gebhart/patrepeval huggingface dataset:
Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum (2011)

Flow cytometry is an essential tool for dissecting the functional complexity of hematopoiesis. We used single-cell "mass cytometry" to examine healthy human bone marrow, measuring 34 parameters simultaneously in single cells (binding of 31 antibodies, viability, DNA content, and relative cell size). The signaling behavior of cell subsets spanning a defined hematopoietic hierarchy was monitored with 18 simultaneous markers of functional signaling states perturbed by a set of ex vivo stimuli and inhibitors. The data set allowed for an algorithmically driven assembly of related cell types defined by surface antigen expression, providing a superimposable map of cell signaling responses in combination with drug inhibition. Visualized in this manner, the analysis revealed previously unappreciated instances of both precise signaling responses that were bounded within conventionally defined cell subsets and more continuous phosphorylation responses that crossed cell population boundaries in unexpected manners yet tracked closely with cellular phenotype. Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.
Finite difference time domain calculations of antenna mutual coupling (1992)

The finite-difference-time-domain (FD-TD) technique is applied to calculations of self and mutual admittances between wire antennas. The results are compared with results obtained using the method of moments. The agreement is quite good, indicating the possibilities for FDTD application to antenna impedance and coupling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inverter VAR control for distribution systems with renewables (2011)

Motivated by the need to cope with rapid and random fluctuations of renewable generation, we presents a model that augments the traditional Volt/VAR control through switched controllers on a slow timescale with inverter control on a fast timescale. The optimization problem is generally nonconvex and therefore hard to solve. We propose a simple convex relaxation and prove that it is exact provided over-satisfaction of load is allowed. Hence Volt/VAR control over radial networks is efficiently solvable. Simulations of a real-world distribution circuit illustrates that the proposed inverter control achieves significant improvement over the IEEE 1547 standard in terms of power quality and power savings.
Inherited congenital adrenal hyperplasia in the rabbit: absent cholesterol side-chain cleavage cytochrome P450 gene expression. (1992)

We investigated adrenal steroidogenic enzymes, their activity and mRNA expression, and in vitro biosynthesis of an enzyme in rabbits with congenital adrenal hyperplasia (CAH; weight: CAH, 19 +/- 5 mg/adrenal; normal, 2.7 +/- 1.0 mg/adrenal). Serum pregnenolone (delta 5-P) levels in CAH newborn rabbits (12-36 h) were normal (mean/range, 438/51-2191 ng/dl), but corticosterone levels were low [0.05 +/- 0.05 microgram/dl; P less than 0.001 vs. normal (0.66 +/- 0.57)]. Serum Na+ levels in CAH newborn rabbits were in the normal range (143 +/- 30 meq/liter), but K+ levels were elevated [7 +/- 1.1 meq/liter; P less than 0.05 vs. normal (5.9 +/- 0.6 meq/liter)]. Minced normal adrenal tissue incubated with [3H] cholesterol (30-100 pmol/flask) and ACTH (100 mU/flask) produced [3H]delta 5-P (newborn, 21 and 45 fmol/100 mg; adult, 3 and 5 fmol/100 mg) and [3H]corticosterone (newborn, 23 fmol/100 mg; adult, 11.3 fmol/100 mg), but CAH adrenals produced no product (less than 1.3 fmol/100 mg). Adrenal mitochondria from normal newborn rabbits produced delta 5-P (4.4-7 nmol/mg protein), but CAH adrenals did not, while CAH adrenal mitochondria demonstrated over 4 times greater 11 beta-hydroxylase activity. A Western blot of adrenal homogenate from normal newborn rabbits revealed a cholesterol side-chain cleavage cytochrome P450 (P450scc)-immunoreactive species (mol wt, 53 x 10(3), but this species was absent in CAH adrenals; CAH adrenals had a normal adrenodoxin and intensified 17 alpha-hydroxylase cytochrome P450 (P450(17)alpha) band compared to normal adrenals. In vitro translation of RNA in a cell-free rabbit reticulocyte lysate system containing [35S] methionine yielded a precursor P450scc protein (mol wt, 58.5 x 10(3)) with normal adrenal RNA, but not with CAH adrenal RNA. P450scc mRNA was detected in all normal adrenals, but was not detected in all CAH adrenals. 21-Hydroxylase cytochrome P450 mRNA expression was detected at a similar level in both normal and CAH adrenals. We conclude that CAH in the rabbit is caused by inherited absent P450scc gene expression. The clinical, pathological, and biochemical manifestations of P450scc deficiency in the rabbit are nearly identical to the human disorder. Increased 11 beta-hydroxylase activity and increased P450(17)alpha on Western blot of CAH adrenals indicate altered gene expression of other steroidogenic enzymes due to CAH. Further molecular analysis of the P450scc gene in this animal CAH model will facilitate understanding of P450scc deficiency CAH.
Role of Cdk5 in Amyloid-beta Pathology of Alzheimer’s Disease (2019)

