gebhart/patrepeval huggingface dataset:
PCNA-interacting peptides reduce Akt phosphorylation and TLR-mediated cytokine secretion suggesting a role of PCNA in cellular signaling (2015)

Proliferating cell nuclear antigen (PCNA), commonly known as a nuclear protein essential for regulation of DNA replication, DNA repair, and epigenetics, has recently been associated with multiple cytosolic functions. Many proteins containing one of the two known PCNA-interacting motifs, the AlkB homologue 2 PCNA interacting motif (APIM) and the PCNA-interacting peptide (PIP)-box, are considered to be mainly cytosolic. APIM is found in more than 20 kinases and/or associated proteins including several direct or indirect members of the mitogen-activated protein kinase (MAPK) and PI3K/Akt pathways. Mass spectrometry analysis of PCNA-pull downs verified that many cytosolic proteins involved in the MAPK and PI3K/Akt pathways are in complex with PCNA. Furthermore, treatment of cells with a PCNA-interacting APIM-containing peptide (APIM-peptide) reduced Akt phosphorylation in human peripheral blood monocytes and a human keratinocyte cell line (HaCaT). Additionally, the APIM-peptide strongly reduced the cytokine secretion from monocytes stimulated with toll like receptor (TLR) ligands and potentiated the effects of MAPK and PI3K/Akt inhibitors. Interestingly, the protein level of the APIM-containing PKR/RIG-1 activator protein (PACT) was initially strongly reduced in HaCaT cells stimulated with APIM-peptide in combination with the TLR ligand polyinosinic-polycytidylic acid (polyIC). Our results suggest that PCNA has a platform role in cytosol affecting cellular signaling.
Arthroscopic Bankart‐Bristow‐Latarjet Procedure: The Development and Early Results of a Safe and Reproducible Technique (2010)

Level IV, therapeutic case series.
Predicting flow state in daily work through continuous sensing of motion rhythm (2009)

We have constructed a new application of continuous sensing of human physiological data during daily a business setting. By capturing the subtle changes and differences in motion rhythm detected through an accelerator rather than trying to identify the context of human activities, we are envisioning the prediction of a person's psychological flow state, i.e., the engagement in one's task. A badge-shaped wearable sensor device called ¿Business Microscope¿ was developed and deployed in a real organization, an office supply firm, for one month to study how effectively flow states could be measured during daily work. We found that even though each subject behaved at different motion rhythms when they were in flow, the consistency of motion rhythm around 2 to 3 Hz was correlated with the richness of flow during work (r=0.47, p<0.01).
Unified Reaction–Diffusion Model for Accurate Prediction of Negative Bias Temperature Instability Effect (2012)

In this study, we developed a unified reaction–diffusion (R–D) model for the negative bias temperature instability (NBTI) effect over a wide range of stress times. The newly developed model provides a physics-based uniform solution and overcomes the limitations of the classical R–D models that cannot describe both the short and the long term stress regions simultaneously. In our modeling framework, the chemical reaction between inversion channel carriers and Si–H bonds at the Si/SiO2 interface dominates the short-term NBTI effects at the beginning of the stress application. Then the H2 diffusion into the polycrystalline silicon (poly-Si) gate becomes responsible for long term stress degradation. Finally, the developed R–D model is implemented into the advanced metal oxide semiconductor field effect transistor (MOSFET) model HiSIM to enable accurate circuit-aging simulation. Simulation results for the current degradation and their comparison with measurements verify the achieved high accuracy and the practical applicability of the developed NBTI model.
Characterization of CdS-quantum dot particles using sedimentation field-flow fractionation (SdFFF) (2015)

