gebhart/patrepeval huggingface dataset:
Large-scale purification of Japanese encephalitis virus from infected mouse brain for preparation of vaccine (1980)

Large volumes of Japanese encephalitis (JE) virus propagated in mouse brain can be easily purified by polyethylene glycol 6,000. By using the polyethylene glycol precipitation method, mouse hemoglobin was almost all separated from the viral suspension, and consequently the total amount of nonviral protein in the viral suspension decreased. The recovery of infectivity was about 100%. The removal of residual polyethylene glycol in the viral suspension was possible without difficulty by means of ethanol precipitation. This method is recommended as an initial step in large-scale purification of Japanese encephalitis virus propagated in mouse brain because it is simple, rapid, and inexpensive.
Increased C5a receptor expression in sepsis (2002)

Excessive production of the complement activation product C5a appears to be harmful during the development of sepsis in rodents. Little is known about the role of the C5a receptor (C5aR) and its presence in different organs during sepsis. Using the cecal ligation/puncture (CLP) model in mice, we show here that C5aR immunoreactivity was strikingly increased in lung, liver, kidney, and heart early in sepsis in both control and neutrophil-depleted mice. C5aR mRNA expression in these organs was also significantly increased during sepsis. Immunohistochemical analysis revealed patterns of increased C5aR expression in parenchymal cells in all four organs following CLP. Mice injected at the start of CLP with a blocking IgG to C5aR (αC5aR) showed dramatically improved survival when compared with animals receiving nonspecific IgG, as did mice injected with αC5a. In αC5aR-treated mice, serum levels of IL-6 and TNF-α and bacterial counts in various organs were significantly reduced during CLP when compared with control CLP animals. These studies demonstrate for the first time that C5aR is upregulated in lung, liver, kidney, and heart during the early phases of sepsis and that blockade of C5aR is highly protective from the lethal outcome of sepsis.
Cell cycle analysis of normal, atrophic, and hyperplastic breast epithelium using two-color multiparametric flow cytometry. (1996)

We performed two-color flow cytometric synthesis phase fraction (SPF) determinations on cytokeratin-labeled benign epithelial populations from 142 breast specimens (41 mastectomy, 70 diagnostic biopsy, 31 reduction mammoplasty). There was wide variability of SPF, ranging from 0.1 to 3.5%, with a frequency distribution skewed to higher values (mean 0.75%, median 0.5%). The mean SPE for women less than 29 years was 0.91%, vs. 0.89% for 30-42 years, 0.66% for 43-49 years, and 0.56% for > or = 50 years (P = 0.05). Histologically atrophic tissue samples exhibited a mean SPF approximately half that of morphologically normal tissue from premenopausal age women (0.79% vs. 0.36%, P = 0.02). Tissues showing histologically proliferative fibrocystic features had a greater mean SPF than non-proliferative fibrocystic tissues (0.59% vs. 0.92%); however, due to the wide spread of values within each of these categories, this difference was not statistically significant and neither group was significantly different from 'normal' tissue samples. Patients with histologically normal breast tissue, though, were significantly younger (mean = 34.6 years) than those with fibrocystic changes (non-proliferative mean = 53.4 years vs. proliferative mean = 42.8 years, P = 0.005). Synchronous right- and left-sided specimens obtained from reduction mammoplasty demonstrated significantly correlated SPF determinations (R = 0.77). We conclude that selective analysis of epithelial populations using two-color flow cytometry provides cell cycle information in benign breast tissue which is analogous to that obtained by labor-intensive nucleotide labeling studies. This study also confirms the biologic variability and age-dependence of breast epithelial proliferation. Finally, the data imply that derangements of cell proliferation in fibrocystic conditions are heterogeneous, complex and incompletely correlated with histologic parameters such as hyperplasia.
“Pruning” of Alloreactive CD4+ T Cells Using 5- (and 6-)Carboxyfluorescein Diacetate Succinimidyl Ester Prolongs Skin Allograft Survival (2004)

