gebhart/patrepeval huggingface dataset:
Zwitterion Stationary Phases (2009)

This chapter contains sections titled: Introduction Simultaneous Separation of Anions and Cations Separation of Anions Separation of Cations Mechanism
Optical coherence tomography detection of shear wave propagation in MCF7 cell modules (2014)

In this work, we explored the potential of measuring shear wave propagation using Optical Coherence Elastography (OCE) in MCF7 cell modules (comprised of MCF7 cells and collagen) and based on a swept-source optical coherence tomography (OCT) system. Shear waves were generated using a piezoelectric transducer transmitting sine-wave bursts of 400 μs, synchronized with an OCT swept source wavelength sweep imaging system. Acoustic radiation force was applied to the MCF7 cell constructs. Differential OCT phase maps, measured with and without the acoustic radiation force, demonstrate microscopic displacement generated by shear wave propagation in these modules. The OCT phase maps are acquired with a swept-source OCT (SS-OCT) system. We also calculated the tissue mechanical properties based on the propagating shear waves in the MCF7 + collagen phantoms using the Acoustic Radiation Force (ARF) of an ultrasound transducer, and measured the shear wave speed with the OCT phase maps. This method lays the foundation for future studies of mechanical property measurements of breast cancer structures, with applications in the study of breast cancer pathologies.
New Methodology to Evaluate the Performance of Ring Resonators Using Optical Low-Coherence Reflectometry (2004)

This paper describes the efficient implementation of optical low-coherence reflectometry (OLCR) measurements to evaluate the performance of InP-based high-index contrast ring resonators. Using examples of racetrack ring resonators, this paper shows here for the first time that all characteristic parameters relevant to resonator design (coupling coefficient k, propagation losses a, and optical cavity length L), and ultimately its performance, can be extracted in a straightforward manner. This is accomplished by introducing a new methodology that implicates OLCR measurements in transmission and also reflection modes as an alternative approach, in comparison with conventional spectral analysis, to extract resonator design parameters.
Supp Figure Captions from Targeted AKT Inhibition in Prostate Cancer Cells and Spheroids Reduces Aerobic Glycolysis and Generation of Hyperpolarized [1-<sup>13</sup>C] Lactate (2023)

&lt;p&gt;Supp Figure Captions&lt;/p&gt;
Determination of tobacco-specificN-nitrosamines in urine of smokers and non-smokers (2009)

Tobacco-specific N-nitrosamines (TSNA) include 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), N'-nitrosonornicotine (NNN), N'-nitrosoanabasine (NAB) and N'-nitrosoanatabine (NAT) and are found in tobacco and tobacco smoke. TSNA are of interest for biomonitoring of tobacco-smoke exposure as they are associated with carcinogenesis. Both NNK and NNN are classified by IARC as Group 1 carcinogens. Samples of 24 h urine collections (n = 108) were analysed from smokers and non-smokers, using a newly developed and validated LC-MS/MS method for determining total 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL, the major metabolite of NNK), and total NNN, NAB and NAT. TSNA levels in smokers' urine were significantly higher than in non-smokers. In smokers, urinary excretion of total TSNA correlated significantly (r > 0.5) with markers of smoking dose, such as daily cigarette consumption, salivary cotinine and urinary nicotine equivalents and increased with the ISO tar yield of cigarettes smoked. The correlation between urinary total NNN and the smoking dose was weaker (r = 0.4-0.5). In conclusion, this new method is suitable for assessing tobacco use-related exposure to NNK, NNN, NAB and NAT.
Scale robust IMU-assisted KLT for stereo visual odometry solution (2016)

