gebhart/patrepeval huggingface dataset:
Very high density of Chinese hamster ovary cells in perfusion by alternating tangential flow or tangential flow filtration in WAVE bioreactor™—part II: Applications for antibody production and cryopreservation (2013)

A high cell density perfusion process of monoclonal antibody (MAb) producing Chinese hamster ovary (CHO) cells was developed in disposable WAVE Bioreactor™ using external hollow fiber (HF) filter as cell separation device. Tangential flow filtration (TFF) and alternating tangential flow (ATF) systems were compared and process applications of high cell density perfusion were studied here: MAb production and cryopreservation. Operations by perfusion using microfiltration (MF) or ultrafiltration (UF) with ATF or TFF and by fed-batch were compared. Cell densities higher than 10(8) cells/mL were obtained using UF TFF or UF ATF. The cells produced comparable amounts of MAb in perfusion by ATF or TFF, MF or UF. MAbs were partially retained by the MF using ATF or TFF but more severely using TFF. Consequently, MAbs were lost when cell broth was discarded from the bioreactor in the daily bleeds. The MAb cell-specific productivity was comparable at cell densities up to 1.3 × 10(8) cells/mL in perfusion and was comparable or lower in fed-batch. After 12 days, six times more MAbs were harvested using perfusion by ATF or TFF with MF or UF, compared to fed-batch and 28× more in a 1-month perfusion at 10(8) cells/mL density. Pumping at a recirculation rate up to 2.75 L/min did not damage the cells with the present TFF settings with HF short circuited. Cell cryopreservation at 0.5 × 10(8) and 10(8) cells/mL was performed using cells from a perfusion run at 10(8) cells/mL density. Cell resuscitation was very successful, showing that this system was a reliable process for cell bank manufacturing.
Starling: Minimizing Communication Overhead in Virtualized Computing Platforms Using Decentralized Affinity-Aware Migration (2010)

Virtualization is being widely used in large-scale computing environments, such as clouds, data centers, and grids, to provide application portability and facilitate resource multiplexing while retaining application isolation. In many existing virtualized platforms, it has been found that the network bandwidth often becomes the bottleneck resource, causing both high network contention and reduced performance for communication and data-intensive applications. In this paper, we present a decentralized affinity-aware migration technique that incorporates heterogeneity and dynamism in network topology and job communication patterns to allocate virtual machines on the available physical resources. Our technique monitors network affinity between pairs of VMs and uses a distributed bartering algorithm, coupled with migration, to dynamically adjust VM placement such that communication overhead is minimized. Our experimental results running the Intel MPI benchmark and a scientific application on a 7-node Xen cluster show that we can get up to 42% improvement in the runtime of the application over a no-migration technique, while achieving up to 85% reduction in network communication cost. In addition, our technique is able to adjust to dynamic variations in communication patterns and provides both good performance and low network contention with minimal overhead.
Characterization of a fluoroscopic imaging system for kV and MV radiography (2000)

An on-line kilovoltage (kV) imaging system has been implemented on a medical linear accelerator to verify radiotherapy field placement. A kV x-ray tube is mounted on the accelerator at 90 degrees to the megavoltage (MV) source and shares the same isocenter. Nearly identical CCD-based fluoroscopic imagers are mounted opposite the two x-ray sources. These systems are being used in a clinical study of patient setup error that examines the advantage of kV imaging for on-line localization. In the investigation reported here, the imaging performance of the kV and MV systems are characterized to provide support to the conclusions of the studies of setup error. A spatial-frequency-dependent linear systems model is used to predict the detective quantum efficiencies (DQEs) of the two systems. Each is divided into a series of gain and spreading stages. The parameters of each stage are either measured or obtained from the literature. The model predicts the system gain to within 7% of the measured gain for the MV system and to within 10% for the kV system. The systems' noise power spectra (NPSs) and modulation transfer functions (MTFs) are measured to construct the measured DQEs. X-ray fluences are calculated using modeled polyenergetic spectra. Measured DQEs agree well with those predicted by the model. The model reveals that the MV system is well optimized, and is x-ray quantum noise limited at low spatial frequencies. The kV system is suboptimal, but for purposes of patient positioning yields images superior to those produced by the MV system. This is attributed to the kV system's higher DQE and to the inherently higher contrasts present at kV energies.
The adsorption of a bacterial cellulase and its two isolated domains to crystalline cellulose. (1992)

CenA is a bacterial cellulase (beta-1,4-glucanase) comprised of a globular catalytic domain joined to an extended cellulose-binding domain (CBD) by a short linker peptide. The adsorption of CenA and its two isolated domains to crystalline cellulose was analyzed. CenA and CBD.PTCenA' (the CBD plus linker) adsorbed rapidly to cellulose at 30 degrees C, and no net desorption of protein was observed during the following 16.7 h. There was no detectable adsorption of the catalytic domain. Scatchard plots of adsorption data for CenA and for CBD.PTCenA were nonlinear (concave upward). The adsorption of CenA and CBD.PTCenA exceeded 7 and 8 mumol/g cellulose, respectively, but saturation was not attained at the highest total protein concentrations employed. A new model for adsorption was developed to describe the interaction of a large ligand (protein) with a lattice of overlapping potential binding sites (cellobiose residues). A relative equilibrium association constant (Kr) of 40.5 and 45.3 liter.g cellulose-1 was estimated for CenA and CBD.PTCenA, respectively, according to this model. A similar Kr value (33.3 liter.g-1) was also obtained for Cex, a Cellulomonas fimi enzyme which contains a related CBD but which hydrolyzes both beta 1,4-xylosidic and beta-1,4-glucosidic bonds. It was estimated that the CBD occupies approximately 39 cellobiose residues on the cellulose surface.
Incomplete lysis of thrombus in the moderate underlying atherosclerotic lesion during intracoronary infusion of streptokinase for acute myocardial infarction: quantitative angiographic observations. (1986)

Thrombolytic recanalization of the obstructed coronary lumen was studied in 32 patients receiving intracoronary streptokinase for 60 to 90 min during acute myocardial infarction. The process was viewed at high arteriographic magnification and was quantified with computer-assisted measurements from repeated single-plane views. The variability of the method for this application was 0.15 to 0.18 mm on minimum diameter estimates. Structural details were seen that are not commonly appreciated at conventional magnification. The recanalized lumen appears to form along an interface between the thrombus and the vessel wall, progressively enlarging its minimum arteriographic diameter to 0.65 +/- 0.24 mm (+/- 1 SD) at the end of the short-term infusion of streptokinase reflecting a final percent stenosis of 77 +/- 10%. In nine infarct lesions found patent 5 +/- 3 weeks later, the recanalized lumen further improved an average of 0.34 mm in minimum diameter (p less than .005) and 13% stenosis (p less than .01). A thin film of contrast medium surrounding the obstructing thrombus faintly defined the boundaries of the original atherosclerotic lumen in all but two cases. The "original stenosis" measured 1.25 +/- 0.32 mm in minimum diameter and 56 +/- 14% stenosis when first visualized; it was unchanged throughout the course of infusion of streptokinase. In five patients catheterized 10 +/- 12 weeks before their infarction, the original stenosis averaged 1.15 +/- 0.22 mm in the preinfarct angiogram, as compared with 1.17 +/- 0.23 mm in its faintly defined form during thrombolytic therapy (p = NS). In 10 cases, this original lesion was less than a 50% stenosis, and in 21 cases less than 60%.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel microchip for in situ TEM imaging of living organisms and bio-reactions in aqueous conditions (2008)

A novel and disposable microchip (K-kit) with SiO(2) nano-membranes was developed and used as a specimen kit for in situ imaging of living organisms in an aqueous condition using transmission electron microscopy (TEM) without equipment modification. This K-kit enabled the successful TEM observation of living Escherichia coli cells and the tellurite reduction process in Klebsiella pneumoniae. The K. pneumoniae and Saccharomyces cerevisiae can stay alive in K-kit after continuous TEM imaging for up to 14 s and 42 s, respectively. Besides, different tellurite reduction profiles in cells grown in aerobic and anaerobic environments can be clearly revealed. These results demonstrate that the K-kit developed in this paper can be useful for observing living organisms and monitoring biological processes in situ.
Shift error correcting modulation codes (1991)

5A class of codes that perform bit-shift error detection/correction directly on run-length-limited (RLL) binary channel data is described. These highly efficient, variable-rate codes can be used with RLL sequences having d,k constraints of d>0 and (k-d)>or=2, and they are fully compatible with conventional signal processing, e.g., peak detection can be used. The simplest and most efficient of these codes are effective only against bit-shift error, i.e., the predominant type of channel data error caused by intersymbol interference and noise in saturation recording systems that employ RLL modulation coding.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Inhibition of endogenous TGF-β signaling enhances lymphangiogenesis (2008)

Lymphangiogenesis is induced by various growth factors, including VEGF-C. Although TGF-beta plays crucial roles in angiogenesis, the roles of TGF-beta signaling in lymphangiogenesis are unknown. We show here that TGF-beta transduced signals in human dermal lymphatic microvascular endothelial cells (HDLECs) and inhibited the proliferation, cord formation, and migration toward VEGF-C of HDLECs. Expression of lymphatic endothelial cell (LEC) markers, including LYVE-1 and Prox1 in HDLECs, as well as early lymph vessel development in mouse embryonic stem cells in the presence of VEGF-A and C, were repressed by TGF-beta but were induced by TGF-beta type I receptor (TbetaR-I) inhibitor. Moreover, inhibition of endogenous TGF-beta signaling by TbetaR-I inhibitor accelerated lymphangiogenesis in a mouse model of chronic peritonitis. Lymphangiogenesis was also induced by TbetaR-I inhibitor in the presence of VEGF-C in pancreatic adenocarcinoma xenograft models inoculated in nude mice. These findings suggest that TGF-beta transduces signals in LECs and plays an important role in the regulation of lymphangiogenesis in vivo.
Notch Signaling in Leukemia (2008)

Recent discoveries indicate that gain-of-function mutations in the Notch1 receptor are very common in human T cell acute lymphoblastic leukemia/lymphoma. This review discusses what these mutations have taught us about normal and pathophysiologic Notch1 signaling, and how these insights may lead to new targeted therapies for patients with this aggressive form of cancer.
Evidence for Degenerative and Regenerative Changes in Neostriatal Spiny Neurons in Huntington's Disease (1985)

Golgi impregnations of neostriatum from deceased Huntington's disease patients and controls were examined. In all cases of Huntington's disease the morphology of dendrites of medium-sized spiny neurons was markedly altered by the appearance of recurved endings and appendages, a decrease or increase in the density of spines, and abnormalities in the size and shape of spines. Pathological changes were rarely observed in medium-sized and large aspiny neostriatal neurons. The findings provide evidence for simultaneous degeneration and growth of spiny neurons in Huntington's disease and support the view that a specific population of neostriatal neurons is selectively involved in its pathogenesis.
Immunotherapy Against HPV16/18 Generates Potent T H 1 and Cytotoxic Cellular Immune Responses (2012)

Despite the development of highly effective prophylactic vaccines against human papillomavirus (HPV) serotypes 16 and 18, prevention of cervical dysplasia and cancer in women infected with high-risk HPV serotypes remains an unmet medical need. We report encouraging phase 1 safety, tolerability, and immunogenicity results for a therapeutic HPV16/18 candidate vaccine, VGX-3100, delivered by in vivo electroporation (EP). Eighteen women previously treated for cervical intraepithelial neoplasia grade 2 or 3 (CIN2/3) received a three-dose (intramuscular) regimen of highly engineered plasmid DNA encoding HPV16 and HPV18 E6/E7 antigens followed by EP in a dose escalation study (0.3, 1, and 3 mg per plasmid). Immunization was well tolerated with reports of mild injection site reactions and no study-related serious or grade 3 and 4 adverse events. No dose-limiting toxicity was noted, and pain was assessed by visual analog scale, with average scores decreasing from 6.2/10 to 1.4 within 10 min. Average peak interferon-γ enzyme-linked immunospot magnitudes were highest in the 3 mg cohort in comparison to the 0.3 and 1 mg cohorts, suggesting a trend toward a dose effect. Flow cytometric analysis revealed the induction of HPV-specific CD8(+) T cells that efficiently loaded granzyme B and perforin and exhibited full cytolytic functionality in all cohorts. These data indicate that VGX-3100 is capable of driving robust immune responses to antigens from high-risk HPV serotypes and could contribute to elimination of HPV-infected cells and subsequent regression of the dysplastic process.
Second and third order hyperpolarizabilities of organic molecules (1975)

We have used the technique of static field induced second harmonic generation in liquids to determine the second order hyperpolarizability β, and the third order hyperpolarizability γ, for a wide range of conjugated and nonconjugated organic molecules. The adequacy of the Onsager local field formulation was tested as was the accuracy of the bond additivity approximation. The large π-electron nonlinearities which are possible in substituted benzene molecules were investigated by measuring a large number of benzene derivatives and subtracting out the σ-electron contributions.
Transcript Analysis of the Citrate Synthase and Succinate Dehydrogenase Genes of Escherichia coli K12 (1986)

A transcript analysis of the citrate synthase and succinate dehydrogenase genes (gltA-sdhCDAB) of Escherichia coli was done by nuclease S1 mapping. Evidence was obtained for two monocistronic gltA transcripts extending anti-clockwise, to a common terminus, from independent promoters with start points 196 bp (major) and 299 bp (minor) upstream of the gltA coding region. Evidence was also obtained for two polycistronic sdh transcripts, sdhCDAB (minor) and sdhDAB (major), extending clockwise, from sites 219 bp upstream of sdhC and 1455 bp upstream of sdhD (i.e. within sdhC), to a common terminus. The synthesis of all of the transcripts was repressed by growth in the presence of glucose, and this is consistent with the well-established fact that both enzymes are subject to catabolite repression. Sequences resembling known binding sites for the cAMP-CRP (cyclic AMP-cyclicAMP receptor protein) complex occur in the vicinity of each promoter suggesting that they are activated by the cAMP-CRP complex.
A key role for Toll-like receptor-3 in disrupting the hemostasis balance on endothelial cells (2008)

Various virus infections cause dysfunctional hemostasis and in some instances lead to the development of viral hemorrhagic fever syndrome. How do diverse viruses induce the expression of tissue factor on vascular cells? We hypothesize that a direct stimulation of pattern recognition receptors (PRR) by viral nucleic acids may be the key. Double-stranded RNA (dsRNA) is produced by many viruses and is recognized by various PRR, including Toll-like receptor-3 (TLR3). We have investigated whether poly I:C, a model for viral dsRNA, can influence cellular hemostasis. Poly I:C could up-regulate tissue factor and down-regulate thrombomodulin expression on endothelial cells but not on monocytes. The response to poly I:C was diminished upon small interfering RNA (siRNA)-mediated inhibition of TLR3, but not other PRR. In vivo, application of poly I:C induced similar changes in the aortic endothelium of mice as determined by enface microscopy. D-dimer, a circulating marker for enhanced coagulation and fibrinolysis, and tissue fibrin deposition was elevated. All the hemostasis-related responses to poly I:C, but not cytokine secretion, were blunted in TLR3(-/-) mice. Hence, the activation of TLR3 can induce the procoagulant state in the endothelium, and this could be relevant for understanding the mechanisms of viral stimulation of hemostasis.
Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays. (1998)

Several forms of human sarcoma, lymphoma, and leukemia are characterized by somatically acquired chromosome translocations that result in fusion genes that encode chimeric transcription factors with oncogenic properties. We have used cDNA microarrays containing 1238 cDNAs to investigate the gene expression profile of a group of seven alveolar rhabdomyosarcoma (ARMS) cell lines characterized by the presence of the PAX3-FKHR fusion gene. Using the method of multidimensional scaling to represent the relationships among the cell lines in two-dimensional Euclidean space, we determined that ARMS cells show a consistent pattern of gene expression, which allows the cells to be clustered together. By searching across the seven ARMS cell lines, we found that 37 of 1238 genes were most consistently expressed in ARMS relative to a reference cell line. Only three of these genes have been previously reported to be expressed in ARMS. Among these 37 were genes related to both primary (PAX3-FKHR) and secondary (CDK4) genetic alterations in ARMS. These results in ARMS demonstrate the potential of cDNA microarray technology to elucidate tumor-specific gene expression profiles in human cancers.
Gut microbiota as a regulator of energy homeostasis and ectopic fat deposition: mechanisms and implications for metabolic disorders (2010)

Gut microbiota manipulation yielded encouraging results for the treatment of different metabolic disorders in experimental models. However, changing intestinal microbiota may be more difficult in free-living individuals compared to standardized laboratory models, and its long-term consequences are unknown. To safely and effectively change human gut microflora, future research should highlight the complex hormonal, immunomodulatory and metabolic mechanisms underlying microbiota-host interactions in different tissues and candidate treatments should be evaluated in well designed trials with patient-oriented end-points.
Expression of Cdx‐2 in the mouse embryo and placenta: Possible role in patterning of the extra‐embryonic membranes (1995)

Three mouse homologues of the Drosophila homeotic gene Caudal (Cad) have been described. They are currently designated Cdx-1, Cdx-2, and Cdx-4. Cdx-1 and 2 are both strongly expressed in the adult mid- and hindgut, while Cdx-1 and 4 have been shown to be activated in the embryonic primitive streak. Using a polyclonal antibody against a fusion protein containing the amino terminal 109 amino acids of murine Cdx-2, we here describe the topographical location of the gene product from early cleavage to 12.5 days of embryonic development. Cdx-2 expression begins at 3.5 days and is confined to the trophectoderm, being absent from the inner cell mass. Subsequently, staining is located in the extra-embryonic ectoderm adjacent to the epiblast, but sparing the more superficially placed polar, as well as the mural trophoblastic cells. Continuing expression in the fetal membranes involves the chorion, the allantoic bud, and, at even later stages, the spongiotrophoblast. From 8.5 days, Cdx-2 begins to be expressed in embryonic tissues, principally (unlike Cdx-1) in the posterior part of the gut from its earliest formation, as well as in the tail bud and in the caudal part of the neural tube. Cdx-2 is, therefore, transcribed well before any other membrane of the Cad homologue group and of the related Hox-C group; its expression in the extra-embryonic membranes and in the hindgut reflects the phylogenetic relationship between the cloaca and the chorio-allantois and suggests the possibility that homeobox genes may be involved in placental development and/or patterning.
π-Conjugated Nickel Bis(dithiolene) Complex Nanosheet (2013)

A π-conjugated nanosheet comprising planar nickel bis(dithiolene) complexes was synthesized by a bottom-up method. A liquid-liquid interfacial reaction using benzenehexathiol in the organic phase and nickel(II) acetate in the aqueous phase produced a semiconducting bulk material with a thickness of several micrometers. Powder X-ray diffraction analysis revealed that the crystalline portion of the bulk material comprised a staggered stack of nanosheets. A single-layer nanosheet was successfully realized using a gas-liquid interfacial reaction. Atomic force microscopy and scanning tunneling microscopy confirmed that the π-conjugated nanosheet was single-layered. Modulation of the oxidation state of the nanosheet was possible using chemical redox reactions.
Role of glycolipids in the metastatic process: Characteristics of neutral glycolipids in clones with different metastatic potentials isolated from a murine fibrosarcoma cell line (1990)

We investigated whether metastatic phenotype is associated with a characteristic glycolipid pattern. For this study, we developed a system of variants with different metastatic potentials that we isolated from the highly metastatic T3 murine fibrosarcoma line by culture in 0.3% agar or on plastic. The glycolipid profiles of T3 cells and of their highly metastatic isolates were characterized by a high level of globotriaosylceramide (Gb3ose). On the other hand, Gb3ose was reduced in a weakly metastatic clone isolated from T3 cells. A reduced level of Gb3ose was also found in a weakly metastatic subclone isolated from a highly metastatic T3 clone. Propagation of this subclone led to the emergence of a series of variants which expressed a high metastatic potential together with a high Gb3ose level. We also observed that Gb3ose was 10 times more prevalent on the cell surface in T3 cells than in a weakly metastatic clone. On the whole, these findings indicate that, in our system of metastatic cells, a high Gb3ose level correlates with metastatic phenotype. It is possible that the highly exposed Gb3ose in metastatic cells is relevant to the metastatic process in view of the role played by the unique molecular structure of this glycolipid in other models of cell-to-cell interaction.