nonlinear terms are approximately proportional to the range between the source and receiver and to the square of the eddy anomaly. At a 1084-km range in the east Atlantic at 24 °N (36 °N) the nonlinear terms can account for 17% (90%) of the exact travel time change where the temperature anomalies associated with the eddies are typically ±0.5 °C (±1 °C). Linearized inversions (based on the linear estimator of the travel time difference) which use the exact travel time differences for data should yield biased results since the average values of the nonlinear terms are not zero. If an a priori knowledge of the eddy spectrum is known, the nonlinear terms could be computed for each ray and subtracted from the exact travel time change. It may then be beneficial to use the corrected set of travel time differences in a linear inversion which would require no iteration.
Variations in ambient light emission from black smokers and flange pools on the Juan De Fuca Ridge (2000)

Ambient light emitted by high‐temperature black smokers and flange pools on the Juan de Fuca Ridge was imaged using a new spectral imaging camera. Most of the light is emitted at long wavelengths (700–1000 nm) and corresponds well to thermal radiation from a body at the same temperature as the vents/flanges. However, black smokers also emit time‐varying radiation in the visible region (400–650 nm) which cannot be explained by a thermal source. This visible radiation is 1–2 orders of magnitude greater than would be expected for purely thermal radiation; it exhibits variation with time, despite relatively constant vent temperatures; and it is not associated with the hottest part of the plume (i.e. the orifice). Flange pools do not exhibit excess visible light over that for a thermal source, suggesting that the light at smokers is caused by mechanisms related to turbulence, mixing, or precipitation.
Label-free high-throughput imaging flow cytometry (2014)

Flow cytometry is an optical method for studying cells based on their individual physical and chemical characteristics. It is widely used in clinical diagnosis, medical research, and biotechnology for analysis of blood cells and other cells in suspension. Conventional flow cytometers aim a laser beam at a stream of cells and measure the elastic scattering of light at forward and side angles. They also perform single-point measurements of fluorescent emissions from labeled cells. However, many reagents used in cell labeling reduce cellular viability or change the behavior of the target cells through the activation of undesired cellular processes or inhibition of normal cellular activity. Therefore, labeled cells are not completely representative of their unaltered form nor are they fully reliable for downstream studies. To remove the requirement of cell labeling in flow cytometry, while still meeting the classification sensitivity and specificity goals, measurement of additional biophysical parameters is essential. Here, we introduce an interferometric imaging flow cytometer based on the world’s fastest continuous-time camera. Our system simultaneously measures cellular size, scattering, and protein concentration as supplementary biophysical parameters for label-free cell classification. It exploits the wide bandwidth of ultrafast laser pulses to perform blur-free quantitative phase and intensity imaging at flow speeds as high as 10 meters per second and achieves nanometer-scale optical path length resolution for precise measurements of cellular protein concentration.
Tandem GC/MS: A useful tool for studying end‐capping reactions of oligo(styryl)lithium anions (1995)

Abstract Anionic living polymerization methods, using organometallic initiators such as butyllithium reagents, have proven useful for, inter alia , styrene polymerization and are amenable to subsequent functionalization of poly(styryl)lithium in the termination step. In this study, general methods for the selective preparation of small styrene oligomers and termination of the intermediate oligo(styryl)lithium anions were investigated. The crude reaction mixtures were analyzed directly by tandem gas chromatography/mass spectrometry (GC/MS). Of the carbon‐ and silicon‐based electrophiles tested, chloro(chloroalkyl)silanes, Cl‐SiR 2 (CH 2 ) n Cl in particular, were shown by GC/MS to be regioselective end‐capping reagents, thus allowing subsequent transformation to the primary amine. The combined GC/MS data allow not only an estimate of the degree of functionalization, but also the identification of by‐products, thus providing insight into the end‐capping process that otherwise might be difficult to access. © 1995 John Wiley &amp; Sons, Inc.
Oxide layer dependent orbital torque efficiency in ferromagnet/Cu/Oxide heterostructures (2023)

The utilization of orbital transport provides a versatile and efficient spin manipulation mechanism. As interest in orbital-mediated spin manipulation grows, we face a new issue to identify the underlying physics that determines the efficiency of orbital torque (OT). In this study, we systematically investigate the variation of OT governed by orbital Rashba-Edelstein effect at the Cu/Oxide interface, as we change the Oxide material. We find that OT varies by a factor of ~2, depending on the Oxide. Our results suggest that the active electronic interatomic interaction (hopping) between Cu and oxygen atom is critical in determining OT. This also gives us an idea of what type of material factors is critical in forming a chiral orbital Rashba texture at the Cu/Oxide interface.
Critical Roles of ASC Inflammasomes in Caspase-1 Activation and Host Innate Resistance to Streptococcus pneumoniae Infection (2011)

