gebhart/patrepeval huggingface dataset:
A Comparison of Protocols Used to Generate Insulin-Producing Cell Clusters from Mouse Embryonic Stem Cells (2008)

Embryonic stem cells (ESCs) have the capacity to generate a panoply of tissue types and may therefore provide an alternative source of tissue in regenerative medicine to treat potentially debilitating conditions like Type 1 diabetes mellitus. However, the ability of mouse ESCs to generate insulin-producing cell clusters (IPCCs) remains highly contentious. In an attempt to clarify this issue, three protocols for the ESC-based generation of IPCCs (referred to as Blyszczuk, Hori, and Lumelsky protocols) were modified and evaluated for their ability to express pancreatic islet genes and proteins and their capacity to function. Herein, we show that the Blyszczuk protocol reproducibly generated IPCCs with gene-expression characteristics that were qualitatively and quantitatively most reminiscent of those found in pancreatic islets. Furthermore, compared to the Hori and Lumelsky protocols, Blyszczuk-derived IPCCs exhibited superior expression of c-peptide, a by-product of de novo insulin synthesis. Functionally, Blyszczuk IPCCs, in contrast to Hori and Lumelsky IPCCs, were able to transiently restore normal blood glucose levels in diabetic mice (<1 week). Longer normoglycemic rescue (>2 weeks) was also achieved in a third of diabetic recipients receiving Blyszczuk IPCCs. Yet Blyszczuk IPCCs were less able to rescue experimental diabetes than isolated syngeneic pancreatic islet tissue. Therefore, depending on the mode of differentiation, ESCs can be driven to generate de novo IPCCs that possess limited functionality. Further modifications to differentiation protocols will be essential to improve the generation of functional IPCCs from mouse ESCs.
Effect of Lipopolysaccharide on Indices of Peripheral and Hepatic Metabolism in Lactating Cows (2003)

Four multiparous lactating cows (175 to 220 d in milk [DIM]) were used in a 4 x 4 Latin square design to assess the effects of four doses (0.0, 0.5, 1.0, and 1.5 microg/kg of body weight) of lipopolysaccharide (LPS; Escherichia coli 0111:B4) on performance and plasma metabolite and hormone concentrations. In addition, effects of immune activation on in vitro hepatic metabolic capacity were evaluated in 12 multiparous lactating cows (150 to 220 DIM) infused with 0 (n = 6), 1.0 (n = 4) or 2.0 (n = 2) microg of LPS/kg. Milk production and DMI decreased linearly with LPS dose for 24 h after LPS infusion. Overall mean plasma tumor necrosis factor-alpha, insulin, glucagon, and cortisol concentrations increased linearly with LPS dose, and plasma beta-hydroxybutyrate decreased linearly by dose after LPS infusion. Infusion of LPS decreased the insulin:glucagon molar ratio, but did not affect plasma concentrations of growth hormone, insulin-like growth factor-1, leptin, or L-(+)-lactate. Plasma concentrations of glucose tended to increase initially and subsequently decrease, and there was a quadratic tendency for increased plasma nonesterified fatty acid concentrations after LPS administration. In vitro hepatic capacity for conversion of [1-(14)C]L-(+)-lactate and [1-(14)C]palmitate, but not [1-(14)C]propionate or [1-(14)C]L-alanine, to CO2 increased after LPS administration. Hepatic capacity to convert [1-(14)C]propionate to glucose tended to increase, but neither esterification nor the conversion of palmitate to acid soluble products was altered by LPS. The LPS infusion resulted in significant changes of endocrine mediators responsible for regulation of energy metabolism of lactating cows and tended to alter subsequent in vitro hepatic metabolic capacity.
Differential Polarization of C-Terminal Src Kinase between Naive and Antigen-Experienced CD8+ T Cells (2013)

