gebhart/patrepeval huggingface dataset:
Cord blood-derived CD34+ hematopoietic cells with low mitochondrial mass are enriched in hematopoietic repopulating stem cell function (2013)

The homeostasis of the hematopoietic stem/progenitor cell pool relies on a fine-tuned balance between self-renewal, differentiation and proliferation. Recent studies have proposed that mitochondria regulate these processes. Although recent work has contributed to understanding the role of mitochondria during stem cell differentiation, it remains unclear whether the mitochondrial content/function affects human hematopoietic stem versus progenitor function. We found that mitochondrial mass correlates strongly with mitochondrial membrane potential in CD34(+) hematopoietic stem/progenitor cells. We, therefore, sorted cord blood CD34(+) cells on the basis of their mitochondrial mass and analyzed the in vitro homeostasis and clonogenic potential as well as the in vivo repopulating potential of CD34(+) cells with high (CD34(+) Mito(High)) versus low (CD34(+) Mito(Low)) mitochondrial mass. The CD34(+) Mito(Low) fraction contained 6-fold more CD34(+)CD38(-) primitive cells and was enriched in hematopoietic stem cell function, as demonstrated by its significantly greater hematopoietic reconstitution potential in immuno-deficient mice. In contrast, the CD34(+) Mito(High) fraction was more enriched in hematopoietic progenitor function with higher in vitro clonogenic capacity. In vitro differentiation of CD34(+) Mito(Low) cells was significantly delayed as compared to that of CD34(+) Mito(High) cells. The eventual complete differentiation of CD34(+) Mito(Low) cells, which coincided with a robust expansion of the CD34(-) differentiated progeny, was accompanied by mitochondrial adaptation, as shown by significant increases in ATP production and expression of the mitochondrial genes ND1 and COX2. In conclusion, cord blood CD34(+) cells with low levels of mitochondrial mass are enriched in hematopoietic repopulating stem cell function whereas high levels of mitochondrial mass identify hematopoietic progenitors. A mitochondrial response underlies hematopoietic stem/progenitor cell differentiation and proliferation of lineage-committed CD34(-) cells.
Design and implementation of an adaptive controller for torque ripple minimization in PM synchronous motors (2000)

This paper addresses the problem of torque ripple minimization in permanent magnet synchronous motors (PMSMs) and proposes an adaptive feedback structure as a solution. A model of PMSM that includes a torque ripple phenomenon is first developed and tested. While slightly different from the conventional one, our model is still compact and suitable for control. All parameters of the model have physical interpretation, and can either be measured directly or estimated in a numerically reliable procedure. An adaptive control algorithm is then described, enabling speed tracking while minimizing the torque ripple. Finally, the proposed algorithm is verified in simulations and implemented in a hardware setup. Experimental results show significant reduction of torque ripple (by 27 dB). Extensive analysis and simulations of hardware imposed limitations were performed as well, revealing and quantifying the issues that might affect practical ripple minimization performance.
Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach (2005)

Overdispersed log-linear models provide an attractive and reliable framework for analyzing SAGE experiments involving multiple libraries. For convenience, the implementation of this method is available through a user-friendly web-interface available at http://www.cbcb.duke.edu/sage.
Generation of substrate-free III–V nanodisks from user-defined multilayer nanopillar arrays for integration on Si (2013)

High material quality InP-based multilayer nanopillar (NP) arrays are fabricated using a combination of self-assembly of silica particles for mask generation and dry etching. In particular, the NP arrays are made from user-defined epitaxial multilayer stacks with specific materials and layer thicknesses. An additional degree of flexibility in the structures is obtained by changing the lateral diameters of the NP multilayer stacks. Pre-defined NP arrays made from InGaAsP/InP and InGaAs/InP NPs are then used to generate substrate-free nanodisks of a chosen material from the stack by selective etching. A soft-stamping method is demonstrated to transfer the generated nanodisks with arbitrary densities onto Si. The transferred nanodisks retain their smooth surface morphologies and their designed geometrical dimensions. Both InP and InGaAsP nanodisks display excellent photoluminescence properties, with line-widths comparable to unprocessed reference epitaxial layers of similar composition. The multilayer NP arrays are potentially attractive for broad-band absorption in third-generation solar cells. The high optical quality, substrate-free InP and InGaAsP nanodisks on Si offer a new path to explore alternative ways to integrate III-V on Si by bonding nanodisks to Si. The method also has the advantage of re-usable III-V substrates for subsequent layer growth.
Nonneural Markers in Alzheimer Disease (1992)