Streptococcus pneumoniae is a Gram-positive, extracellular bacterium that is responsible for significant mortality and morbidity worldwide. Pneumolysin (PLY), a cytolysin produced by all clinical isolates of the pneumococcus, is one of the most important virulence factors of this pathogen. We have previously reported that PLY is an essential factor for activation of caspase-1 and consequent secretion of IL-1β and IL-18 in macrophages infected with S. pneumoniae. However, the host molecular factors involved in caspase-1 activation are still unclear. To further elucidate the mechanism of caspase-1 activation in macrophages infected with S. pneumoniae, we examined the involvement of inflammasomes in inducing this cellular response. Our study revealed that apoptosis-associated specklike protein containing a caspase recruitment domain (ASC), an adaptor protein for inflammasome receptors such as nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3) and absent in melanoma 2 (AIM2), is essentially required for the induction of caspase-1 activation by S. pneumoniae. Caspase-1 activation was partially impaired in NLRP3(-/-) macrophages, whereas knockdown and knockout of AIM2 resulted in a clear decrease in caspase-1 activation in response to S. pneumoniae. These results suggest that ASC inflammasomes, including AIM2 and NLRP3, are critical for caspase-1 activation induced by S. pneumoniae. Furthermore, ASC(-/-) mice were more susceptible than wild-type mice to S. pneumoniae, with impaired secretion of IL-1β and IL-18 into the bronchoalveolar lavage after intranasal infection, suggesting that ASC inflammasomes contribute to the protection of host from infection with PLY-producing S. pneumoniae.
Shot-noise limited operation of a monomode high cavity Q semiconductor laser (2007)

hot-noise-limited laser operation over a wide spectral bandwidth is demonstrated by using a semiconductor active medium inserted into a high-Q external cavity. This approach ensures, with a compact design, a sufficiently long photon lifetime to reach the oscillation-relaxation-free class A regime. The laser relative intensity noise is limited to the shot-noise relative floor, −156 dB/Hz for a 1 mA detected photocurrent, over the 100 MHz to 18 GHz bandwidth. The optimization of the laser cavity is discussed, and convenient shot-noise-limited operation is shown to be a trade-off between the cavity length and laser mode filtering.
Solution Processed p-Doped Hole Transport Layer for Polymer Light-Emitting Diodes (2011)

A solution processed p-doped hole transport layer was developed using a poly(9,9'-dioctylfluorene-co-bis-N,N'-(4-ethoxycarbonylphenyl)-bis-N,N'-phenyl benzidine (PFO-co-NEPB) as the hole transport material and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) as the p type dopant. The F4-TCNQ doped PFO-co-NEPB layer was insoluble to organic solvent after baking and showed an ohmic contact behavior due to p doping effect of the solution processed F4-TCNQ. Yellow polymer emitting materials could be spin coated on the F4-TCNQ doped PFO-co-NEPB layer, and the driving voltage, power efficiency and lifetime of yellow polymer light-emitting diodes were greatly improved by the F4-TCNQ doping in the PFO-co-NEPB layer.
Holland (2011)

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
Model for arm movements during myoclonic seizures (2007)

A model is formulated for arm movements during myoclonic (epileptic) seizures. The system described in the model, consists of a mechanical and an electrophysiological part. The model output is compared to real patient accelerometry (ACM)-data from six epilepsy patients. Eight out of ten myoclonic seizures have a good fit to the model. The values of the model parameters tuned to the real seizures are physiologically feasible. Using mean parameter values leads to agreeable fits in six out of ten myoclonic seizures. Two of the four parameters seem to be robust for variation in patient and seizure. The presented model approach leads to a better understanding of patterns in ACM-recordings that are associated with myoclonic seizures and in the future can contribute to automated detection of these patterns.
Peripheral tachykinin receptors as potential therapeutic targets in visceral diseases (2003)

More than 10 years of intensive preclinical investigation of selective tachykinin (TK) receptor antagonists has provided a rationale to the speculation that peripheral neurokinin (NK)-1, -2 and -3 receptors may be involved in the pathophysiology of various human diseases at the visceral level. In the airways, despite promising effects in animal models of asthma, pilot clinical trials with selective NK-1 or -2 receptor antagonists in asthmatics have been ambiguous, whereas the potential antitussive effects of NK-1, -2 or -3 antagonists have not yet been verified in humans. In the gastrointestinal (GI) tract, irritable bowel syndrome (IBS) and pancreatitis are appealing targets for peripherally-acting NK-1 and -2 antagonists, respectively. In the genito-urinary tract, NK-1 receptor antagonists could offer some protection against nephrotoxicity and cytotoxicity induced by chemotherapeutic agents, whereas NK-2 receptor antagonists appear to be promising new agents for the treatment of neurogenic bladder hyperreflexia. Finally, there is preclinical evidence for hypothesising an effect of NK-3 receptor antagonists on the cardiovascular disturbance that characterises pre-eclampsia. Other more speculative applications are also mentioned.
Exploiting structured data for learning contagious diseases under incomplete testing (2021)