In CD8(+) T cells, engagement of the TCR with agonist peptide:MHC molecules causes dynamic redistribution of surface molecules including the CD8 coreceptor to the immunological synapse. CD8 associates with the Src-family kinase (SFK) Lck, which, in turn, initiates the rapid tyrosine phosphorylation events that drive cellular activation. Compared with naive T cells, Ag-experienced CD8(+) T cells make shorter contacts with APC, are less dependent on costimulation, and are triggered by lower concentrations of Ag, yet the molecular basis of this more efficient response of memory T cells is not fully understood. In this article, we show differences between naive and Ag-experienced CD8(+) T cells in colocalization of the SFKs and their negative regulator, C-terminal Src kinase (Csk). In naive CD8(+) T cells, there was pronounced colocalization of SFKs and Csk at the site of TCR triggering, whereas in Ag-experienced cells, Csk displayed a bipolar distribution with a proportion of the molecules sequestered within a cytosolic area in the distal pole of the cell. The data show that there is differential redistribution of a key negative regulator away from the site of TCR engagement in Ag-experienced CD8(+) T cells, which might be associated with the more efficient responses of these cells on re-exposure to Ag.
Photodependent release from poly(vinyl alcohol)/epoxypropoxy coumarin hydrogels (2011)

Abstract To obtain a photoresponsive hydrogel, poly(vinyl alcohol) (PVA) having coumarin residue as a pending group was crosslinked by photodimerizing the coumarin pendants. PVA having coumarin pendants was prepared by reacting the polymer with epoxypropoxy coumarin (EPC) in a strong alkali condition with EPC/PVA molar ratio of 200/1. According to the 1H NMR spectrum of PVA‐EPC conjugate, the molar ratio of EPC residue to PVA was about 4.3/1, indicating that EPC was attached to PVA every 444 repeating units of vinyl alcohol. An aqueous solution of PVA‐EPC (5%, w/v) became a semi‐solid hydrogel by the irradiation of a light (λ = 365 nm; 400 W) for 1 hr. The dimerization degree of EPC residues of the hydrogel decreased and increased in a periodical manner under the cyclic irradiation between two UV lights (λ = 365 nm and λ = 254 nm). The release of 5(6)‐carboxyfluorescein (CF) from PVA‐EPC hydrogel was significantly enhanced by the 5 min‐irradiation of λ = 254 nm (6 W), possibly due to the photodedimerization of EPC residues of the hydrogel. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Exploring computer viruses (1988)

The author presents some thoughts on viruses and explores the anatomy of a sample computer virus. He details, using C language programs, some of the fundamental parts associated with viruses and how these viruses can be detected. It is concluded that the final decision for virus control rests with risk management. It is suggested that, at the very least, contingency plans for virus recovery along with configuration control and software screening will be found to be cost effective.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Recessive Resistance to Tomato yellow leaf curl virus from the Tomato Cultivar Tyking Is Located in the Same Region as Ty-5 on Chromosome 4 (2012)

Tomato yellow leaf curl virus (TYLCV), a Begomovirus in the family Geminiviridae, is an important disease of cultivated tomato ( Solanum lycopersicum L.) in many parts of the world. Disease is managed primarily by chemical control of the vector, the sweetpotato whitefly, Bemisia tabaci (Genn.), and by growing resistant varieties. Resistance derived from the cultivar Tyking is being used in many breeding programs, but the location of resistance factors has not been reported. The breeding lines Fla. 8753 and Fla. 344 both have high levels of resistance to TYLCV derived from ‘Tyking’ and from S. chilense accession LA 1938, but none of their parent lines contain any of the known genes Ty-1 to Ty-4 . An additional resistance locus, Ty-5 , was recently identified, and to determine if this locus controls TYLCV resistance in Fla. 8753 and Fla. 344, appropriate segregating populations were analyzed using the Ty-5 marker, SlNAC1 . Results show that SlNAC1 cosegregates with a recessive allele derived from ‘Tyking’. We suggest the gene symbol ty-5 be used to describe this gene. Mean disease severity of progeny homozygous for either the resistant or susceptible alleles did not equal parental levels of resistance and susceptibility, respectively, suggesting the involvement of an additional gene that is likely derived from LA1938.
PET Image Reconstruction Using Kernel Method (2014)