CdS 양자점 입자는 특정 파장의 빛을 방출하는 반도체 나노 결정으로 이러한 광학적 특성 때문에 질병 진단 시약, 광학기술, 미디어 산업 및 태양전지와 같은 다양한 분야에서 응용되는 물질이다. 방출하는 빛의 색은 입자의 크기에 의존하기 때문에 CdS 양자점 입자의 크기 및 크기분포를 정확하게 분석하는 것이 필요하다. 본 연구에서는 CdS 양자점 입자를 감마-선 조사법(<TEX>${\gamma}$</TEX>-ray irradiation method)을 이용하여 합성하고, 크기 및 크기 분포도를 결정하기 위하여 침강 장-흐름 분획법 (SdFFF)를 이용하였다. 침강 장-흐름 분획법을 이용한 CdS 양자점 입자의 정확한 분석을 위하여 분석조건의 최적화(유속, 외부장 세기, field-programming)에 대하여 조사되었다. 투과 전자 현미경(transmission electron microscopy, TEM)으로 확인된 단일 입자의 크기는 ~4 nm 였으며, 단일 입자의 응집으로 생성된 2차 입자 크기의 평균은 159 nm로 확인되었다. 첨가된 입자 안정제의 농도가 증가할수록 CdS 양자점 입자의 크기가 감소하는 경향성을 확인하였다. 침강 장-흐름 분획법, 투과 전자 현미경, 그리고 동적 광 산란법(dynamic light scattering, DLS)으로 결정된 CdS 양자점 크기는 각각 126, 159, 그리고 152 nm 였다. 본 연구의 결과로 침강 장-흐름 분획법은 비교적 넓은 크기분포를 갖는 다양한 종류의 무기입자의 크기 및 크기 분포도를 결정하는데 유용한 방법임을 확인하였다. CdS-QD particles are a nano-sized semiconducting crystal that emits light. Their optical properties show great potential in many areas of applications such as disease-diagnostic reagents, optical technologies, media industries and solar cells. The wavelength of emitting light depends on the particle size and thus the quality control of CdS-QD particle requires accurate determination of the size distribution. In this study, CdS-QD particles were synthesized by a simple <TEX>${\gamma}$</TEX>-ray irradiation method. As a particle stabilizer polyvinyl pyrrolidone (PVP) were added. In order to determine the size and size distribution of the CdS-QD particles, sedimentation field-flow fractionation (SdFFF) was employed. Effects of carious parameters including the the flow rate, external field strength, and field programming conditions were investigated to optimize SdFFF for analysis of CdS-QD particles. The Transmission electron microscopy (TEM) analysis show the primary single particle size was ~4 nm, TEM images indicate that the primarty particles were aggregated to form secondary particles having the mean size of about 159 nm. As the concentration of the stabilizer increases, the particle size tends to decrease. Mean size determined by SdFFF, TEM, and dynamic light scattering (DLS) were 126, 159, and 152 nm, respectively. Results showed SdFFF may become a useful tool for determination of the size and its distribution of various types of inorganic particles.
Optical coherence tomography noise modeling and fundamental bounds on human retinal layer segmentation accuracy(Conference Presentation) (2016)

The human retina is composed of several layers, visible by in vivo optical coherence tomography (OCT) imaging. To enhance diagnostics of retinal diseases, several algorithms have been developed to automatically segment one or more of the boundaries of these layers. OCT images are corrupted by noise, which is frequently the result of the detector noise and speckle, a type of coherent noise resulting from the presence of several scatterers in each voxel. However, it is unknown what the empirical distribution of noise in each layer of the retina is, and how the magnitude and distribution of the noise affects the lower bounds of segmentation accuracy. Five healthy volunteers were imaged using a spectral domain OCT probe from Bioptigen, Inc, centered at 850nm with 4.6µm full width at half maximum axial resolution. Each volume was segmented by expert manual graders into nine layers. The histograms of intensities in each layer were then fit to seven possible noise distributions from the literature on speckle and image processing. Using these empirical noise distributions and empirical estimates of the intensity of each layer, the Cramer-Rao lower bound (CRLB), a measure of the variance of an estimator, was calculated for each boundary layer. Additionally, the optimum bias of a segmentation algorithm was calculated, and a corresponding biased CRLB was calculated, which represents the improved performance an algorithm can achieve by using prior knowledge, such as the smoothness and continuity of layer boundaries. Our general mathematical model can be easily adapted for virtually any OCT modality.
Bcl-2 Targets Protein Phosphatase 1α to Bad (2001)

The diverse forms of protein phosphatase 1 (PP1) in vivo result from the association of the catalytic subunit with different regulatory subunits. We recently have described that PP1alpha is a Ras-activated Bad phosphatase that regulates IL-2 deprivation-induced apoptosis. With the yeast two-hybrid system, GST fusion proteins, indirect immunofluorescence, and coimmunoprecipitation, we found that Bcl-2 interacts with PP1alpha and Bad. In contrast, Bad did not interact with 14-3-3 protein. Bcl-2 depletion decreased phosphatase activity and association of PP1alpha to Bad. Bcl-2 contains the RIVAF motif, analogous to the well characterized R/KXV/IXF consensus motif shared by most PP1-interacting proteins. This sequence is involved in the binding of Bcl-2 to PP1alpha. Disruption of Bcl-2/PP1alpha association strongly decreased Bcl-2 and Bad-associated phosphatase activity and formation of the trimolecular complex. These results suggest that Bcl-2 targets PP1alpha to Bad.
Reorientation and fusion of cytotoxic T lymphocyte granules after interaction with target cells as determined by high resolution cinemicrography. (1986)