SUMMARY We propose a novel stereo visual IMU-assisted (Inertial Measurement Unit) technique that extends to large inter-frame motion the use of KLT tracker (Kanade–Lucas–Tomasi). The constrained and coherent inter-frame motion acquired from the IMU is applied to detected features through homogenous transform using 3D geometry and stereoscopy properties. This predicts efficiently the projection of the optical flow in subsequent images. Accurate adaptive tracking windows limit tracking areas resulting in a minimum of lost features and also prevent tracking of dynamic objects. This new feature tracking approach is adopted as part of a fast and robust visual odometry algorithm based on double dogleg trust region method. Comparisons with gyro-aided KLT and variants approaches show that our technique is able to maintain minimum loss of features and low computational cost even on image sequences presenting important scale change. Visual odometry solution based on this IMU-assisted KLT gives more accurate result than INS/GPS solution for trajectory generation in certain context.
Mesenchymal Stem/Stromal Cells Protect against Autoimmunity via CCL2-Dependent Recruitment of Myeloid-Derived Suppressor Cells (2015)

Exogenously administered mesenchymal stem/stromal cells (MSCs) suppress autoimmunity despite transient engraftment. However, the mechanism is unclear. In this study, we report a novel mechanism by which MSCs modulate the immune system by recruiting myeloid-derived suppressor cells in a mouse model of experimental autoimmune uveitis (EAU). Intravenous infusion of MSCs blocked EAU development and reduced Th1 and Th17 responses. Time course analysis revealed an increase of MHC class II(lo)Ly6G(-)Ly6C(hi)CD11b(+) cells in draining lymph nodes by MSCs. These Ly6C(hi)CD11b(+) cells suppressed CD4(+) cell proliferation and Th1/Th17 differentiation and induced CD4(+) cell apoptosis. Adoptive transfer of Ly6C(hi)CD11b(+) cells ameliorated EAU, whereas depletion of Ly6C(hi)CD11b(+) cells abrogated the effects of MSCs. 1.8% of MSCs were present in draining lymph nodes 1 d after infusion, and MSCs with CCL2 knockdown did not increase MHC class II(lo)Ly6G(-)Ly6C(hi)CD11b(+) cells and failed to attenuate EAU. Therefore, our findings demonstrate that MSCs suppress autoimmunity by recruiting myeloid-derived suppressor cells into sites of inflammation in a CCL2-dependent manner.
[Differential diagnosis of rejection and cyclosporin nephrotoxicity in organ transplantation using exfoliative urinary cytology]. (1985)

Although the successful results sealing with Cyclosporin therapy in organ transplantation, side effects such as nephrotoxicity due to drug administration, are still partially solved especially concerning differential diagnosis versus rejection in kidney allograft. On this basis the authors evaluated the application of urinary exfoliative cytology for the monitoring of 110 patients who underwent kidney transplant under Cyclosporin regimen. Among them 33 cases showed direct and/or indirect cytopathic signs of nephrotoxicity induced by Cyclosporin, never observed on over 6000 urinary specimens of renal graphed patients treated with conventional therapy. The authors conclude that urinary exfoliative cytology is a useful, safe and easily repeatable method for the differential diagnosis between rejection and Cyclosporin nephrotoxicity at early stage in kidney transplantation.
Benefits of Active Debris Removal on the LEO Debris Population (2010)

Since the launch of Sputnik, orbital debris population continues to increase due to ongoing space activities, on-orbit explosions, and accidental collisions. In the future, a great deal of fragments can be expected to be created by explosions and collisions. In spite of prevention of satellite and rocket upper stage explosions and other mitigation measures, debris population in low Earth orbit may not be stabilized. To better limit the growth of the future debris population, it is necessary to remove the existing debris actively. This paper studies about the effectiveness of active debris removal in low Earth orbit where the collision rate with and between space debris is high. This study does not consider economic problems, but investigates removing debris which may stabilize well the current debris population based on the concept of Japan Aerospace Exploration Agency.
Enantioselective Broensted Acid Catalyzed Transfer Hydrogenation: Organocatalytic Reduction of Imines. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Supplementary Figure 4 from Promyelocytic Leukemia Protein is Required for Gain of Function by Mutant p53 (2023)

Supplementary Figure 4 from Promyelocytic Leukemia Protein is Required for Gain of Function by Mutant p53
Characteristics of JMV Marek's Disease Tumor: A Nonproductively Infected Transplantable Cell Lacking in Rescuable Virus2 (1976)