Image reconstruction from low-count positron emission tomography (PET) projection data is challenging because the inverse problem is ill-posed. Prior information can be used to improve image quality. Inspired by the kernel methods in machine learning, this paper proposes a kernel based method that models PET image intensity in each pixel as a function of a set of features obtained from prior information. The kernel-based image model is incorporated into the forward model of PET projection data and the coefficients can be readily estimated by the maximum likelihood (ML) or penalized likelihood image reconstruction. A kernelized expectation-maximization algorithm is presented to obtain the ML estimate. Computer simulations show that the proposed approach can achieve better bias versus variance trade-off and higher contrast recovery for dynamic PET image reconstruction than the conventional maximum likelihood method with and without post-reconstruction denoising. Compared with other regularization-based methods, the kernel method is easier to implement and provides better image quality for low-count data. Application of the proposed kernel method to a 4-D dynamic PET patient dataset showed promising results.
Differential expression and activation of NF‐κB family proteins during oral carcinogenesis: Role of high risk human papillomavirus infection (2006)

Oral cancer is one of the most common cancers in India and south-east Asian region consisting of more than 50% of all malignant tumors. Along with many known risk factors, infection of Human Papillomavirus (HPV) has been associated with the development of oral cancer and is suggested to modulate host cell transcription. Reciprocally, cellular transcription factors, such as NF-kappaB and AP-1 are known to modulate the expression of viral and other genes involved in the development of cancer. In the absence of data on NF-kappaB in relation to HPV in oral cancer, we studied the DNA binding activity and expression pattern of NF-kappaB family of proteins in different stages of oral cancer and correlated with HPV infection that has been associated with better prognosis of the disease. A total of 110 fresh oral tissue biopsies were collected comprising 10 normal controls, 34 precancer and 66 oral cancer lesions prior to chemotherapy/radiotherapy. Diagnosis of HPV was done by both consensus and type-specific PCR. Electrophoretic mobility shift assays, western blots and immunohistochemical analysis were performed to assess the binding activity and expression pattern of NF-kappaB family of proteins (p50, p65, p52, c-Rel, RelB and Bcl-3) in oral tissue biopsies. Twenty seven percent (18/66) of the oral cancer biopsies showed the presence of HPV infection exclusively of high risk HPV type 16, which was primarily associated with the well differentiated squamous cell carcinomas (WDSCC). We observed a high constitutive activation of NF-kappaB with concomitant upregulated expression of all the NF-kappaB members in oral cancer tissues. Expression of NF-kappaB components gradually increased as the severity of lesion increased from precancer to invasive cancer. NF-kappaB p50 was found to be the major DNA binding component, which is indicative of homodimerization of p50 subunits. Interestingly, in HPV16 infected oral cancers although p50 showed high binding activity, p65 also showed a partial involvement as evidenced in supershift assay. Both by western blotting and immunohistochemistry, a differential overexpression and nuclear localization of p50, p65 and partially of Bcl-3 were observed in HPV16 positive oral cancer patients that also showed an over-expression of p21. We therefore, demonstrate a constitutive activation and differential expression of NF-kappaB proteins, which change as a function of severity of oral lesions during development of oral cancer. The NF-kappaB DNA binding is primarily due to homodimerization of p50 but infection of high risk HPV promotes participation of p65 in NF-kappaB complex formation, leading to heterodimerization of p50/p65. We propose that the involvement of p65 in HPV infected oral cancer may be linked to improved differentiation and better prognosis of the disease when treated.
Impaired response of fibroblasts from patients with hyperapobetalipoproteinemia to acylation-stimulating protein. (1990)

Acylation-stimulating protein (ASP) is a small, basic, human plasma protein that markedly stimulates triglyceride synthesis in human adipocytes and cultured human skin fibroblasts. The present studies examine the response to ASP of cultured skin fibroblasts from normal subjects patients with hyperapobetalipoproteinemia, patients with familial hypercholesterolemia, and patients with hypertriglyceridemia without hyperapobetalipoproteinemia. Triglyceride synthesis induced by ASP did not differ significantly among the normals, the patients with familial hypercholesterolemia, and the patients with hypertriglyceridemia with normal low density lipoprotein (LDL) apolipoprotein B levels; however, on average, it was markedly reduced in the patients with hyperapobetalipoproteinemia. In all groups studied, evidence of specific saturable binding of radioiodinated ASP was present. Binding, however, was significantly reduced in the groups with hyperapobetalipoproteinemia whereas the other three groups were indistinguishable. By contrast, LDL-specific binding was reduced only in the patients with familial hypercholesterolemia. There was a significant direct relation between the degree of ASP binding and the triglyceride synthesis inducible by ASP. In addition, with the exception of the patients with familial hypercholesterolemia, there was an inverse relation between both ASP-specific binding and ASP-induced triglyceride synthesis in fibroblasts to LDL levels in plasma whereas no relation was evident to plasma high density lipoprotein and very low density lipoprotein.
Estrogenic actions of RU486 in hormone-responsive MCF-7 human breast cancer cells (1993)

