gebhart/patrepeval huggingface dataset:
Rapid changes in specific estrogen binding elicited by cGMP or cAMP in cytosol from human endometrial cells. (1983)

Addition of cGMP to cytosol of human endometrium or to cells of the endometrial cancer line HEC-1 produced severalfold increases in specific estrogen binding (EB) levels. This effect was maximal with 1 microM cGMP in the presence of 0.1 mM isobutylmethylxanthine (a phosphodiesterase inhibitor) during incubations with [3H]estradiol. In contrast, cAMP decreased EB levels under similar conditions. The effects of cyclic nucleotides on EB levels were complete in less than 15 min in the presence of Mg2+, Mn2+, or Ca2+. The EB sites generated by the addition of cGMP during labeling of cytosol with 10 nM [3H]estradiol were found to sediment in the 8S and 4S regions of low-salt glycerol gradients. No changes in EB levels were observed when cyclic nucleotides were added to cytosol depleted of ATP by preincubation at 4 degrees C for 3 hr, but responsiveness was restored by addition of exogenous ATP. The ATP requirement and the pattern of dependence of cyclic nucleotide actions on divalent cation concentrations suggest that cGMP and cAMP effects may be mediated by kinases and may involve phosphorylations. Another possibility is that the cyclic nucleotides interact allosterically with the binder in the presence of ATP. Addition of sodium molybdate, ATP, and GTP to homogenates of endometrial tissue or HEC-1 cells produces increases in EB levels similar to those obtained by the addition of cGMP. However, these compounds are much less active when added to cytoplasm or cytosol. On the basis of these and other observations, it is hypothesized that molybdate, ATP, and GTP affect EB levels primarily by increasing cGMP concentrations through processes involving a plasma membrane-bound guanylate cyclase.
Large number of CD19+/CD23+ B cells and small number of CD8+ T cells as early markers for cow's milk allergy (CMA) (1998)

Assessment of activation of immune mechanisms is valuable in the early diagnosis of cow's milk allergy (CMA). The purpose of this study was to evaluate peripheral blood lymphocyte subclasses in children suspected of having CMA and healthy infants in order to detect an early marker for food allergy. Altogether 47 breast-fed infants, aged from 0.4 to 10 months were followed-up prospectively from birth because of atopic heredity. Twenty-three of the infants were healthy and 24 infants had a strong suspicion of and later challenge-proven cow's milk allergy. Leucocyte subsets were determined from peripheral blood mononuclear cells by flow cytometry. In response to a clinical cow's milk challenge, seven infants developed urticaria, 11 infants had eczema, three patients had loose stools, diarrhoea or vomiting and three infants had eczema and diarrhoea, loose stools or vomiting. The total percentage of B cells and also the proportion of B cells bearing a low-affinity IgE receptor as a marker for activation were significantly higher, whereas the percentage of CD8+ T cells was significantly lower in infants with challenge-proven CMA than in healthy controls. These results imply that infants with active CMA have a defect in regulation of B-cell function. Further, they suggest that imbalance of the ratio of suppressor and helper T cells might be an important factor in the etiopathogenesis of CMA. Our results show that large numbers of activated CD19+ B cells and low numbers of CD8+ T cells could be considered as early markers for food allergy since they are already detectable in peripheral blood during the earliest symptoms of CMA.
INCORPORATING MACHINE VISION IN PRECISION DAIRY FARMING TECHNOLOGIES (2016)