Alzheimer's Disease (AD) is a progressive neurodegenerative disease with irreversible cognitive impairment. So far, successful treatment and prevention for this disease are deficient in spite of delaying the progression of cognitive impairment and dementia. Cyclin dependent kinase 5 (Cdk5), a unique member of the cyclin-dependent kinase family, is involved in AD pathogenesis and may be a pathophysiological mediator that links the major pathological features of AD. Cdk5 dysregulation interferes with the proteolytic processing of Amyloid-beta Protein Precursor (APP) and modulates amyloidbeta (Aβ) by affecting three enzymes called α-, β- and γ-secretase, which are critical for the hydrolysis of APP. Given that the accumulation and deposition of Aβ derived from APP are a common hinge point in the numerous pathogenic hypotheses of AD, figuring out that influence of specific mechanisms of Cdk5 on Aβ pathology will deepen our understanding of AD.
Circulating Tumor Cells—New Challenges Ahead (2012)

The presence of circulating tumor cells (CTCs)2 was first described by Thomas Ashworth in 1869 (1). In 1889, Stephen Paget proposed in the first issue of The Lancet the “seed and soil” hypothesis, according to which “metastasis depends on cross-talk between selected cancer cells (the ‘seeds’) and specific organ microenvironments (the ‘soil’),” a hypothesis revisited many years later by Isaiah Fidler [(2); quotation from Fidler]. It took more than a century to recognize the critical role that CTCs play in the metastatic spread of carcinomas, that the detection of CTCs is associated with prognosis for many cancers (such as those of the breast, colon, and prostate), and that their enumeration is useful in follow-up (3). On the basis of these developments, the evaluation of CTCs now represents a promising new diagnostic tool, especially for advanced-stage cancer patients, for whom CTCs can be used as a “liquid biopsy” that allows physicians to follow cancer changes over time and tailor treatment accordingly (3).

Given that CTCs are very rare, the very limited amount of available biological sample presents a unique analytical and technical challenge. CTCs can now be isolated, detected, and enumerated with a plethora of highly sensitive analytical methods, such as quantitative reverse-transcription PCR, image-based approaches, and techniques that use microfilter and microchip devices (4). In most cases, the isolation and detection of CTCs depend primarily on their epithelial characteristics, and antibodies to epithelial cell adhesion molecule (EpCAM) and cytokeratins (CKs), respectively, are used for this purpose. At present, the CellSearch® system (Veridex) is the only technology that has been cleared by the US Food and Drug Administration for the detection and enumeration of CTCs in patients with metastatic …
Peptide Requirement for CTL Activation Reflects the Sensitivity to CD3 Engagement: Correlation with CD8αβ Versus CD8αα Expression (2001)