Journal Article Estrogenic actions of RU486 in hormone-responsive MCF-7 human breast cancer cells Get access M H Jeng, M H Jeng 1Department of Human Oncology, University of Wisconsin Comprehensive Cancer Center, Madison 53792. Search for other works by this author on: Oxford Academic Google Scholar S M Langan-Fahey, S M Langan-Fahey 1Department of Human Oncology, University of Wisconsin Comprehensive Cancer Center, Madison 53792. Search for other works by this author on: Oxford Academic Google Scholar V C Jordan V C Jordan 1Department of Human Oncology, University of Wisconsin Comprehensive Cancer Center, Madison 53792. Search for other works by this author on: Oxford Academic Google Scholar Endocrinology, Volume 132, Issue 6, 1 June 1993, Pages 2622–2630, https://doi.org/10.1210/endo.132.6.8504763 Published: 01 June 1993
Through-the-Wall Sensing of Personnel Using Passive Bistatic WiFi Radar at Standoff Distances (2011)

In this paper, we investigate the feasibility of uncooperatively and covertly detecting people moving behind walls using passive bistatic WiFi radar at standoff distances. A series of experiments was conducted which involved personnel targets moving inside a building within the coverage area of a WiFi access point. These targets were monitored from outside the building using a 2.4-GHz passive multistatic receiver, and the data were processed offline to yield range and Doppler information. The results presented show the first through-the-wall (TTW) detections of moving personnel using passive WiFi radar. The measured Doppler shifts agree with those predicted by bistatic theory. Further analysis of the data revealed that the system is limited by the signal-to-interference ratio (SIR), and not the signal-to-noise ratio. We have also shown that a new interference suppression technique based on the CLEAN algorithm can improve the SIR by approximately 19 dB. These encouraging initial findings demonstrate the potential for using passive WiFi radar as a low-cost TTW detection sensor with widespread applicability.
Efficient coupling of incoherent light into optical fibers and bundles (1978)

The excitation efficiencies of a few lower order modes in a W-type fiber have been studied when the modes are excited with tilted as well as off-set Gaussian beams. The effect of beam size, angle of incidence, the radius of curvature of the incident wavefront, and the off-axis displacement on the excitation efficiencies has been obtained. It is found that in order to couple maximum power into the fundamental mode, the incident wavefront must be plane and the beam must be incident axially along the fiber with a suitable value of the beam size.
Catalytic Dehydration of Methanol to Dimethyl Ether (DME) over Solid-Acid Catalysts (2002)

The conversion of dimethyl ether(DME) has been carried out over <TEX>$\gamma-alumina$</TEX>, silica-alumina, and modified <TEX>$\gamma-aluminal$</TEX> catalysts. Especially, the water effect has been investigated on purpose to develop a suitable catalyst for one-step synthesis of DME from <TEX>$CO_2$</TEX> hydrgenation, The <TEX>$\gamma-Al_2O_3$</TEX> modified with 1 wt% silica is more active and less deactivated by water than unmodified one. <TEX>$CO_2has$</TEX> no effect on catalytic dehydration of methanol to DME.
Mechanical properties of powder metallurgy Ti-829 and Ti-25Al-10Nb-3V-1Mo produced by rapid omnidirectional compaction (1991)

Two powder metallurgy, high temperature titanium alloys, one based on a near-alpha composition and the other on an alpha-2 ordered intermetallic compound, were compared in this study. The evaluation of room temperature tensile properties, and the high temperature creep strength of the alloys IMI-829 (near-alpha) and Ti-25Al-10Nb-3V-1Mo (Ti{sub 3}Al), were the objective of this work. Pre-alloyed powders produced by the plasma rotating electrode process were compacted by rapid omnidirectional consolidation for both compositions. The properly heat-treated IMI-829 compacts performed as well as comparable near-alpha wrought alloys with similar microstructures. The as-compacted Ti{sub 3}Al showed substantially improved ductility in comparison to the wrought alloy of the same composition, 6%. While it demonstrated good strength levels (approximately 1,100 MPa) upon heat treatment, the room temperature ductility of the Ti{sub 3}Al was severely reduced to less than 1% for all heat treatment conditions. Larsen-Miller comparison of the creep strength of the Ti{sub 3}Al placed it within the scatterband of wrought values.
Congenital hyperinsulinism: Molecular basis of a heterogeneous disease (1999)