The interaction of murine cytotoxic T lymphocyte (CTL) clones with human lymphoblastoid target cells was studied in thin preparations by using high resolution cinemicrography. CTL not bound to target cells were morphologically polar, possessing a broad leading edge containing the nucleus, and a tapered tail containing a large number of granules. The CTL were observed to move by the extension of pseudopods from the leading edge. Initial contact with a target cell was made via the leading edge of the CTL. If the human target cell expressed the appropriate HLA antigen, distinct morphologic changes occurred in the CTL as early as 2 min after initial contact. The CTL rounded up, and the nucleus moved from a position adjacent to the zone of contact to be replaced by the cytoplasmic granules. Redistribution of the granules was completed as early as 10 min after initial contact was made. These morphologic changes did not occur when the CTL made contact with other CTL, or with target cells that did not express the appropriate HLA antigens. In studies that make use of Nomarski optics, an apparent fusion of CTL cytoplasmic granules with the membrane in the vicinity of the target cell contact area was observed 4 min after binding, and before granule reorientation was complete. These data provide direct evidence for the occurrence of both reorientation of the cytoplasmic contents and granule fusion in CTL with a time course similar to that of administration of the lethal hit.
Holographic Microscopy: From the Idea to the Market (2010)

LOA
Convalescent plasma therapy in aHUS patient with SARS-CoV-2 infection (2022)

Endotheliosis, thrombotic microangiopathy and complement system over activation have been described as pathologic features of tissue damage in the setting of coronavirus disease. Interestingly, complement-mediated cell injury is also a typical feature of atypical Hemolytic Uremic Syndrome. Indeed, a growing body of literature has described a higher risk of microangiopathy recurrence, in aHUS patients who test positive for SARS-CoV-2. The correct clinical and therapeutic management patients with a history of HUS and SARS-CoV-2 infection is not well established. We report a case of SARS-CoV-2 infection in an aHUS patient who did not develop a recurrence of the disease and that was successfully treated with convalescent immune plasma therapy.
Understanding Shared Speech-Text Representations (2023)

Recently, a number of approaches to train speech models by incorporating text into end-to-end models have been developed, with Maestro advancing state-of-the-art automatic speech recognition (ASR) and Speech Translation (ST) performance. In this paper, we expand our understanding of the resulting shared speech-text representations with two types of analyses. First we examine the limits of speech-free domain adaptation, finding that a corpus-specific duration model for speech-text alignment is the most important component for learning a shared speech-text representation. Second, we inspect the similarities between activations of unimodal (speech or text) encoders as compared to the activations of a shared encoder. We find that the shared encoder learns a more compact and overlapping speech-text representation than the uni-modal encoders. We hypothesize that this partially explains the effectiveness of the Maestro shared speech-text representations.
Differentially Flat Design of Bipeds Ensuring Limit-Cycles (2007)

In bipedal walking, a trajectory is acceptable as long as it is repetitive and allows the foot to clear the ground, while allowing the biped to move forward. Since the actual trajectory followed by a biped is not as important, a biped having more than one passive joints can also meet the motion requirements. Due to physical constraints, a biped is under-actuated at the ground contact with the feet. A biped should exhibit limit cycles when moving continuously in an environment. In general, it is difficult to prove existence of limit cycles for nonlinear systems. In this work, we generate limit cycles for a class of nonlinear underactuated bipeds using differential flatness. A specific inertia distribution renders the biped design differentially flat. Differential Flatness allows generation of a family of limit cycles amenable to numerical optimization. The results are illustrated by two DOF biped.
Icosahedral galloxane clusters (2007)

Hydrolysis of 'tris(aryl or alkyl)gallium(III)' species results in the formation of spheroidal dodecameric galloxane mixed oxide-hydroxide clusters, and shows that the gallium centres and associated residual alkyl/aryl groups are arranged at the polyhedral vertices of pseudo-icosahedra.
Interactions between transport inhibitors at the anion binding sites of the band 3 dimer (1981)