One of the ways that machine learning algorithms can help control the spread of an infectious disease is by building models that predict who is likely to get infected whether or not they display any symptoms, making them good candidates for preemptive isolation. In this work we ask: can we build reliable infection prediction models when the observed data is collected under limited, and biased testing that prioritizes testing symptomatic individuals? Our analysis suggests that under favorable conditions, incomplete testing might be sufficient to achieve relatively good out-of-sample prediction error. Favorable conditions occur when untested-infected individuals have sufficiently different characteristics from untested-healthy, and when the infected individuals are potent, meaning they infect a large majority of their neighbors. We develop an algorithm that predicts infections, and show that it outperforms benchmarks on simulated data. We apply our model to data from a large hospital to predict Clostridioides difficile infections; a communicable disease that is characterized by asymptomatic (i.e., untested) carriers. Using a proxy instead of the unobserved untested-infected state, we show that our model outperforms benchmarks in predicting infections.
Production and localization of mammary-derived growth factor 1 in the normal and malignant mammary gland (1994)

Previously, we have detected a human milk and breast cancer-derived, acidic, 62 kDa, N-glycosylated growth factor named mammary-derived growth factor 1 (MDGF1). The N-terminal amino acid sequence of MDGF1 showed it to be a new growth factor. The factor stimulated collagen synthesis by fibroblasts and proliferation in normal and malignant mammary epithelial cells. Polyclonal antisera raised against the N-terminal synthetic peptide has been used to demonstrate that some human breast cancer and normal mammary epithelial cell strains and cell lines secrete the factor into their conditioned media. The antibody could adsorb the biological activity of the factor present in conditioned media. The objective of the present study was to utilize this high titre polyclonal anti-MDGF1 antisera to establish the presence and distribution of the factor in benign and malignant human breast tissues as determined by immunohistochemical analysis and enzymelinked immunosorbent assay (ELISA) assays. Frozen sections of normal and malignant breast tissue were used for immunostaining, while homogenized soluble fractions were used for ELISA testing. Antigen absorption confirmed the antibody staining to be specific. MDGF1 is localized in the duct and lobular epithelial cells of the mammary gland. Staining was nuclear and cytoplasmic in tumour and normal specimens. All of the breast tumour specimens demonstrated intense staining of the tumour cells. Localization of MDGF1 in benign and malignant human breast tissue suggests that it is universally present in breast epithelial derived cells. Study of MDGF1 could eventually provide new insights into breast development and/or tumour formation and progression.
Distributed Stochastic Phase-Shift Optimization in a RIS-Assisted Cellular Network (2021)

Reconfigurable intelligent surfaces (RIS) technology, as the name implies, is a grid of many small intelligent surfaces that can be reconfigured. It is a new and promising concept in wireless communications, expected to help realize the requirements of the future cellular generations. Numerous studies have been done to prove its added advantages and to control these surfaces in beneficial ways. However, these control schemes come with difficulties related to efficient and practical implementation. In this paper, we propose to control multiple RISs in a multi-user scheme with an algorithm that leads to a simple implementation. We formulate a stochastic optimization problem and we propose a new method using a distributed stochastic algorithm that allows the optimization to be done locally at each RIS with low computational requirements and without the need for instantaneous channel knowledge at the RIS. Also, the signaling between the base station (BS) and each RIS is limited to the exchange of a scalar only. Simulation results prove the success and efficiency of this algorithm.
A Method to Extract the Complete Fiber Network Topology of Planar Fibrous Tissues and Scaffolds (2010)

Improving fabrication protocols and design strategies, investigating on how fibrous ECM and synthetic architectures affect cell morphology, metabolism and phenotypic expression, predicting mechanical behaviors, have increasingly become crucial goals in the understanding of native tissues and in the development of engineered tissue. In the present study, an image-based analysis approach that provides an automatic tool to fully characterize engineered tissue fiber network topology was developed. The following micro architectural features were detected: fiber angle distribution, fiber connectivity, fiber overlap spatial density, and fiber diameter. In order to demonstrate the potential of this approach Electrospun poly(ester urethane)urea (ES-PEUU) scaffolds were studied. Electrospun scaffolds were chosen for their recognized capability to recapitulate native soft tissue extra cellular matrix (ECM) morphology.
Repeated Ramp Tests on Stable LVAD Patients Reveal Patient-Specific Hemodynamic Fingerprint (2017)