Cells of the JMV Marek's disease (MD) tumor, originally produced by rapid serial passage of MD lymphoma cells in chickens, were characterized to determine whether they were of host or donor origin and to ascertain certain virus-host cell interrelationships. Differences noted in blood group B surface alloantigens between tumor cells and host lymphocytes indicated a probable nonhost origin (i.e., transplantability) of the tumor. JMV spleen tumors contained predominantly large lymphoblasts bearing MD tumor-associated surface antigen. DNA from JMV tumor cell suspensions hybridized significantly with MD virus cRNA, which indicated that JMV cells contained at least a portion of the MD virus genome. No MD virus was rescued from JMV tumors by techniques suitable for rescue of virus from MD lymphomas. The JMV tumor cells were also devoid of MD virus-specific antigens. These properties differed markedly from those of MD lymphoma cells and make the JMV tumor cell a unique, potentially valuable, tool for further study of oncogenic herpesvirus infection and tumor immunity in the chicken.
Enzalutamide, an Oral Androgen Receptor Inhibitor for Treatment of Castration-Resistant Prostate Cancer (2019)

Androgen receptor (AR) signaling is a key pathway in prostate cancer, and patients are initially treated with androgen deprivation therapy. Patients who have stopped responding to androgen deprivation therapy are considered to have castration-resistant prostate cancer (CRPC), which is still dependent on AR signaling. Enzalutamide, an orally available AR inhibitor, was initially approved by the US FDA for the treatment of patients with metastatic CRPC who have previously received docetaxel. The indication was subsequently extended to include all patients with metastatic CRPC, and most recently to include patients with nonmetastatic CRPC. This review summarizes the body of evidence supporting enzalutamide efficacy and safety in CRPC.
g-Factor analysis of protein secondary structure in solutions and thin films (2003)

The biological activity of proteins is structure dependent. In this discussion, we describe development of g-factor analysis for characterizing the secondary structure of proteins in solutions and films. In g-factor analysis, experimental circular dichroism (CD) and UV absorbance spectra are converted to dimensionless g-factor spectra by dividing the differential absorbance of circularly polarized light (AL - AR) by the UV absorbance (A) at each wavelength. The spectra can be deconvolved and the secondary structure estimated without information on the protein molecular weight, sample concentration, or sample path length. We have refined g-factor spectral acquisition and deconvolution parameters to improve the precision and accuracy of experimental g-factor spectra and the subsequent secondary structure estimations. In general, slower scan rates and longer response times are required to obtain high quality g-factor spectra than to obtain ordinary CD spectra, particularly for data at wavelengths longer than 230 nm. The spectral acquisition and deconvolution procedures have been validated for aqueous bovine serum albumin (BSA) and poly(L-proline). The secondary structures of fibronectin and laminin in buffer solutions are predicted. When BSA and poly(L-proline) form films on quartz, their secondary structures change significantly: 13% for BSA and 32% for poly(L-proline). By contrast, the secondary structure of fibronectin is the same in solution and films. The g-factor method is an easy, rapid, accurate and precise method for determining secondary structure and structural changes in protein solutions and films. Potential applications range from proteomics and structure-based drug discovery, to the design and fabrication of biosensors, biomaterials and biofluidic devices.
Neutrophil Extracellular Traps Promote the Development and Growth of Human Salivary Stones (2020)

Salivary gland stones, or sialoliths, are the most common cause of the obstruction of salivary glands. The mechanism behind the formation of sialoliths has been elusive. Symptomatic sialolithiasis has a prevalence of 0.45% in the general population, is characterized by recurrent painful periprandial swelling of the affected gland, and often results in sialadenitis with the need for surgical intervention. Here, we show by the use of immunohistochemistry, immunofluorescence, computed tomography (CT) scans and reconstructions, special dye techniques, bacterial genotyping, and enzyme activity analyses that neutrophil extracellular traps (NETs) initiate the formation and growth of sialoliths in humans. The deposition of neutrophil granulocyte extracellular DNA around small crystals results in the dense aggregation of the latter, and the subsequent mineralization creates alternating layers of dense mineral, which are predominantly calcium salt deposits and DNA. The further agglomeration and appositional growth of these structures promotes the development of macroscopic sialoliths that finally occlude the efferent ducts of the salivary glands, causing clinical symptoms and salivary gland dysfunction. These findings provide an entirely novel insight into the mechanism of sialolithogenesis, in which an immune system-mediated response essentially participates in the physicochemical process of concrement formation and growth.
A novel technique to correct kyphosis in cervical myelopathy due to continuous-type ossification of the posterior longitudinal ligament (2016)