Removal of alloreactive cells by either thymic deletion or deletion/anergy in the periphery is regarded as crucial to the development of tolerance. Dyes, such as CFSE, that allow monitoring of cell division suggest that in vitro proliferation could be a used as a way of "pruning" alloreactive cells while retaining a normal immune repertoire with retention of memory to previously encountered pathogens. This would overcome the problems occurring as a result of therapies that use massive depletion of T cells to allow acceptance of organ transplants or bone marrow grafts. We therefore used a skin graft model of CD4-mediated T cell rejection across a major H-2 mismatch (C57BL/6 (H-2(b)) to BALB/c (H-2(d)) mice) to evaluate whether nondividing CD4(+) T cells derived from a mixed lymphocyte culture would exhibit tolerance to a skin graft from the initial stimulator strain. We demonstrate that selective removal of dividing alloreactive CD4(+) T cells resulted in marked specific prolongation of allogeneic skin graft survival, and that the nondividing CD4(+) T cells retained a broad TCR repertoire and the ability to maintain memory. This novel way of depleting alloreactive T cells may serve as a useful strategy in combination with other mechanisms to achieve transplant tolerance.
Warfarin-Resistance Genotype Determination in the Norway Rat, Rattus Norvegicus (1979)

The 2-stage determination is based on changes in blood coaggulation activity brought about both by the administration of warfarin in conjunction with vitamin K1 epoxide and by feeding a vitamin K-free diet for 4 days. When it was applied to laboratory-bred rats of known warfarin-resistance genotype, 35/35 homozygous susceptible, 44/44 homozygous resistant and 131/133 heterozygous rats were correctly classified. This method was equally effective in identifying the genotype of wild rats carrying the warfarin-resistance gene, Rw2. The procedure is rapid and accurate.
Temperature, pH, and Spore Load Effects on the Ability of Nisin to Prevent the Outgrowth of Clostridium botulinum Spores (1981)

ABSTRACT The effectiveness of nisin in preventing the outgrowth of spores of Clostridium botulinum types A, B, and E in TPYG broth was profoundly affected by pH, temperature of heat‐shocking, length of the heat‐shocking period, and spore load. Nisin was considerably more effective at pH 6 than at either pH 7 or pH 8 in limiting the outgrowth of all six tested strains. Heat‐damaged spores were also more sensitive to nisin. Both higher heat‐shocking temperatures in the range 20‐30°C higher than the optimal heat‐shocking temperatures for the particular strain and longer heat‐shocking periods served to lower the levels of nisin required to inhibit spore outgrowth. Nisin was more effective against spore loads of 10 2 spores/ml. than higher spore loads of 10 3 or 10 4 spores/ml with all of these variables taken into consideration, the order of sensitivity of the spores of the various strains of C. botulinum was strain 56A &lt; strain 69A &lt; strain 113 B = strain 213 B &lt; strain Beluga E &lt; strain Minnesota E
The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity (2009)

We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene.
Effects of blocking contacts on generation-recombination noise and responsivity in intrinsic photoconductors (1984)

A theory is presented of generation-recombination (g-r) noise, responsivity, and detectivity D* in intrinsic photoconductors, including for the first time the effects of recombination at the contacts as a variable parameter. The contacts are described using a contact recombination velocity. Increasing the blocking at the contacts can significantly increase the responsivity, and also push the detectivity toward the background limited value since blocking contacts increase responsivity and the background contribution to the noise voltage faster than the thermal contribution. Blocking contacts also cause both the responsivity and g-r noise voltage to roll off at lower frequencies. Numerical calculations are presented for X∼0.2 HgCdTe photoconductors. Blocking contacts are found to increase the range of material parameters which can be used to make detectors. For example, under typical conditions, to reach responsivities of 105 V/W and detectivities of 6×1010 cm(Hz)1/2/W at T=77 °K, blocking contacts can increase the maximum allowed carrier density from about 4×1014 to about 2×1015 cm−3, and enlarge the required composition window from about 0.200&amp;lt;x&amp;lt;0.212 to about 0.188&amp;lt;x&amp;lt;0.212 for typical device geometries.
Antiangiogenic gene therapy targeting the endothelium-specific receptor tyrosine kinase Tie2 (1998)

Angiogenesis is required for tumor growth and metastasis, and inhibition of angiogenesis is a promising approach for anticancer therapy. Tie2 (a.k.a Tek) is an endothelium-specific receptor tyrosine kinase known to play a role in tumor angiogenesis. To explore the therapeutic potential of blocking the Tie2 pathway, an adenoviral vector was constructed to deliver a recombinant, soluble Tie2 receptor (AdExTek) capable of blocking Tie2 activation. Two days after i.v. injection of AdExTek, the plasma concentration of ExTek exceeded 1 mg/ml and was maintained for about 8 days. Administration of AdExTek to mice with two different well established primary tumors, a murine mammary carcinoma (4T1) or a murine melanoma (B16F10.9), significantly inhibited the growth rate of both tumors (64% and 47%, respectively). To study the effect of ExTek on tumor metastasis, both tumor cell lines were coinjected i.v. with either AdExTek or a control virus. Mice coinjected with control virus developed numerous large, well vascularized lung metastases. In contrast, mice coinjected with AdExTek virus developed few, if any, grossly apparent metastases, and histologic examination revealed only small avascular clusters of tumor cells. Administration of AdExTek also inhibited tumor metastasis when delivered at the time of surgical excision of primary tumors in a clinically relevant model of tumor metastasis. This study demonstrates the potential utility of gene therapy for systemic delivery of an antiangiogenic agent targeting an endothelium-specific receptor, Tie2.
Icodextrin-associated peritonitis among CAPD patients (2003)

nephropathy, as suggested by focally collapsed tufts and focal and segmental areas of glomerular sclerosis.In conclusion, Leishmania behaves as an opportunistic infection in HIV-infected individuals.It should be suspected in African people in a case of acute renal failure, when no other causes can be advocated.ARF can be due to direct invasion of parenchyma and to tubulo-interstitial and glomerular structures involvement.
Immune Activation during Measles: 2-microglobulin in Plasma and Cerebrospinal Fluid in Complicated and Uncomplicated Disease (1992)

Beta 2-microglobulin (beta 2m) is a small protein that forms the light chain of the class I major histocompatibility molecule and is also present in soluble form in serum and cerebrospinal fluid (CSF). Measles is associated with immune activation and evidence of immunologic abnormalities that persist for several weeks. To assess further the immunologic changes occurring during measles, beta 2m was measured in plasma and CSF. beta 2m became elevated during measles before the onset of the rash and was highest during the rash. Elevations persisted for several weeks and correlated well with levels of soluble interleukin-2 receptor and neopterin and less well with soluble CD8. CSF beta 2m was elevated in postmeasles encephalomyelitis. Plasma levels of beta 2m did not correlate with spontaneous proliferation of peripheral blood mononuclear cells (PBMC) or with in vitro production of beta 2m by cultured PBMC. The data suggest that increases in beta 2m in measles correlate better with cytokine production than with cell proliferation.
Treatment of Hepatic Encephalopathy (1997)

Hepatic encephalopathy is a complex neuropsychiatric syndrome that may occur in such diverse clinical situations as inherited errors of the urea cycle, acute or chronic liver disease, and spontaneous or iatrogenic portosystemic venous shunting, including that following procedures to establish a transjugular intrahepatic portosystemic shunt. The clinical manifestations of this syndrome range from subtle abnormalities detectable only by psychometric testing to deep coma. Several grading systems have been proposed; one based on clinical and electroencephalographic abnormalities is shown in Table 1.1 Hepatic encephalopathy may be present in 50 to 70 percent of all patients with cirrhosis, including those with abnormalities demonstrable . . .
Transcriptional Profiling of Human Hematopoiesis During In Vitro Lineage‐Specific Differentiation (2005)

To better understand the transcriptional program that a ccompanies orderly lineage-specific hematopoietic differentiation, we performed serial oligonucleotide microarray analysis of human normal CD34+ bone marrow cells during lineage-specific differentiation. CD34+ bone marrow cells isolated from healthy individuals were selectively stimulated in vitro with the cytokines erythropoietin (EPO), thrombopoietin (TPO), granulocyte colony-stimulating factor (G-CSF), and granulocyte macrophage colony-stimulating factor (GM-CSF). Cells from each of the lineages were harvested after 4, 7, and 11 days of culture for expression profiling. Gene expression was analyzed by oligonucleotide microarrays (HG-U133A; Affymetrix, Santa Clara, CA). Experiments were done in triplicates. We identified 258 genes that are consistently upregulated or downregulated during the course of lineage-specific differentiation within each specific lineage (horizontal change). In addition, we identified 52 genes that contributed to a specific expression profile, yielding a genetic signature specific for successive stages of differentiation within each of the three lineages. Analysis of horizontal changes selected 21 continuously upregulated genes for EPO-induced differentiation (including GTPase activator proteins RAP1GA1 and ARHGAP8, which regulate small Rho GTPases), 21 for G-CSF-induced/GM-CSF-induced differentiation, and 91 for TPO-induced differentiation (including DLK1, of which the role in normal hematopoiesis is not defined). During the lineage-specific differentiation, 58 (erythropoiesis), 30 (granulopoiesis), and 37 (thrombopoiesis) genes were significantly downregulated, respectively. The expression of selected genes was confirmed by real-time polymerase chain reaction. Our data encompass the first extensive transcriptional profile of human hematopoiesis during in vitro lineage-specific differentiation.
Absence of hematopoietic tissue factor pathway inhibitor mitigates bleeding in mice with hemophilia (2012)

Tissue factor pathway inhibitor (TFPI) blocks thrombin generation via the extrinsic blood coagulation pathway. Because the severe bleeding in patients with hemophilia occurs from deficiency of intrinsic blood coagulation pathway factor VIII or IX, pharmacological agents that inactivate TFPI and, therefore, restore thrombin generation via the extrinsic pathway, are being developed for treatment of hemophilia. Murine models of combined TFPI and factor VIII deficiency were used to examine the impact of TFPI deficiency on bleeding and clotting in hemophilia. In breeding studies, Factor VIII null (F8(-/-)) did not rescue the embryonic death of TFPI null (Tfpi(-/-)) mice. Tfpi(+/-) did not alter the bleeding phenotype of F8(-/-) mice. However, total inhibition of intravascular TFPI through injection of anti-TFPI antibody mitigated tail vein bleeding. Interestingly, tail blood loss progressively decreased at doses greater than needed to totally inhibit plasma TFPI, suggesting that inhibition of a sequestered pool of TFPI released at the injury site mitigates bleeding. Because TFPI is sequestered within platelets and released following their activation, the function of platelet TFPI was examined in F8(-/-) mice lacking hematopoietic cell TFPI that was generated by fetal liver transplantation. Blood loss after tail transection significantly decreased in Tfpi(+/-);F8(-/-) mice with hematopoietic Tfpi(-/-) cells compared with Tfpi(+/-);F8(-/-) mice with Tfpi(+/+) hematopoietic cells. Additionally, following femoral vein injury, Tfpi(+/-);F8(-/-) mice with Tfpi(-/-) hematopoietic cells had increased fibrin deposition compared with identical-genotype mice with Tfpi(+/+) hematopoietic cells. These findings implicate platelet TFPI as a primary physiological regulator of bleeding in hemophilia.
The Handbook of Antenna Design (1986)

These books present the fundamental background, theory and analytical techniques of antenna design, dealing with a very wide range of antenna types from very low frequencies to millimeter waves.
COX-2 expression is associated with an aggressive phenotype in ductal carcinoma in situ (2004)

Cyclooxygenase type-2 (COX-2) is overexpressed in malignant tumours including breast cancers, though the mechanism of upregulation is unclear. This study aimed to determine COX-2 expression in ductal carcinoma in situ (DCIS) in comparison to invasive breast cancer (IBC) and normal breast, and also to investigate the relationship of COX-2 expression with HER-2 expression, oestrogen receptor (ER), tumour grade and cellular proliferation (Ki67) in DCIS. Cyclooxygenase type-2, HER-2, ER and Ki67 expression were determined by immunohistochemistry on paraffin tissue sections of DCIS (n=187), IBC (n=65) and normal breast reduction tissue (n=60). Cyclooxygenase type-2 expression in DCIS (67%, P<0.001) and IBC (63%, P<0.001) was significantly greater than in normal breast (23%). There was no difference in COX-2 expression level between DCIS and IBC (P=0.87) or between normal breast from reduction mammoplasty tissue and normal breast ducts around DCIS (22%, P=0.29). In DCIS, COX-2 expression was associated with higher cellular proliferation rates (P<0.0001), nuclear grade (P=0.003), with ER negativity (P=0.003) and with HER-2 positivity (P<0.0001). Cyclooxygenase type-2 expression is upregulated in in situ breast cancer and is associated with surrogate markers of an aggressive DCIS phenotype including nonoestrogen-regulated signalling pathways. Cyclooxygenase type-2 inhibition may potentially prevent the development of ER-positive and ER-negative breast cancers.
Fabrication and testing of planar chalcogenide waveguide integrated microfluidic sensor (2007)

We have fabricated and tested, to the best of our knowledge, the first microfluidic device monolithically integrated with planar chalcogenide glass waveguides on a silicon substrate. High-quality Ge(23)Sb(7)S(70) glass films have been deposited onto oxide coated silicon wafers using thermal evaporation, and high-index-contrast channel waveguides have been defined using SF(6) plasma etching. Microfluidic channel patterning in photocurable resin (SU8) and channel sealing by a polydimethylsiloxane (PDMS) cover completed the device fabrication. The chalcogenide waveguides yield a transmission loss of 2.3 dB/cm at 1550 nm. We show in this letter that using this device, N-methylaniline can be detected using its well-defined absorption fingerprint of the N-H bond near 1496 nm. Our measurements indicate linear response of the sensor to varying N-methylaniline concentrations. From our experiments, a sensitivity of this sensor down to a N-methylaniline concentration 0.7 vol. % is expected. Given the low-cost fabrication process used, and robust device configuration, our integration scheme provides a promising device platform for chemical sensing applications.
Capture of a Single Molecule in a Nanocavity (2001)

We describe a heptameric protein pore that has been engineered to accommodate two different cyclodextrin adapters simultaneously within the lumen of a transmembrane beta barrel. The volume between the adapters is a cavity of approximately 4400 cubic angstroms. Analysis of single-channel recordings reveals that individual charged organic molecules can be pulled into the cavity by an electrical potential. Once trapped, an organic molecule shuttles back and forth between the adapters for hundreds of milliseconds. Such self-assembling nanostructures are of interest for the fabrication of multianalyte sensors and could provide a means to control chemical reactions.
The Gas-Phase Acidity of 2(3H)-Oxepinone:  A Step toward an Experimental Heat of Formation for the 2-Oxepinoxy Radical (2005)

In an effort to gain further insight into the oxidation of the phenyl radical, this contribution details the first of three experiments designed to establish the heat of formation of the 2-oxepinoxy radical. We report here the synthesis of the previously unknown 2(7H)-oxepinone (12a) and 2(3H)-oxepinone (12b). We have determined the gas-phase acidity (Delta(acid)H(298)) of 12b by means of a bracketing study employing a flowing afterglow apparatus with quadrupole mass spectrometric detection. In this experiment, compound 12b was reacted in the gas phase with a series of bases of varying strength. A proton-transfer reaction was observed when 12b was reacted with t-BuS(-), but not when 12b was reacted with HS(-). We conclude that the gas-phase acidity of 12b lies between those of t-BuSH and H(2)S, and it is thereby assigned a value of Delta(acid)H(298) = 352 +/- 2 kcal/mol. Additional support for this value was found by performing the reverse reactions (i.e. the 2-oxepinoxy anion (15a) was reacted with proton sources of differing acidities). Anion 15a underwent a proton-transfer reaction with H(2)S but not with t-BuSH, in agreement with the results from the forward reactions. The experimental value of the gas-phase acidity agrees well with those from DFT calculations, which predicted Delta(acid)H(298) = 348.9 kcal/mol at the B3LYP/6-31+G(d) level and 349.2 kcal/mol at the B3LYP/aug-cc-pVTZ level.
General approach to hitless switching and FSR extension resonators in integrated photonic circuits (2006)

A hitless bypass switch for microphotonic channel add-drop filters that is based on /spl Delta//spl beta/ switches is described. We generalize the design to a large class of devices enabling variants of the switch and application to free-spectral-range extension in tunable filters.