Nonneural tissues are now widely used to search for abnormalities in genes as well as for other markers of dementia of the Alzheimer type (DAT). Studies of nonneural tissues can experimentally circumvent problems inherent in the study of autopsy brain, but to be meaningful, abnormalities identified in the periphery must be correlated with abnormalities in the brain, which is the tissue of clinical interest. Among the topics in DAT research that can be readily studied in nonneural cells (including tissue cultures) are molecular genetics, amyloid precursor protein formation and metabolism, systemic manifestations of immunological and inflammatory mechanisms, proteolysis, membranes, signal transduction, and mitochondria and metabolism. Although phenomena suggesting the possibility of cytoskeletal abnormalities in nonneural DAT cells have been described, the tau molecules involved in paired helical filament formation are relatively brain-specific. Since the neuropathological diagnosis of DAT depends on recognizing a pattern of changes rather than any single abnormality, it seems unlikely that any one laboratory abnormality in peripheral tissues will correlate precisely with the clinicopathological entity of DAT. However, abnormalities found in nonneural DAT cells that correlate with the existence of similar abnormalities in the brain are likely to be informative about the disease process in the patients in whom they occur.
Effects of local cytochalasin D delivery on smooth muscle cell migration and on collar‐induced intimal hyperplasia in the rabbit carotid artery (2001)

1. Smooth muscle cell (SMC) migration has been implicated in neointima formation after angioplasty. Therefore, we investigated whether cytochalasin D, a fungal metabolite that inhibits actin filament formation, suppressed SMC migration and collar-induced intimal hyperplasia in the rabbit carotid artery. 2. To establish effective concentrations, contractions of carotid artery rings to phenylephrine were determined after incubation with cytochalasin D (10(-8) - 10(-6) M) for 30 min or 3 days. In vitro cell migration was studied using carotid artery explants and a modified Boyden chamber with SMCs isolated from the rabbit aorta. The in vivo effect was tested after infusion of 10(-8) - 10(-4) M cytochalasin D into collars placed around the left carotid artery; collars placed around the right artery served as controls. 3. Contractions to phenylephrine decreased after 30 min or 3 days exposure to 10(-7) and 10(-6) M cytochalasin D; the effect was partly reversible. These concentrations also inhibited cellular outgrowth and SMC migration in the in vitro assays. 4. Immunohistochemistry showed that local delivery of 10(-5) or 10(-4) M cytochalasin D for 2 weeks suppressed collar-induced alpha-SMC actin expression in the intima by 68% and 84% respectively. However, the cross-sectional area of the intima was not reduced due to an influx of T-lymphocytes and macrophages. 5. It is concluded that cytochalasin D suppressed SMC contractility and migration in vitro. Although perivascular infusion of cytochalasin D inhibited collar-induced SMC migration from media to intima in vivo as well, the intimal hyperplasia was not reduced due to concomitant development of an inflammatory response.
Autophosphorylation-dependent Targeting of Calcium/ Calmodulin-dependent Protein Kinase II by the NR2B Subunit of theN-Methyl-d-aspartate Receptor (1998)

Activation and Thr286 autophosphorylation of calcium/calmodulindependent kinase II (CaMKII) following Ca2+ influx via N-methyl-D-aspartate (NMDA)-type glutamate receptors is essential for hippocampal long term potentiation (LTP), a widely investigated cellular model of learning and memory. Here, we show that NR2B, but not NR2A or NR1, subunits of NMDA receptors are responsible for autophosphorylation-dependent targeting of CaMKII. CaMKII and NMDA receptors colocalize in neuronal dendritic spines, and a CaMKII.NMDA receptor complex can be isolated from brain extracts. Autophosphorylation induces direct high-affinity binding of CaMKII to a 50 amino acid domain in the NR2B cytoplasmic tail; little or no binding is observed to NR2A and NR1 cytoplasmic tails. Specific colocalization of CaMKII with NR2B-containing NMDA receptors in transfected cells depends on receptor activation, Ca2+ influx, and Thr286 autophosphorylation. Translocation of CaMKII because of interaction with the NMDA receptor Ca2+ channel may potentiate kinase activity and provide exquisite spatial and temporal control of postsynaptic substrate phosphorylation.
Stress, NK Receptors, and Immune Surveillance (2001)

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Indomethacin inhibits cholera toxin-induced cyclic AMP accumulation in Chinese hamster ovary cells (1988)

Indomethacin was examined for its capacity to inhibit increases in adenosine-3′,5′-monophosphate (cAMP) concentrations in Chinese hamster ovary (CHO) cells treated with cholera toxin. When added to the culture medium 1 h prior to cholera toxin (100 ng/ml), indomethacin (500 µg/ml) exhibited maximum protection against the typical increase in cAMP. Application of indomethacin at the same time as cholera toxin or up to 3 h after the toxin progressively decreased the drug's capacity to block further increases in cAMP. The drug appeared to block adenylate cyclase activity because addition of forskolin to drug-treated cells did not elicit a cAMP response. Binding of 125I-labeled cholera toxin to indomethacin-treated cells was also reduced by at least 50%. These data indicate that indomethacin's inhibitory effect on cAMP formation in cholera toxin-treated cells could be explained by its capacity to alter adenylate cyclase activity and cholera toxin binding.
Expression of Toll‐like receptor 9 in mouse and human lungs (2013)

Toll-like receptors (TLR) recognize conserved molecular motifs of microorganisms, and constitute an important part of the innate immune system. Numerous studies have shown the importance of these receptors, including TLR9, in establishing effective immune responses to a broad range of infections, and in disorders such as COPD. TLR9 detects unmethylated DNA and is expressed in a wide range of immune cells in mice and humans, as well as other species. Most TLR9 expression studies have been done on cultured or isolated cells, but none that we know of on intact lung. Because cell-specific expression of TLR9 is important to understand its precise role in lung physiology, we tested mouse and human lung tissues for expression of TLR9 mRNA and protein with in situ hybridization and immunohistochemistry, respectively. We found TLR9 mRNA and protein expression in bronchial epithelium, vascular endothelium, alveolar septal cells and alveolar macrophages in both species. Immuno-electron microscopy delineated TLR9 expression in plasma membrane, cytoplasm and the nucleus of various lung cells. Lungs from human cases of COPD had significantly increased numbers of TLR9-positive cells. These are the first data showing TLR9 mRNA and protein expression in intact human and mouse lungs. The data may be useful for clarifying the role of TLR9 in the contributions of specific cells to lung physiology.
Immunologic responses of progressive multiple sclerosis patients treated with an anti‐T‐cell monoclonal antibody, anti‐T12 (1986)

Twelve patients with progressive MS were treated with a murine IgM pan-T-cell monoclonal antibody reactive against T12, a determinant present on most post-thymic T-cells. Circulating T12+ cells could not be detected from days 1 to 7, although T3+T11+T12- cells appeared by day 3. Human anti-mouse antibodies were detected in 78% of patients by day 7 and correlated with a decrease in anti-T12 MAb blood levels and the reappearance of T12+ cells in the blood. Although there were high levels of anti-T12 MAb in the serum, there were only barely detectable levels in the CSF and no decrease in the proportion of T12+ cells in the CSF with treatment. Immunologic studies demonstrated a decrease of in vitro pokeweed mitogen-driven Ig synthesis on day 3 with an increase on day 10 that consisted in part of human anti-mouse antibodies. Eleven of 12 patients completed therapy. Prednisone was administered with the treatment after mild allergic reactions occurred in the first two patients. Because this was an open phase one study and patients were treated with prednisone, the effect of treatment on the progression of disease is difficult to assess, and no definitive conclusions concerning clinical effects can be made.
A finite states Markov quantizer for speech coding (2002)