OBJECTIVE Although posterior decompressive surgery is widely used to treat patients with cervical myelopathy and multilevel ossification of the posterior longitudinal ligament (OPLL), a poor outcome is anticipated if the sagittal alignment is kyphotic (or K-line negative). Accordingly, it is mandatory to perform anterior decompression and fusion in patients with cervical kyphosis. However, it can be difficult to perform anterior surgery because of the high risk of complications. This present report proposes a novel "greenstick fracture technique" to change the K-line from negative to positive in patients with cervical myelopathy, OPLL, and kyphotic deformity. METHODS Four patients with cervical myelopathy, continuous-type OPLL, and kyphotic sagittal alignment (who were K-line negative) were indicated for surgery. Posterior laminectomy and lateral mass screw insertions using a posterior approach were performed, followed by anterior surgery. Multilevel discectomy and thinning of the OPLL mass by bur drilling was performed, then an intentional greenstick fracture at each disc level was made to convert the cervical K-line from negative to positive. Finally, posterior instrumentation using a rod was carried out to maintain cervical lordosis. RESULTS MRI showed complete decompression of the cord by posterior migration in all cases, which had been caused by cervical lordosis. Restoration of neurological defects was confirmed at the 1-year follow-up assessment. No specific complications were identified that were associated with this technique. CONCLUSIONS A greenstick fracture technique may be effective and safe when applied to patients with cervical myelopathy, continuous-type OPLL, and kyphotic deformity (K-line negative). However, further studies with more cases will be required to reveal its generalizability and safety.
Portal hypertensive gastropathy as a prognostic index in patients with liver cirrhosis (2016)

PHG was well correlated with portal hypertension and could be used as a prognostic factor for LC but not for the prediction of HCC.
BRCA in breast cancer: From risk assessment to therapeutic prediction (2009)

BRCA1/2 mutations are the most commonly identified germ line gene mutations in patients with hereditary breast cancer. These proteins have many critical cellular functions, including repair of DNA double-strand breaks. The role of defective BRCA1/2 as a predictor of response to DNA-damaging agents has been studied extensively in preclinical models, but prospective clinical validation is lacking. Poly [ADP-ribose] polymerase (PARP) inhibitors illustrate the concept of synthetic lethality in cells with defective BRCA1/2 and numerous PARP inhibitors are being evaluated in patients with BRCA1/2-associated tumors. BRCA1/2 mutation or functional loss will likely serve as a useful predictive biomarker of response to treatment with PARP inhibitors.
Improving 1D optical proximity effect matching for 45-nm node by scatterometry metrology (2009)

The fingerprint of the optical proximity effect, OPE, is required to develop each process node's optical proximity correction (OPC) model. This model should work equally well on different exposure systems. However, small differences in optical and mechanical properties in the lithographic system can lead to a different CD characteristic for a given OPC. It becomes beneficial to match the OPE of one scanner to the scanner population in a fab. Here, we focus on aspects of angle resolving scatterometry metrology used for OPE matching of two XT:1700i scanners and compare those to SEM metrology. The capability of the scatterometry tool for monitoring the stability of OPE is evaluated. Scatterometry allows measuring the side wall angle, SWA, of a resist profile and this can be used as a measure for focus. Here, focus comparison by SWA is included into the matching process. For the application used here, the residual RMS mismatch through pitch for scatterometry could be reduced to 0.2nm compared to 0.5nm for CD-SEM.
Cdk1 and Okadaic Acid-sensitive Phosphatases Control Assembly of Nuclear Pore Complexes inDrosophilaEmbryos (2005)