Hemodynamic speed ramp tests are used in left ventricular assist device (LVAD) patients to guide speed adjustment and medical therapies. However, the reproducibility of these tests is unknown. In this prospective study, clinically stable LVAD patients underwent echocardiography and right heart catheterization ramp tests followed by a repeat test within 2 years as per institutional protocol. Sixteen patients (61.8 ± 10.5 years old, 50% male, eight with HeartMate II and eight with HVAD) underwent repeated ramp testing. The first test was performed 187 (42-1857) days from LVAD implant and the second test was performed 278 (126-560) days from the first test. All hemodynamic variables measured at the baseline speed remained statistically unchanged between the first and second ramp test (p > 0.05 for all). Changes in hemodynamic parameters, as assessed by the slopes of their changes over the range of speeds tested, were also the same at the two timepoints (p > 0.05 for all). Stable LVAD patients had similar hemodynamic profiles over the course of years including similar responses to speed changes. This suggests that ramp tests may represent a hemodynamic fingerprint; deviations from a baseline test can aid diagnosis at times of clinical deterioration or device malfunction.
Low-Dose Anti-Thymocyte Globulin for Graft-Versus-Host-Disease Prophylaxis in Matched Unrelated Allogeneic Hematopoietic Stem Cell Transplant (2017)

Background: Prophylactic in-vivo T-Cell depletion with antithymocyte globulin (ATG) has been reported to decrease graft-versus-host disease (GVHD) in matched related (MRD) and unrelated donor (MUD) hematopoietic stem cell transplant (HSCT). Our institution has had a longstanding policy of administering low-dose ATG to MUD HSCT patients to mitigate donor disparity-related GVHD risk. Here we report our experience using an unconventionally low-dose ATG by comparing outcomes in patients who did (MUD) and did not (MRD) receive prophylactic ATG as part of their HSCT regimen. Methods: We conducted a retrospective study comparing 110 MUD (ATG exposed) and 78 MRD (ATG unexposed) HSCT patients transplanted for any malignant indication at The Ottawa Hospital from 2009 to 2014. MUD HSCT patients received rabbit ATG (Thymoglobulin ®) at .5 mg/kg on pre-transplant day −2 and 2.0 mg/kg on day −1, to total 2.5 mg/kg. Primary outcomes assessed were incidence of acute and chronic GVHD, defined as GVHD requiring systemic immunosuppression at less or more than 100 days post HSCT. Secondary outcomes included relapse, survival, and infectious outcomes. Results: There were no baseline differences in age, sex, HSCT indication, disease risk index, graft source, or conditioning intensity between cohorts. Significant differences were observed between ATG exposed and unexposed cohorts in proportion of 7/8 mismatches (14 v 6%; P = .015) and median CD34+ dose (4.9 v 7.6 × 108 cells; P < .001). No differences were noted in platelet engraftment, however ATG exposed patients had significantly faster neutrophil engraftment (16 v 19 days; P = .007). None of these differences were associated with GVHD, relapse, or survival outcomes in multivariate analysis. ATG exposed patients had significantly lower GVHD rates (57 v 79%; P = .005), with differences noted primarily in chronic GVHD (18 v 44%, P = .009). At median follow-up of 15 (1-73) and 20 (0-69) months for ATG exposed and unexposed cohorts, there were no differences in overall survival (median OS not met), cumulative incidence of relapse (26 v 29%; P = .73) or relapse-free survival (median not met v 26.2 months; P = .22). ATG exposed patients had significantly better GVHD-Free Relapse-Free Survival (GRFS), with a two-year GRFS of 23% v 3% (P = .003; Figure 1). There were no differences in ICU admission rates or in incidence or type of infections. In multivariate analysis ATG exposure was not associated with relapse or survival outcomes, but was independently associated with decreased incidence of chronic GVHD (HR .33, 95% CI .14–.78; P = .012). Conclusions: Here we report significantly lower chronic GVHD rates and improved GRFS in an ATG exposed MUD HSCT cohort compared to an unexposed MRD counterpart. Our findings suggest that low dose ATG may be effective at preventing GVHD without compromising relapse or survival, and that broader exploration of its optimal dosing is warranted.
Augmentation of Musculoskeletal Regeneration: Role for Pluripotent Stem Cells (2018)

The rise in the incidence of musculoskeletal diseases is attributed to an increasing ageing population. The debilitating effects of musculoskeletal diseases, coupled with a lack of effective therapies, contribute to huge financial strains on healthcare systems. The focus of regenerative medicine has shifted to pluripotent stem cells (PSCs), namely, human embryonic stem cells and human-induced PSCs, due to the limited success of adult stem cell-based interventions. PSCs constitute a valuable cell source for musculoskeletal regeneration due to their capacity for unlimited self-renewal, ability to differentiate into all cell lineages of the three germ layers and perceived immunoprivileged characteristics. This review summarizes methods for chondrogenic, osteogenic, myogenic and adipogenic differentiation of PSCs and their potential for therapeutic applications.