Congenital hyperinsulinism (CHI) is a disease phenotype characterized by increased, usually irregular, insulin secretion leading to hypoglycemia, coma, and severe brain damage, left untreated. Hyperinsulinism may be caused by a range of biochemical disturbances and molecular defects. In pancreatic β cells, insulin secretion is stimulated by closure of the ATP-dependent potassium channel (KATP channel). KATP channel is a complex composed of at least two subunits: the sulfonylurea receptor SUR1 and Kir6.2, an inward rectifier K+ channel member. Mutations in both subunits have been identified in patients with the autosomal recessive form of hyperinsulinism, including 28 different mutations in the SUR1 gene and two mutations in the Kir6.2 gene. These mutations co-segregated with disease phenotype, also known as persistent hyperinsulinemic hypoglycemia of infancy (PHHI), and with attenuated KATP channel function. Inadequately high insulin secretion in one family with an autosomal dominant mode of inheritance is caused by a mutation in the glucokinase gene, resulting in increased affinity of the enzyme for glucose. Five different mutations have been identified in the glutamate dehydrogenase gene, resulting in overactivity of this enzyme and causing a syndrome of hyperinsulinism and hyperammonemia. In 13 cases, hyperinsulinism was caused by one or more focal pancreatic lesions with specific loss of maternal alleles of the imprinted chromosome region 11p15. In five patients, this loss of heterozygosity unmasked a paternally inherited recessive SUR1 mutation. The new molecular approaches in PHHI give further insight into the mechanism of pancreatic β cell insulin secretion. The heterogeneous group of patients with CHI may now be classified according to their basic defects in the four different genes, with potential implications for a more specific treatment. Hum Mutat 13:351–361, 1999. © 1999 Wiley-Liss, Inc.
Two-level logic minimization for low power (1995)

Abstract: We study the problem of two-level logic minimization for low power in static CMOS circuits. We start by defining Power Prime Implicants (PPIs) which identify the set of all implicants that are sufficient and necessary for obtaining a minimum power solution. We then provide an efficient algorithm for generating the set of all PPIs of a function. The set of all PPIs is then used in a minimum covering problem to find the best power solution. The feasibility of generating the set of all PPIs and the increased complexity of solving the minimum covering problem are analyzed by deriving an upper bound on the expected number of PPIs which shows it to be linearly proportional to the number of prime implicants of the function. The results of our experiments are then used to draw conclusions on the effectiveness of low power two-level logic minimization.
Effects of Keratinocyte and Hepatocyte Growth Factor <i>In Vivo:</i> Implications for Retrovirus-Mediated Gene Transfer to Liver (1998)

We have previously shown that intravenous administration of keratinocyte growth factor (KGF) induces hepatocyte proliferation, allowing for efficient and noninvasive in vivo gene transfer with high-titer retroviral vectors in mice. The distinctive periportal distribution of transduced cells led us to investigate the ability of virus-sized particles to perfuse the liver adequately after growth factor treatment. We found that perfusion was adequate, and that transduction was limited to the periportal region because only those cells were stimulated to divide. Cells in this region also showed increased expression of Ram-1, the receptor for the murine Moloney leukemia virus (MoMLV) amphotropic envelope, after KGF treatment. In further studies we found that recombinant hepatocyte growth factor (HGF) induces a different population of hepatocytes to divide and upregulate Ram-1. The differential pattern of induction suggested that combining KGF and HGF would improve gene transfer efficiency further. Indeed, simultaneous delivery of both growth factors leads to an overall increase in the number of proliferating cells. Importantly, when coupled with MoMLV delivery, efficiency of gene transfer increased. These results confirm the utility of growth factors for noninvasive hepatic gene transfer in mice, and demonstrate how experiments to define the mechanism of transduction can be taken advantage of to develop improved gene transfer protocols.