Disassembly and reassembly of the nuclear pore complexes (NPCs) is one of the major events during open mitosis in higher eukaryotes. However, how this process is controlled by the mitotic machinery is not clear. To investigate this we developed a novel in vivo model system based on syncytial Drosophila embryos. We microinjected different mitotic effectors into the embryonic cytoplasm and monitored the dynamics of disassembly/reassembly of NPCs in live embryos using fluorescently labeled wheat germ agglutinin (WGA) or in fixed embryos using electron microscopy and immunostaining techniques. We found that in live embryos Cdk1 activity was necessary and sufficient to induce disassembly of NPCs as well as their cytoplasmic mimics: annulate lamellae pore complexes (ALPCs). Cdk1 activity was also required for keeping NPCs and ALPCs disassembled during mitosis. In agreement recombinant Cdk1/cyclin B was able to induce phosphorylation and dissociation of nucleoporins from the NPCs in vitro. Conversely, reassembly of NPCs and ALPCs was dependent on the activity of protein phosphatases, sensitive to okadaic acid (OA). Our findings suggest a model where mitotic disassembly/reassembly of the NPCs is regulated by a dynamic equilibrium of Cdk1 and OA-sensitive phosphatase activities and provide evidence that mitotic phosphorylation mediates disassembly of the NPC.
High-throughput imaging and analysis of root system architecture inBrachypodium distachyonunder differential nutrient availability (2012)

Nitrogen (N) and phosphorus (P) deficiency are primary constraints for plant productivity, and root system architecture (RSA) plays a vital role in the acquisition of these nutrients. The genetic determinants of RSA are poorly understood, primarily owing to the complexity of crop genomes and the lack of sufficient RSA phenotyping methods. The objective of this study was to characterize the RSA of two Brachypodium distachyon accessions under different nutrient availability. To do so, we used a high-throughput plant growth and imaging platform, and developed software that quantified 19 different RSA traits. We found significant differences in RSA between two Brachypodium accessions grown on nutrient-rich, low-N and low-P conditions. More specifically, one accession maintained axile root growth under low N, while the other accession maintained lateral root growth under low P. These traits resemble the RSA of crops adapted to low-N and -P conditions, respectively. Furthermore, we found that a number of these traits were highly heritable. This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions.
USE OF NEPHROSTOMY TUBES IN URETERIC OBSTRUCTION FROM INCURABLE MALIGNANCY (2003)

Malignancy may produce ureteric obstruction. This obstruction may be relieved by inserting a nephrostomy tube. All 31 cases of malignant ureteric obstruction from a single institution were retrospectively analysed. The commonest indications for nephrostomy tube insertion were renal failure (87%) and flank pain with hydronephrosis (13%). The mean serum creatinine levels pre and post insertion were 481 and 170 micromol/l, representing significant improvement (p<0.01). The complication rate was 13%, relating to tube blockage or dislodgement. Survival of patients was significantly worse if their malignancy was not resectable or suitable for chemotherapy (p=0.01). However, incurable patients still survived for a mean of 232 days, and although 46% of this time was spent as an inpatient, it did not differ significantly from the inpatient rate of curable patients (31%, p=0.1). Nephrostomy tube insertion should be considered for all palliative cases of malignant ureteric obstruction.
MGait : Model-Based Gait Analysis Using Wearable Bend and Inertial Sensors (2021)

Movement disorders, such as Parkinson’s disease, affect more than 10 million people worldwide. Gait analysis is a critical step in the diagnosis and rehabilitation of these disorders. Specifically, step and stride lengths provide valuable insights into the gait quality and rehabilitation process. However, traditional approaches for estimating step length are not suitable for continuous daily monitoring since they rely on special mats and clinical environments. To address this limitation, this article presents a novel and practical step-length estimation technique using low-power wearable bend and inertial sensors. Experimental results show that the proposed model estimates step length with 5.49% mean absolute percentage error and provides accurate real-time feedback to the user.