The inclusion of precision dairy farming technologies in dairy operations is an area of increasing research and industry direction. Machine vision based systems are suitable for the dairy environment as they do not inhibit workflow, are capable of continuous operation, and can be fully automated. The research of this dissertation developed and tested 3 machine vision based precision dairy farming technologies tailored to the latest generation of RGB+D cameras. The first system focused on testing various imaging approaches for the potential use of machine vision for automated dairy cow feed intake monitoring. The second system focused on monitoring the gradual change in body condition score (BCS) for 116 cows over a nearly 7 month period. Several proposed automated BCS systems have been previously developed by researchers, but none have monitored the gradual change in BCS for a duration of this magnitude. These gradual changes infer a great deal of beneficial and immediate information on the health condition of every individual cow being monitored. The third system focused on automated dairy cow feature detection using Haar cascade classifiers to detect anatomical features. These features included the tailhead, hips, and rear regions of the cow body. The features chosen were done so in order to aid machine vision applications in determining if and where a cow is present in an image or video frame. Once the cow has been detected, it must then be automatically identified in order to keep the system fully automated, which was also studied in a machine vision based approach in this research as a complimentary aspect to incorporate along with cow detection. Such systems have the potential to catch poor health conditions developing early on, aid in balancing the diet of the individual cow, and help farm management to better facilitate resources, monetary and otherwise, in an appropriate and efficient manner. Several different applications of this research are also discussed along with future directions for research, including the potential for additional automated precision dairy farming technologies, integrating many of these technologies into a unified system, and the use of alternative, potentially more robust machine vision cameras.
Metabolic toxicity of fluorescent stains on thawed cryopreserved bovine sperm cells. (1991)

Several fluorescent probes, including derivatives of carboxyfluorescein, carbocyanine, ethidium, and rhodamine, have been used to assess sperm viability. However, the effects of these fluorescent dyes on the metabolic activity of sperm cells have not been systematically examined. This study was conducted to determine the effect of specific fluorescent stains on the metabolic processes of sperm. Cryopreserved bovine sperm cells were thawed, fluorescently stained, and examined using metabolic and flow cytometric techniques. Sperm were stained with either rhodamine 123 (Rhod-123), the aliphatic cell-tracking compound PKH2-GL, dihydro-ethidium (HED), the bisbenzimide stain Hoechst 33342 (Ho33342), or left unstained. The stained samples were compared for metabolic activity, cell staining pattern, and fluorescent intensity over a 180-min period. Samples stained with HED, Ho33342, and PKH2-GL had less oxygen uptake when compared with the unstained sperm samples (p greater than 0.05). Unstained samples and samples stained with Rhod-123 had similar oxygen consumption. The carbon dioxide produced during the 180 min was not different between controls and stained samples. Therefore, some fluorescent probes inhibit the oxygen metabolism of thawed, cryopreserved bovine sperm cells.
DNA gene vaccination for HIV (1997)

The human immunodeficiency virus-1 (HIV-1) is a retrovirus which preferentially infects and kills CD4+ T cells and macrophages, ultimately resulting in immune system failure and multi-pathogen infections. Recent breakthroughs in combination therapy using three different anti-retroviral agents have generated optimism regarding the ability to control viral replication in vivo [46]. However, this therapeutic regimen is costly, and it is too early to tell whether this approach can eradicate established infection [26, 46]. The costs and the stringent administration regimen requirements of these pharmaceutical agents make it clear that these drugs will only be effectively utilized in a limited part of the world population. Therefore, to address the worldwide problem of HIV-1 infection, there remains a need for a prophylactic vaccination strategy designed to control the epidemic through mass immunization campaigns [115].
Randomized Trial of C5a Receptor Inhibitor Avacopan in ANCA-Associated Vasculitis (2017)