Evidence is presented that the binding of aromatic disulfonates to the external transport sites of the red cell anion-exchange protein (band 3) can exhibit negative cooperativity. Fluorescence resonance energy transfer has been used to compare the affinities of an aromatic disulfonate 4,4'-bis-(4-nitro-2,1,3-benzoxadiazolyl)dihydrostilbene-2,2'-disulfonate[H2(NBD)2DS] for "empty" band 3 dimers (in which neither external transport site is occupied) and for "half-filled" dimers (in which one site per dimer is occupied by a covalently attached fluorescent stilbenedisulfonate). H2(NBD)2DS apparently binds to the external anion transport site since it is a potent inhibitor of [35S]sulfate influx into red cells (Ki = 20-50 nM), binds reversibly to approximately one site per band 3 monomer (1.6 X 10(6) sites/cell), and is displaced by covalent labeling with a disulfonic stilbene. The affinity of H2(NBD)2DS for membranes in which 80% of the transport sites are occupied by covalently attached 4-benzamido-4'-isothiocyanostilbene-2,2'-disulfonate (BIDS) was approximately 1 order of magnitude lower than that for unmodified membranes. However, when a similar proportion of the transport sites on red cells was blocked by reaction with BIDS, [35S]sulfate was taken up with a lower Vmax but with a Km identical with that observed for unmodified cells, suggesting that no subunit interactions are necessary for transport. Therefore, in order to test whether the observed negative cooperativity of aromatic disulfonate binding could be ascribed simply to steric hindrance, the distance between transport sites was measured by fluorescence resonance energy transfer. H2(NBD)2DS and eosin maleimide were used as acceptors, with BIDS as donor. Transfer efficiencies were determined by donor fluorescence quenching, by acceptor fluorescence enhancement, and from donor lifetime changes. Uncertainties in the distance were estimated from measured depolarization factors. The donor-acceptor distance was found to be only 28-52 A. Since the probes are large molecules, they could therefore be very close together, and the observed negative cooperativity might be explained by overlapping sites. The results suggest that the subunits of a band 3 dimer transport anions independently but that access to the transport sites may be provided by a cavity between the subunits.
CD206+ M2-like macrophages regulate systemic glucose metabolism by inhibiting proliferation of adipocyte progenitors (2017)

Adipose tissue resident macrophages have important roles in the maintenance of tissue homeostasis and regulate insulin sensitivity for example by secreting pro-inflammatory or anti-inflammatory cytokines. Here, we show that M2-like macrophages in adipose tissue regulate systemic glucose homeostasis by inhibiting adipocyte progenitor proliferation via the CD206/TGFβ signaling pathway. We show that adipose tissue CD206<sup>+</sup> cells are primarily M2-like macrophages, and ablation of CD206<sup>+</sup> M2-like macrophages improves systemic insulin sensitivity, which was associated with an increased number of smaller adipocytes. Mice genetically engineered to have reduced numbers of CD206<sup>+</sup> M2-like macrophages show a down-regulation of TGFβ signaling in adipose tissue, together with up-regulated proliferation and differentiation of adipocyte progenitors. Our findings indicate that CD206<sup>+</sup> M2-like macrophages in adipose tissues create a microenvironment that inhibits growth and differentiation of adipocyte progenitors and, thereby, control adiposity and systemic insulin sensitivity.Adipose tissue contains macrophages that can influence both local and systemic metabolism via the secretion of cytokines. Here, Nawaz et al. report that M2-like macrophages, present in adipose tissue, create a microenvironment that inhibits proliferation of adipocyte progenitors due to the secretion of TGF-β1.
Orthogonal assays for the identification of inhibitors of the single-stranded nucleic acid binding protein YB-1 (2019)

We have previously shown that high expression of the nucleic acid binding factor YB-1 is strongly associated with poor prognosis in a variety of cancer types. The 3-dimensional protein structure of YB-1 has yet to be determined and its role in transcriptional regulation remains elusive. Drug targeting of transcription factors is often thought to be difficult and there are very few published high-throughput screening approaches. YB-1 predominantly binds to single-stranded nucleic acids, adding further difficulty to drug discovery. Therefore, we have developed two novel screening assays to detect compounds that interfere with the transcriptional activation properties of YB-1, both of which may be generalizable to screen for inhibitors of other nucleic acid binding molecules. The first approach is a cell-based luciferase reporter gene assay that measures the level of activation of a fragment of the <i>E2F1</i> promoter by YB-1. The second approach is a novel application of the AlphaScreen system, to detect interference of YB-1 interaction with a single-stranded DNA binding site. These complementary assays examine YB-1 binding to two discrete nucleic acid sequences using two different luminescent signal outputs and were employed sequentially to screen 7360 small molecule compounds leading to the identification of three putative YB-1 inhibitors.
Gradient descent algorithm applied to wavefront retrieval from through-focus images by an extreme ultraviolet microscope with partially coherent source (2014)