A low-bit-rate codec based on an ergodic hidden Markov model (EHMM) is presented. A 256-state autoregressive Gaussian EHMM is trained on speech uttered by eight different speakers by means of the Baum-Welch algorithm. Initial estimates are obtained from vector quantization. The resulting EHMM is then utilized for a Viterbi decoding of incoming speech data. The state sequence obtained is frame synchronously encoded. The bit rate is gradually lowered by cutting off low-probability transitions and thus reducing the destination state encoding bit allocation requirements. The encoded spectra sequence is used, on the receiver side of the codec, for linear predictive coding synthesis. Global entropy and distortion measures for different bit rates are reported and compared to vector quantization results. Informal listening tests were performed by comparing the results of the proposed method at various bit rates and vector quantization using the same material.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Altered expression of SIRPγ on the T-cells of relapsing remitting multiple sclerosis and type 1 diabetes patients could potentiate effector responses from T-cells (2020)

Factors regulating self-antigen directed immune-responses in autoimmunity are poorly understood. Signal regulatory protein gamma (SIRPγ) is a human T-cell specific protein with genetic variants associated with type 1 diabetes (T1D). SIRPγ's function in the immune system remains unclear. We show that T1D and relapsing remitting multiple sclerosis (RRMS) subjects have significantly greater frequency of rs2281808 T genetic variant, that correlates with reduced SIRPγ-expression in T-cells. Importantly, reduced SIRPγ-expression in RRMS and T1D subjects was not restricted to T variant, suggesting SIRPγ-expression is also regulated by disease specific factors in autoimmunity. Interestingly, increased frequencies of SIRPγlow T-cells in RRMS and T1D positively correlated with proinflammatory molecules from T-cells. Finally, we show that SIRPγlow T-cells have enhanced pathogenecity in vivo in a GVHD model. These findings suggest that decreased-SIRPγ expression, either determined by genetic variants or through peripherally acquired processes, may have a mechanistic link to autoimmunity through induction of hyperactive T-cells.
Controlling angiogenesis by two unique TGF-β type I receptor signaling pathways. (2011)

Genetic studies in mice and humans have revealed a pivotal function for transforming growth factor-beta (TGF-β) in vascular development and maintenance of vascular homeostasis. Mice deficient for various TGF-β signaling components develop an embryonic lethality due to vascular defects. In patients, mutations in TGF-β receptors have been linked to vascular dysplasia like Hereditary Hemorrhagic Telangiectasia (HHT) and pulmonary arterial hypertension (PAH). Besides indirect effects by regulating the expression of angiogenic regulators, TGF-β also has potent direct effects on endothelial cell growth and migration, and we have proposed that TGF-β regulates the activation state of the endothelium via two opposing type I receptor/Smad pathways, activin receptor-like kinase (ALK)1 and ALK5. TGF-β is also critical for the differentiation of mural precursors into pericytes and smooth muscle cells. Furthermore, defective paracrine TGF-β signaling between endothelial and neighboring mural cells may be responsible for a leaky vessel phenotype that is characteristic of HHT. In this review, we discuss our current understanding of the TGF-β signaling pathway and its regulation of endothelial and vascular smooth muscle cell function.
Thin film disks with transient metal underlayers (1992)

A novel technique for fabricating thin-film disk media with controlled surface roughness and bulk magnetic properties is described. This technique uses a low-melting point metal as an underlayer which is deposited onto a nonwetting substrate to form isolated spherical features. The magnetic layer deposited onto this underlayer is associated with a fine and controllable surface roughness which is desirable for tribological performance. The magnetic and mechanical performances of thin-film disks fabricated with this technique are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experiment and Theory of the Broadband Absorption by a Tapered Hyperbolic Metamaterial Array (2014)

A broadband absorber based on a tapered, alternating metal–dielectric multilayered structure was realized in the visible and IR range. The structure is fabricated by using a versatile method easily scalable to large areas by taking advantage of the line width reduction that occurs naturally in masked evaporation processes. The multilayered structure can be treated as a hyperbolic metamaterial (HMM), and the tapered structure can be regarded as a HMM waveguide with varying width. Light couples into the tapered structure most strongly at the mode cutoff position in the waveguide due to the hyperbolic dispersion and the phase matching condition. Resonant cavities are formed between the top of the tapered structure and the cutoff level, producing strong absorption peaks. These resonances are closely spaced spectrally due to the high k modes in HMM. Finally a broad absorption band is formed due to the broadening of the resonances from an array of coupled HMM tapered structures.
Organ Localization in PET/CT Images using Hierarchical Conditional Faster R-CNN Method (2019)