Alternative C activation is involved in the pathogenesis of ANCA-associated vasculitis. However, glucocorticoids used as treatment contribute to the morbidity and mortality of vasculitis. We determined whether avacopan (CCX168), an orally administered, selective C5a receptor inhibitor, could replace oral glucocorticoids without compromising efficacy. In this randomized, placebo-controlled trial, adults with newly diagnosed or relapsing vasculitis received placebo plus prednisone starting at 60 mg daily (control group), avacopan (30 mg, twice daily) plus reduced-dose prednisone (20 mg daily), or avacopan (30 mg, twice daily) without prednisone. All patients received cyclophosphamide or rituximab. The primary efficacy measure was the proportion of patients achieving a ≥50% reduction in Birmingham Vasculitis Activity Score by week 12 and no worsening in any body system. We enrolled 67 patients, 23 in the control and 22 in each of the avacopan groups. Clinical response at week 12 was achieved in 14 of 20 (70.0%) control patients, 19 of 22 (86.4%) patients in the avacopan plus reduced-dose prednisone group (difference from control 16.4%; two-sided 90% confidence limit, -4.3% to 37.1%; <i>P</i>=0.002 for noninferiority), and 17 of 21 (81.0%) patients in the avacopan without prednisone group (difference from control 11.0%; two-sided 90% confidence limit, -11.0% to 32.9%; <i>P</i>=0.01 for noninferiority). Adverse events occurred in 21 of 23 (91%) control patients, 19 of 22 (86%) patients in the avacopan plus reduced-dose prednisone group, and 21 of 22 (96%) patients in the avacopan without prednisone group. In conclusion, C5a receptor inhibition with avacopan was effective in replacing high-dose glucocorticoids in treating vasculitis.
A study of the use of local interconnect in CMOS leaf cell design (2003)

The authors present a leaf-cell layout methodology for harnessing the potential of the local interconnect (LI) layer in digital CMOS circuits. Based on the line-of-diffusion layout style, LI is used for selected connections, typically at the output of logic gates, in order to free up the metal layer in congested areas. The authors present experimental results based on a variety of logic cells which demonstrate the benefit of the LI in terms of cell area, circuit reliability, and routing flexibility.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Theoretical study of the coherent backscattering of light by disordered media (1988)

A theoretical study of the coherent backscattering effect of light from disordered semi-infinite media is presented for various situations including time-dependent effects as well as absorption and amplitude modulation. Particular attention is devoted to the case of anisotropic scattering and to polarization in order to explain quantitatively experimental results. A microscopic derivation of the coherent albedo is given which strongly supports the heuristic formula previously established. In addition the coherent albedo of a fractal system is predicted. The validity of the different approximations used are discussed and some further theoretical developments are presented.
Revisiting Millikan's Oil-Drop Experiment (2005)

This article revisits the original data from Millikan's oil-drop experiment. The data have been analyzed using Microsoft Excel. As expected, the results show that Millikan obtained almost exactly the same value that is obtained using a modern computer and spreadsheet. Millikan did not use factoring of the measured charges even though this is often the explanation given in discussions of this experiment. The smallest difference observed indicates the charge of the electron and provides an initial value for the computer analysis of the data. This analysis would be a good exercise (or introductory laboratory) to illustrate the use of spreadsheets for analysis of laboratory data in the physical chemistry laboratory. Other chemistry teachers might also benefit from this analysis and by reading Millikan's primary article on this experiment.
Complexes of ruthenium(4) with nicotinic acid; Kompleksy ruteriya(4) s nikotinovoj koslotoj (1997)

Nicotinic acid (HL) interaction with (NH{sub 4}){sub 2}x[RuNOCl{sub 5}] has been studied. Dependence of the composition of the complexes formed on the medium acidity has been shown. The complexes structure has been analyzed by the methods of thermogravimetry, IR- and X-ray electron spectroscopy. A new type of nicotinic acid anion coordination-bidentate-bridge one- has been ascertained: the ligand is coordinated via pyridine nitrogen atom and carboxylate group oxygen with formation of binuclear complexes. 21 refs.
Keloid‐derived keratinocytes exhibit an abnormal gene expression profile consistent with a distinct causal role in keloid pathology (2013)

Keloids are disfiguring scars that extend beyond the original wound borders and resist treatment. Keloids exhibit excessive extracellular matrix deposition, although the underlying mechanisms remain unclear. To better understand the molecular basis of keloid scarring, here we define the genomic profiles of keloid fibroblasts and keratinocytes. In both cell types, keloid-derived cells exhibit differential expression of genes encompassing a diverse set of functional categories. Strikingly, keloid keratinocytes exhibited decreased expression of a set of transcription factor, cell adhesion, and intermediate filament genes essential for normal epidermal morphology. Conversely, they exhibit elevated expression of genes associated with wound healing, cellular motility, and vascular development. A substantial number of genes involved in epithelial-mesenchymal transition were also up-regulated in keloid keratinocytes, implicating this process in keloid pathology. Furthermore, keloid keratinocytes displayed significantly higher migration rates than normal keratinocytes in vitro and reduced expression of desmosomal proteins in vivo. Previous studies suggested that keratinocytes contribute to keloid scarring by regulating extracellular matrix production in fibroblasts. Our current results show fundamental abnormalities in keloid keratinocytes, suggesting they have a profoundly more direct role in keloid scarring than previously appreciated. Therefore, development of novel therapies should target both fibroblast and keratinocyte populations for increased efficacy.
The mRNA and RNA-copy pseudogenes encoding TM30<sub>nm</sub>, a human cytoskdetal tropomyosin (1986)