The wavefront retrieval by gradient descent algorithm that is typically applied to coherent or incoherent imaging is extended to retrieve a wavefront from a series of through-focus images by partially coherent illumination. For accurate retrieval, we modeled partial coherence as well as object transmittance into the gradient descent algorithm. However, this modeling increases the computation time due to the complexity of partially coherent imaging simulation that is repeatedly used in the optimization loop. To accelerate the computation, we incorporate not only the Fourier transform but also an eigenfunction decomposition of the image. As a demonstration, the extended algorithm is applied to retrieve a field-dependent wavefront of a microscope operated at extreme ultraviolet wavelength (13.4 nm). The retrieved wavefront qualitatively matches the expected characteristics of the lens design.
Fabrication of Tunable Duty Cycle Metal Wire Nanograting by Oblique Sputtering (2008)

A method to fabricate metal wire nanogratings of tunable duty cycle (0.5 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">~</sub> 0.9 and even larger) without using e-beam lithography (EBL) is demonstrated. This provides a low cost technology to realize subwavelength metal slit arrays. The fabrication processes and the details of accurately controlling the grating shape are disclosed. The transmission properties of the metal wire nanograting with different duty cycles are discussed. The technique to make multiple layer metal wire grating using oblique deposition is also proposed.
Ventricular remodeling induced by acute nonocclusive constriction of coronary artery in rats (1989)

To determine the consequence of acute nonocclusive constriction of the epicardial coronary artery on the adaptation of the left ventricle and its impact as a function of age, the left main coronary artery was narrowed in rats 4 and 12 mo of age, and the animals were killed 45 min later. Similar reductions in the luminal diameter, averaging 4%, were obtained in both groups of animals, and this change resulted in an increase in left ventricular end-diastolic pressure and a decrease in positive and negative change in pressure overtime (dP/dt) and in peak-developed ventricular pressure. Left ventricular volume increased by 66% and 56% at 4 and 12 mo because of increases in both the longitudinal and transverse chamber diameters. In contrast, wall thickness decreased by 27% and 35%, whereas sarcomere length increased only by 8.0% and 6.0%, respectively. These changes implied the occurrence of side-to-side slippage of myocytes within the wall to accommodate the larger chamber volume. The alterations in myocardial performance combined with the variations in ventricular size and wall thickness produced a marked elevation in diastolic and systolic wall stress. Moreover, myocyte cell damage in the form of contraction bands and disorganization of the intercalated disc region was seen. No consistent difference was found in any of the parameters measured as a function of age. Measurements of resting coronary blood flow across the left ventricular wall before coronary artery narrowing were comparable with those obtained 45 min after constriction. In conclusion, acute nonocclusive coronary artery stenosis has profound detrimental effects on the function and structure of the myocardium in the absence of an impairment of resting coronary blood flow.
Acute carbon dioxide avoidance in Caenorhabditis elegans (2008)

Carbon dioxide is produced as a by-product of cellular respiration by all aerobic organisms and thus serves for many animals as an important indicator of food, mates, and predators. However, whether free-living terrestrial nematodes such as Caenorhabditis elegans respond to CO2 was unclear. We have demonstrated that adult C. elegans display an acute avoidance response upon exposure to CO2 that is characterized by the cessation of forward movement and the rapid initiation of backward movement. This response is mediated by a cGMP signaling pathway that includes the cGMP-gated heteromeric channel TAX-2/TAX-4. CO2 avoidance is modulated by multiple signaling molecules, including the neuropeptide Y receptor NPR-1 and the calcineurin subunits TAX-6 and CNB-1. Nutritional status also modulates CO2 responsiveness via the insulin and TGFbeta signaling pathways. CO2 response is mediated by a neural circuit that includes the BAG neurons, a pair of sensory neurons of previously unknown function. TAX-2/TAX-4 function in the BAG neurons to mediate acute CO2 avoidance. Our results demonstrate that C. elegans senses and responds to CO2 using multiple signaling pathways and a neural network that includes the BAG neurons and that this response is modulated by the physiological state of the worm.