In our previous studies, CTL that were sensitive to low concentrations of peptide Ag were found to be far superior to those requiring high concentrations of Ag for reducing viral burden when adoptively transferred into SCID mice. Thus it is important that we understand the mechanisms that control the requirement for peptide Ag with the long-term goal of selectively expanding these exquisitely sensitive cells in vivo. Although TCR affinity is one parameter that can affect the CTL sensitivity for Ag, we investigated whether additional mechanisms may also be involved. In studies using a TCR transgenic mouse model, we successfully generated CTL with identical TCR affinity that possess distinctly different activation requirements. Using both peptide Ag and anti-CD3 Ab to activate the CTL lines of high vs low avidity, we found that the variations in activation threshold are the result of differences in the required number of engaged TCR. Additionally, we have observed that the ratio of CD8alphabeta to CD8alphaalpha is significantly greater in CTL lines that are more sensitive to TCR engagement, which may contribute to the lower activation threshold of these CTL following CD3 engagement. These studies identify a novel mechanism by which the activation requirements of Ag-specific CTL are determined by demonstrating a direct correlation between the sensitivity to TCR engagement, the expression of levels CD8alphabeta vs alphaalpha, and the amount of peptide Ag required to reach the threshold for activation.
CD133: to be or not to be, is this the real question? (2013)

CD133 (promini-1) is a member of the transmembrane glycoprotein family, was initially described as a specific marker to select human hematopoietic progenitor cells. Then, it was recognised as important marker to identify and isolate the specific cell subpopulation termed "cancer stem cells". Many studies showed that CD133(+) cells have stemness properties such as self-renewal, differentiation ability, high proliferation and they are able also to form tumours in xenografts. Moreover it has been demonstrated that CD133(+) cells more resistant to radiation and standard chemotherapy than CD133(-) cells. Although this, others investigations demonstrated that also CD133(-) cells can show the same characteristics of those positive for CD133(+). Hence, some inconsistencies among published data on CD133 function can be ascribed to different causes questioning the main role as specific marker of cancer stem cells. In fact, many authors indicate that CD133 is expressed both in differentiated and undifferentiated cells, and CD133(-) cancer cells can also initiate tumours. Indeed, it is still a matter of debate whether CD133(+) cells truly represent the ultimate tumourigenic population. However, the belief that CD133 may act as a universal marker of CSCs has been met with a high degree of controversy in the research community. In this review there is an attempt to highlight: i) the role and function of CD133, with an overview on the current stage of knowledge about this molecule, ii) the difficulty often encountered in its identification iii) the utility of CD133 expression as a prognostic marker.
Adaptive fuzzy logic control (1992)

A systematic design procedure for fuzzy linguistic controllers with adaptive or learning capability is introduced. The design is based on stability and hierarchy of identification and control. The fuzzy rule-base is stored in a fuzzy hypercube and the fuzzy control action is computed via a fuzzy inference mechanism. Initial conditions for the elements of a fuzzy hypercube are obtained by an offline fuzzy clustering mechanism with large-grain uncertainty. Two fuzzy algorithms are developed: the first one is a fuzzy identification-learning algorithm and the second is a fuzzy control-inferencing algorithm. The fuzzy identification-learning algorithm updates the membership functions on the action side of the rules and the fuzzy control-inferencing algorithm calculates fuzzy control data. This approach guarantees the stability, convergence, and robustness of the closed-loop feedback system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Neural adaptive content-aware internet video delivery (2018)

Internet video streaming has experienced tremendous growth over the last few decades. However, the quality of existing video delivery critically depends on the bandwidth resource. Consequently, user quality of experience (QoE) suffers inevitably when network conditions become unfavorable. We present a new video delivery framework that utilizes client computation and recent advances in deep neural networks (DNNs) to reduce the dependency for delivering high-quality video. The use of DNNs enables us to enhance the video quality independent to the available bandwidth. We design a practical system that addresses several challenges, such as client heterogeneity, interaction with bitrate adaptation, and DNN transfer, in enabling the idea. Our evaluation using 3G and broadband network traces shows the proposed system outperforms the current state of the art, enhancing the average QoE by 43.08% using the same bandwidth budget or saving 17.13% of bandwidth while providing the same user QoE.
Immunochemical Characterization of Native Polysaccharides from Group B Streptococcus: The Relationship of the Type III and Group B Determinants (1978)

Abstract Three polysaccharides were purified from a type III strain of Group B Streptococcus grown under conditions varying in exposure to acid by washing the cells with an EDTA buffer or extracting with cold 10% TCA. Extraction of cells grown in a medium buffered with a pH titrator resulted in a polysaccharide antigen of 1.2 × 106 daltons having only type III serologic specificity. The antigen extracted with EDTA from cells grown in a medium where acid accumulated had a molecular size of approximately 600,000, and demonstrated both type III and group B serologic activity. The antigen extracted with TCA had a molecular size of approximately 500,000 and also reacted with type III and group B sera. Chemical studies revealed that all three polysaccharides contained varying concentrations of galactose, glucose, glucosamine, and sialic acid. Only the TCA antigen contained rhamnose. Alcohol fractionation of the TCA antigen allowed separation of type III from group B serologic reactivity. However, this method failed to separate the two determinants of the EDTA-non-pH titrated antigen. Other physical, chemical, and immunologic methods similarly failed to separate these two determinants. Mild hydrolysis of the EDTA-pH-titrated antigen exposed a determinant immunologically identical to the formamide-extracted group B antigen. These studies as well as electron microscopy and affinity chromatography demonstrated that two determinants exist on the native polysaccharide antigen of type III, Group B Streptococcus. One is the superficial capsular type specific determinant, which in the most native state masks the second determinant, a common group B determinant. Quantitative precipitation inhibition studies confirmed that l-rhamnose was the immunodominant sugar for the formamide-extracted B antigen. No monosaccharide inhibited the cross-reactive determinant on the EDTA-non pH titrated antigen. Despite this observation, both the formamide-extracted B antigen and the EDTA-non pH titrated antigen were demonstrated to be precipitating antibodies of identical specificity.
Depressed Ventilatory Load Compensation in Sleep Apnea: Reversal by Nasal CPAP (1993)

Abnormal inspiratory load compensation may be one factor leading to development of obstructive sleep apnea (OSA). Alternatively, abnormalities in ventilatory load compensation may be a consequence of the manifestations of OSA. This investigation was designed to determine if impairment of awake inspiratory load compensation exists in OSA and to determine if abnormalities in this parameter are reversible by nasal CPAP therapy. A new technique for assessment of awake inspiratory load compensation was devised to standardize the degree of ventilatory stimulation applied during load compensation assessment in each subject. This eliminates intersubject differences in degree of ventilatory stimulation during testing, which are inevitable with standard techniques and which have been shown to affect the measurement of load compensation. Inspiratory load compensation was assessed during resting room air ventilation and during steady state CO2 and exercise stimulation titrated to provide similar degrees of ventilatory stimulation in each subject. Impairment of awake inspiratory load compensation was found during all conditions in the patients with moderate to severe OSA studied compared with that in weight-matched control subjects. Normalization of awake inspiratory load compensation was observed after 4 wk of nasal CPAP therapy in five patients. These results indicate that impairment of awake inspiratory load compensation is a reversible consequence rather than a cause of OSA.
Interleukin‐18 acts as an angiogenesis and tumor suppressor (1999)

Interleukin-18 (IL-18), also called interferon-gamma (IFN-gamma)-inducing factor, has recently been characterized as a potent IFN-gamma-inducing cytokine. We now report that IL-18 is a novel antiangiogenic and antitumor cytokine. In vitro, IL-18 specifically inhibits fibroblast growth factor-2-stimulated proliferation of capillary endothelial cells. In vivo, IL-18 is sufficiently potent to suppress the fibroblast growth factor-induced corneal neovascularization by systemic administration in mice. This cytokine also inhibits embryonic angiogenesis in the chick chorioallantoic membrane assay. Systemic and intralesional administrations of IL-18 produce a significant suppression of the growth of murine T241 fibrosarcoma in syngeneic C57Bl6/J and immunodeficient SCID mice. The antitumor effect appears to be potent because an average of >75% inhibition of primary tumor growth was observed at a dose of 50 microg/kg/day. In cell culture, murine T241 fibrosarcoma cells are insensitive to recombinant IL-18 at concentrations that significantly inhibit endothelial cell proliferation. Immunohistochemical studies of tumor tissues reveal hypovascularization of the IL-18-treated tumors. These results suggest that IL-18 may participate in the regulation of a switch of tumor angiogenesis.-Cao, R., Farnebo, J., Kurimoto, M., Cao, Y. Interleukin-18 acts as an angiogenesis and tumor suppressor.
Electronic speckle photography: increased accuracy by nonintegral pixel shifting (1994)