We have determined the sequence of a 2.5 kb mRNA in human fibroblasts encoding a 248 amino acid cytoskeletal tropomyosin. The protein product of this mRNA is TM30nm, one of five tropomyosin-like proteins in human fibroblasts. The structural gene encoding this mRNA can also produce a 1.3 kb mRNA encoding a 285 amino acid skeletal muscle alpha-tropomyosin by tissue-specific alternative mRNA splicing. However, the multiple RNA-copy pseudogenes of this gene family are derived largely if not exclusively from transcripts processed according to the pattern observed in non-muscle cells.
Quantum transport modeling in anisotropic semiconductors using Wigner function formulation (2005)

The Wigner transport equation is formulated in anisotropic semiconductor quantum wells. We suggest a formulation in which we can use the conventional Wigner transport equation solvers developed assuming isotropic materials for the actual numerical calculation. The three-dimensional Wigner function involving effective mass tensor can be reduced into one-dimensional form which involves only one diagonal effective mass tensor element and the original three-dimensional Wigner function is given as the convolution of the one-dimensionally reduced Wigner function with a newly defined function related to the off-diagonal effective mass tensor elements.
Probabilistic Evaluation of Counterfactual Queries (2022)

Evaluation of counterfactual queries (e.g., &quot;If A were true, would C have been true?&quot;) is important to fault diagnosis, planning, and determination of liability. We present a formalism that uses probabilistic causal networks to evaluate one&apos;s belief that the counterfactual consequent, C, would have been true if the antecedent, A, were true. The antecedent of the query is interpreted as an external action that forces the proposition A to be true, which is consistent with Lewis&apos; Miraculous Analysis. This formalism offers a concrete embodiment of the &quot;closest world&quot; approach which (1) properly reflects common understanding of causal influences, (2) deals with the uncertainties inherent in the world, and (3) is amenable to machine representation.
Global bifurcation from intervals for Sturm-Liouville problems which are not linearizable (2013)

In this paper, we study unilateral global bifurcation which bifurcates from the trivial solutions axis or from infinity for nonlinear Sturm--Liouville problems of the form \begin{equation} \left\{ \begin{array}{l} -\left(pu'\right)'+qu=\lambda au+af\left(x,u,u',\lambda\right)+g\left(x,u,u',\lambda\right)\,\,\text{for}\,\, x\in(0,1),\\ b_0u(0)+c_0u'(0)=0,\\ b_1u(1)+c_1u'(1)=0, \end{array} \right.\nonumber \end{equation} where $a\in C([0, 1], [0,+\infty))$ and $a(x)\not\equiv 0$ on any subinterval of $[0, 1]$, $f,g\in C([0,1]\times\mathbb{R}^3,\mathbb{R})$. Suppose that $f$ and $g$ satisfy \begin{equation} \vert f(x,\xi,\eta,\lambda)\vert\leq M_0\vert \xi\vert+M_1\vert \eta\vert,\,\, \forall x\in [0,1]\,\,\text{and}\,\,\lambda \in\mathbb{R}, \nonumber \end{equation} \begin{equation} g(x,\xi,\eta,\lambda)=o(\vert \xi\vert+\vert \eta\vert),\,\, \text{uniformly in}\,\, x\in [0,1]\,\,\text{and}\,\,\lambda \in \Lambda,\nonumber \end{equation} as either $\vert \xi\vert+\vert \eta\vert\rightarrow 0$ or $\vert \xi\vert+\vert \eta\vert\rightarrow +\infty$, for some constants $M_0$, $M_1$, and any bounded interval $\Lambda$.
Keyboards and covert channels (2006)