Localization of multiple organs from whole-body PET/CT image is a prerequisite step of automated PET/CT image analysis. However, due to the large image size and the wide body range, multi-organ detection from whole-body image suffers from high computation burden and low searching accuracy. In this paper, we propose an efficient and accurate multi-organ localization method by combining the conditional Gaussian model (CGM) and the Faster R-CNN object detection neural network. Different organs are detected subsequentially following their anatomical hierarchy. The CGM is used model the inter-organ positional correlations between different hierarchical levels. Once an organ at a coarser level is localized, its children organs at the finer level are roughly predicted using the CGM, and then the Faster R-CNN method is used to refine the locations within the predicted regions. To alleviate the computation burden, we project the volumetric image into orthogonal 2D images and perform organ localization in the projected images. The 2D localization results are then back-projected to 3D to obtain the 3D organ region. Experimental results show that our method achieved sub-centimetre detection accuracy of multiple torso organs within 10min. The accuracy and robustness of our method are both superior to the traditional Faster R-CNN method which does not use the hierarchical searching strategy. We applied our method to both the CT and PET images and found that although PET has worse pixel resolution than CT, it yielded better localization accuracy for the organs with high PET tracer contrast. This result means that intensity contrast is more important than image resolution for improving the localization accuracy.
Synthesis, Critical Micelle Concentrations, and Antimycobacterial Properties of Homologous, Dendritic Amphiphiles. Probing Intrinsic Activity and the “Cutoff” Effect (2007)

Newkome-type, 1-->3 C-branched dendrons make an excellent headgroup for amphiphiles with ultralong, saturated, linear alkyl chains. Synthesis of a homologous series of five such amphiphiles from 14 to 22 carbons-RNHCONHC(CH2CH2CO2H)3, R = n-CnH2n+1, n = 14, 16, 18, 20, 22-proceeds readily. These amphiphiles are soluble in aqueous solutions of triethanolamine. Surface-tension measurements on this homologous series reveal an unusually gradual decrease in log critical micelle concentration (CMC) as the chain length increases. In fact, the tetradecyl homologue does not appear to form micelles. Further, measurements of minimal inhibitory concentration (MIC) by broth microdilution against Mycobacterium smegmatis as a function of the initial cell density provide a direct measure of the intrinsic activity (MIC0) of each homologue. The hexadecyl homologue is the most active at inhibiting growth with an MIC0 equal to 3.5 x 10-5 M, which is 100-fold below the CMC.
UMA AVALIAÇÃO CRÍTICA DA NARRATIVA NA HISTÓRIA DO ESPORTE: LENDO O DEBATE SOBRE O SALVAMENTO NO MAR (2012)

Resumo: Esse artigo e uma tentativa de solucionar a disputa e o debate historico sobre o salvamento no mar envolvendo dois especialistas, Ed Jaggard e Douglas Booth. Tendo em vista a base de seus conhecimentos, seus esforcos de pesquisa e suas experiencias de vida, nao e minha intencao criticar seus trabalhos especificamente a partir de uma perspectiva empirica. Minha tatica nao sera a de adotar o caminho tradicional e questionar suas producoes historicas relacionando-as com as evidencias contextualizadas, mas a de olhar para a construcao literaria de suas narrativas historicas, com base nas obras de Hayden White. Palavras-Chave: narrativa e historia, salvamento no mar, teoria da historia A CRITICAL APPRAISAL OF NARRATIVE IN SPORT HISTORY: READING THE SURF LIFESAVING DEBATE Abstract: This article is an attempt of resolving the historical debate and dispute involving surf lifesaving by two experts, Ed Jaggard and Douglas Booth. Given their knowledge bases, their research efforts and their lived experiences, it is not my intention to critique their work specifically from an empirical perspective. The tack I will adopt is not to take the traditional path by questioning their historical production in relation to the contextualized evidence but to look at the literary construction of their historical narratives, based on the works of Hayden White. Keywords: historical narratives, surf lifesaving, theory of history