Electronic speckle photography offers a simple and fast technique for measuring in-plane displacement fields in solid and fluid mechanics. An improved algorithm is presented and analyzed by use of both computer-simulated speckle patterns and real experiments. The idea of the improved algorithm is to maximize the correlation between correlated subimages from different images by shifting one of them by nonintegral pixel values. The improved algorithm was found to determine displacement components with an uncertainty of less than 1% of a pixel and with negligible systematic errors in ideal experimental conditions.
Estrogen Induces c-myc Gene Expression via an Upstream Enhancer Activated by the Estrogen Receptor and the AP-1 Transcription Factor (2011)

c-myc oncogene is implicated in tumorigenesis of many cancers, including breast cancer. Although c-myc is a well-known estrogen-induced gene, its promoter has no estrogen-response element, and the underlying mechanism by which estrogen induces its expression remains obscure. Recent genome-wide studies by us and others suggested that distant elements may mediate estrogen induction of gene expression. In this study, we investigated the molecular mechanism by which estrogen induces c-myc expression with a focus on these distal elements. Estrogen rapidly induced c-myc expression in estrogen receptor (ER)-positive breast cancer cells. Although estrogen had little effect on c-myc proximal promoter activity, it did stimulate the activity of a luciferase reporter containing a distal 67-kb enhancer. Estrogen induction of this luciferase reporter was dependent upon both a half-estrogen response element and an activator protein 1 (AP-1) site within this enhancer, which are conserved across 11 different mammalian species. Small interfering RNA experiments and chromatin immunoprecipitation assays demonstrated the necessity of ER and AP-1 cross talk for estrogen to induce c-myc expression. TAM67, the AP-1 dominant negative, partially inhibited estrogen induction of c-myc expression and suppressed estrogen-induced cell cycle progression. Together, these results demonstrate a novel pathway of estrogen regulation of gene expression by cooperation between ER and AP-1 at the distal enhancer element and that AP-1 is involved in estrogen induction of the c-myc oncogene. These results solve the long-standing question in the field of endocrinology of how estrogen induces c-myc expression.
Catadioptric projective geometry: theory and applications (2002)

Catadioptric cameras are devices which use both mirrors (catadioptric elements) and lenses (dioptric elements) to form images. In computer vision and robotics, catadioptric cameras have been used for their wide field of view. Such cameras often have a field of view greater than 180°, which is unobtainable from perspective cameras. The cost of this extra-wide field of view is a distortion in the image when compared with perspective images. Unless this distortion is known, it is not possible to apply now classical computer vision algorithms to solve the structure-from-motion (SFM) problem, to use just one example. In this dissertation we study the geometry induced by such devices so that we may solve the SFM problem for catadioptric devices. In the first part of the thesis we prove that all central catadioptric devices, those whose mirrors have conic sections as cross-sections, can be decomposed into a central projection to a sphere centered about the viewpoint, followed by central projection from a point on the sphere's axis. This result introduces a unifying model for describing all central catadioptric projections. The second principle result singles out those catadioptric devices with parabolic mirrors, which the previous result shows to be equivalent to projection to the sphere followed by stereographic projection. We demonstrate the existence of a bilinear constraint on the inverse stereographic projection of image points, even in the uncalibrated case. The coefficients of the bilinear constraint are shown to encode the intrinsic parameters of the projection, thus allowing for self-calibration from two views if the intrinsic parameters are equal. Using these results we implement a procedure to estimate the structure and motion from two parabolic views. These results are novel and have important applications in computer vision. In particular, a framework for studying vision in central catadioptric sensors is provided. Using this framework we introduce reconstruction and self-calibration algorithms solving the SFM problem for a class of catadioptric sensors, and furthermore we obtain results which are theoretically impossible to achieve in perspective cameras. The algorithms are shown to be robust to noise and deviations from ideal models.