Previous studies on how we hit moving targets have revealed that the direction in which we move our hand is continuously adjusted on the basis of the target's perceived position, with a delay of about 110 ms. In the present study we show that the acceleration of the hand is also under such continuous control. Subjects were instructed to hit moving targets (running spiders) as quickly as possible with a rod. We found that changing the velocity of the target influenced the speed with which the rod was moved. The influence was noticeable about 200 ms after the target's velocity changed. The extent of the influence was consistent with a direct dependence of the acceleration of the hand on the target's velocity. We conclude that the acceleration of the hand is continuously adjusted on the basis of the speed of the target, with a delay of about 200 ms.
Evaluation of “Credit Card” Libraries for Inhibition of HIV-1 gp41 Fusogenic Core Formation (2006)

Protein-protein interactions are of critical importance in biological systems, and small molecule modulators of such protein recognition and intervention processes are of particular interest. To investigate this area of research, we have synthesized small-molecule libraries that can disrupt a number of biologically relevant protein-protein interactions. These library members are designed upon planar motif, appended with a variety of chemical functions, which we have termed "credit-card" structures. From two of our "credit-card" libraries, a series of molecules were uncovered which act as inhibitors against the HIV-1 gp41 fusogenic 6-helix bundle core formation, viral antigen p24 formation, and cell-cell fusion at low micromolar concentrations. From the high-throughput screening assays we utilized, a selective index (SI) value of 4.2 was uncovered for compound 2261, which bodes well for future structure activity investigations and the design of more potent gp41 inhibitors.
Potent Activity of a Novel Dimeric Heat Shock Protein 90 Inhibitor against Head and Neck Squamous Cell Carcinoma <i>In vitro</i> and <i>In vivo</i> (2005)

Heat shock protein 90 (Hsp90) is a molecular chaperone that promotes the conformational maturation of numerous client proteins, many of which play critical roles in tumor cell growth and survival. The ansamycin-based Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG) is currently in phase I/II clinical testing. However, 17-AAG is difficult to formulate and displays weak activity against some tumors. A novel dimeric ansamycin, EC5, was evaluated for antitumor activity in eight head and neck squamous cell carcinoma (HNSCC) cell lines. Both 17-AAG and EC5 inhibited tumor cell proliferation effectively, but EC5 was more potent, with IC(50) below 200 nmol/L in most cell lines tested, including several lines that were resistant to 17-AAG. The inability of 17-AAG to kill JHU12 cells was linked to a defect in retinoblastoma signaling and could be rescued by ectopic expression of p16(INK4a). EC5 induced G(1) growth arrest of tumor cells and apoptosis, with the degradation of client proteins including epidermal growth factor receptor, c-Raf-1, Akt, and Cdk4 and inhibition of Akt phosphorylation. In vivo, EC5 dramatically reduced the growth rate of established HNSCC xenografts in nude mice and decreased expression of epidermal growth factor receptor and Akt within the xenografts. These results suggest that this novel ansamycin-based Hsp90 inhibitor affects multiple pathways involved in tumor development and progression and may represent a new strategy for the treatment of HNSCC patients.
Checkpoint processing and recovery: an efficient, scalable alternative to reorder buffers (2003)

Processors require a combination of large instruction windows and high clock frequency to achieve high performance. Traditional processors use reorder buffers, but these structures do not scale efficiently as window size increases. A new technique, checkpoint processing and recovery, offers an efficient means of increasing the instruction window size without requiring large, cycle-critical structures, and provides a promising microarchitecture for future high-performance processors.
Validation of a new t2* algorithm and its uncertainty value for cardiac and liver iron load determination from MRI magnitude images (2015)

The proposed algorithm was shown to provide robust T2* measurements and uncertainty estimates over the range of clinically relevant T2* values. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance.