gebhart/patrepeval huggingface dataset:
Automated flow cytometry for acquisition of time‐dependent population data (2003)

Abstract Background The implementation of flow cytometry in many experimental settings can be limited by the extensive amount of sample handling and preparation required for analysis. We describe a system that automatically performs sample handling and flow cytometric analysis, thus allowing one to construct detailed pictures of changes in cell population distributions as a function of time. Methods Cell samples from bioreactors were loaded into a microchamber designed to perform all sample preparation steps including washing, fixation, staining, and dilution. The sample was then transported into a sample loop of known volume from which it was injected into the flow cell for determination of cell counts and measurement of scattering and fluorescence parameters. The apparatus was fully automated and controlled with a personal computer equipped with a data acquisition card. An inexpensive mechanism that continuously replenished the sheath fluid was implemented to ensure continuous and uninterrupted operation of the flow cytometer for several days. The device was interfaced with a FACSCalibur equipped with CellQuest software for data acquisition and analysis. Results The set‐up was tested with batch cultures of Saccharomyces cerevisiae expressing the green fluorescent protein (GFP). On‐line cell counts showed close agreement with off‐line measurements throughout the exponential growth of a yeast culture. The time course of light scattering, GFP fluorescence, and viability distributions provided a detailed description of changes occurring in growing cell cultures based on sampling approximately every 15 min for more than 40 consecutive hours. Therefore, the device could be used to obtain descriptions of the dynamic behavior of cell populations with no user intervention required for several days. Conclusions The system significantly expanded the utility of flow cytometry by eliminating cumbersome and time‐consuming steps that make the application of flow cytometry impractical in certain situations. It is anticipated that the described set‐up will find utility in biotechnology applications such as monitoring of cell cultures, screening of biologically active compounds, and in functional genomics efforts for phenotypic characterizations of cells. Cytometry Part A 51A:87–96, 2003. © 2003 Wiley‐Liss, Inc.
The Role of Apoptosis in the Regulation of Hematopoietic Stem Cells (2000)

Hematopoietic stem cells (HSC) give rise to cells of all hematopoietic lineages, many of which are short lived. HSC face developmental choices: self-renewal (remain an HSC with long-term multilineage repopulating potential) or differentiation (become an HSC with short-term multilineage repopulating potential and, eventually, a mature cell). There is a large overcapacity of differentiating hematopoietic cells and apoptosis plays a role in regulating their numbers. It is not clear whether apoptosis plays a direct role in regulating HSC numbers. To address this, we have employed a transgenic mouse model that overexpresses BCL-2 in all hematopoietic cells, including HSC: H2K-BCL-2. Cells from H2K-BCL-2 mice have been shown to be protected against a wide variety of apoptosis-inducing challenges. This block in apoptosis affects their HSC compartment. H2K-BCL-2-transgenic mice have increased numbers of HSC in bone marrow (2.4x wild type), but fewer of these cells are in the S/G(2)/M phases of the cell cycle (0.6x wild type). Their HSC have an increased plating efficiency in vitro, engraft at least as well as wild-type HSC in vivo, and have an advantage following competitive reconstitution with wild-type HSC.
Recent status on Nano CMOS and future direction (2006)

Recently, CMOS downsizing has been accelerated very aggressively in both production and research level, and even transistor operation of a 5 nm gate length CMOS was reported in a conference. However, many serious problems are expected for implementing small-geometry MOSFETs into large scale integrated circuits even for 45 nm technology node, and it is still questionable if we can successfully introduce sub-10 nm CMOS LSIs into market, because the problems expected at this moment — such as I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</inf> /I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</inf> ratio, current drive, variation in the electrical characteristics, concerns for the yield, reliability and manufacturing cost. Considering the above situation, we formed a leading research group for future ultra-low power Nano-CMOS technology in 2003 – 2006, by the Special Coordination Funds for Promoting Science and Technology sponsored by Ministry of Education, Culture, Sports, Science and Technology, Japan, in order to conduct Nano-CMOS studies in advance to provide possible solutions to the future expected problems. The conclusion obtained by the group study was that, in the Nano-CMOS era, aggressive introduction of new materials, processes, structures, and operation concepts is required to solve the problems. Also, new physical analysis technique and physical model in order to predict and explain the atomic scale phenomena and properties at the new material interfaces are important. Unfortunately, there are no candidates among the so-called ‘beyond CMOS’ new devices, which are believed to really replace CMOS transistors usable for the products of highly integrated circuits within 20 years. Thus, our opinion is that we need to still continue CMOS based transistors — CMOS with FinFET, Nanowire FET, and even CNTFET — with ‘More Moore’ approach with combining that of ‘More than Moore.’
Comparison of E1A CR3-Dependent Transcriptional Activation across Six Different Human Adenovirus Subgroups (2010)

The largest E1A isoform of human adenovirus (Ad) includes a C-4 zinc finger domain within conserved region 3 (CR3) that is largely responsible for activating transcription of the early viral genes. CR3 interacts with multiple cellular factors, but its mechanism of action is modeled primarily on the basis of the mechanism for the prototype E1A protein of human Ad type 5. We expanded this model to include a representative member from each of the six human Ad subgroups. All CR3 domains tested were capable of transactivation. However, there were dramatic differences in their levels of transcriptional activation. Despite these functional variations, the interactions of these representative CR3s with known cellular transcriptional regulators revealed only modest differences. Four common cellular targets of all representative CR3s were identified: the proteasome component human Sug1 (hSug1)/S8, the acetyltransferases p300/CREB binding protein (CBP), the mediator component mediator complex subunit 23 (MED23) protein, and TATA binding protein (TBP). The first three factors appear to be critical for CR3 function. RNA interference against human TBP showed no significant reduction in transactivation by any CR3 tested. These results indicate that the cellular factors previously shown to be important for transactivation by Ad5 CR3 are similarly bound by the E1A proteins of other types. This was confirmed experimentally using a transcriptional squelching assay, which demonstrated that the CR3 regions of each Ad type could compete with Ad5 CR3 for limiting factors. Interestingly, a mutant of Ad5 CR3 (V147L) was capable of squelching wild-type Ad5 CR3, despite its failure to bind TBP, MED23, p300/CBP-associated factor (pCAF), or p300/CBP, suggestive of the possibility that an additional as yet unidentified cellular factor is required for transactivation by E1A CR3.
Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition (2013)

Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat), into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas) proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences) located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism.
Effective Phase Separation of Biomass Pyrolysis Oils by Adding Aqueous Salt Solutions (2009)

Effective separation methods must be developed to generate fractions of similar polarity and to concentrate the undistillable compounds before bio-oils are to be a source of chemicals production. Phase separation is one effective pathway to realize initial separation of bio-oil. By adding a little salt (3 wt % of bio-oil) or aqueous salt solution (10 wt % of bio-oil) including LiCl, CaCl2, FeCl3, (NH4)SO4, K2CO3, and Fe(NO3)3, the pyrolysis bio-oil of rice husk would quickly form two phases (40−80 wt % of the upper phase, 20−60 wt % of the bottom phase). On the basis of elemental analysis, 13C NMR integrations and GC/MS analysis, it has been demonstrated that some major components in the bio-oil are concentrated in upper/bottom phases respectively. The upper layers exhibit high contents of water, acetic acid, and water-soluble compounds; low density, viscosity, and calorific values; and high distillable substances (up to 65%). The bottom layer consists of low water content, high lignin-pyrolysis compounds, and low distillable substances (<10%), with high viscosity and calorific values. The physiochemical properties of two phases from the phase separation depend on the nature and dosage of salt added.
Plasticization of poly(dimethyl siloxane) by high‐pressure gases as studied by NMR relaxation (1974)

Abstract The molecular relaxation behavior of poly(dimethyl siloxane) (PDMS) exposed to various gases pressurized to 207 megapascals (MPa) was investigated by pulsed nuclear magnetic resonance spectroscopy. For a gas of low solubility, such as helium, the gas acts only as a pressurizing medium allowing the effect of pressure on the glass transition to be determined. For gases of high solubility the gas acts not only as a pressurizing medium but also as a plasticizing agent, expanding the polymer lattice and increasing the frequency of molecular motions. The plasticizing effect of argon was found to increase the temperature dependence of the molecular correlation frequency.
1‐Docosanol and other long chain primary alcohols in developing rat brain (1977)

Long chain alcohols were detected in developing rat brain at ages ranging from 5 to 40 days. They were at their highest level of 0.0109% of the total lipids at the age of 10 days and decreased to 0.0036% at the age of 40 days. They consited mainly of hexadecanol, octadecanol, octadecenol, eicosanol, docosanol, and tetracosanol. The fact that substantial amounts of fatty alcohols having more than 20 carbon atoms were present in myelinating rat brain indicated a chain length specificity in their utilization for 0'alkyl and 0'alk-1-enyl glycerolipid biosynthesis.
High-efficiency gene transfer into CD34+ cells with a human immunodeficiency virus type 1-based retroviral vector pseudotyped with vesicular stomatitis virus envelope glycoprotein G (1996)

Currently, amphotropic retroviral vectors are widely used for gene transfer into CD34+ hematopoietic progenitor cells. The relatively low levels of transduction efficiency associated with these vectors in human cells is due to low viral titers and limitations in concentrating the virus because of the inherent fragility of retroviral envelopes. Here we show that a human immunodeficiency virus type 1 (HIV-1)-based retroviral vector containing the firefly luciferase reporter gene can be pseudotyped with a broad-host-range vesicular stomatitis virus envelope glycoprotein G (VSV-G). Higher-efficiency gene transfer into CD34+ cells was achieved with a VSV-G-pseudotyped HIV-1 vector than with a vector packaged in an amphotropic envelope. Concentration of virus without loss of viral infectivity permitted a higher multiplicity of infection, with a consequent higher efficiency of gene transfer, reaching 2.8 copies per cell. These vectors also showed remarkable stability during storage at 4 degrees C for a week. In addition, there was no significant loss of titer after freezing and thawing of the stock virus. The ability of VSV-G-pseudotyped retroviral vectors to achieve a severalfold increase in levels of transduction into CD34+ cells will allow high-efficiency gene transfer into hematopoietic progenitor cells for gene therapy purposes. Furthermore, since it has now become possible to infect CD34+ cells with pseudotyped HIV-1 with a high level of efficiency in vitro, many important questions regarding the effect of HIV-1 on lineage-specific differentiation of hematopoietic progenitors can now be addressed.
Studies on the use of mumps virus for treatment of human cancer. (1978)

Purified mumps virus (Urabe strain) was given mainly by intravenous injection to a total of 200 patients with cancer. The only adverse clinical reaction was transient mild fever in about half the patients. The beneficial clinical effects were as follows; decrease or disappearance of ascites and edema of the lower limbs at high rates (26/37 and 4/4, respectively), usually within a week after treatment: decrease or stoppage of cancerous bleeding in 30 of 35 patients: decrease or disappearance of pain in most of the patients: and tumor regression in 26 patients with cancer of the breast, rectum, ileocaecum, thyroid gland, uterus, skin, etc. Histologically, the virus-treatment caused shrinkage of nuclei and vacuolization of the cytoplasma of tumor cells, but the degenerative changes of tumor cells were not so great as those after chemotherapy or radiotherapy. Infiltration of lymphocytes, fibrosis and collagenesis occurred around tumor tissues, where necrosis or exfoliation of tumor cells was frequently observed.
Chemotherapy for Leishmaniasis: Biochemical Mechanisms, Clinical Efficacy, and Future Strategies (1988)

The 1980s have seen significant advances in the treatment of cutaneous, mucosal, and visceral leishmaniasis. Safe regimens of pentavalent antimony in the form of Pentostam (Wellcome Foundation, London; 20 mg of antimony/[kg.d] for 20-30 days) have produced initial cure rates of greater than 90% in these diseases. Biochemical investigations have demonstrated at least three parasite-specific features relevant to the mechanism of action of chemotherapeutic agents: (1) Organization of glycolytic enzymes and some enzymes of fatty acid catabolism into organelles (glycosomes) occurs in Leishmania but not in mammalian cells. Since antimony inhibits both amastigote catabolism of glucose via glycolytic enzymes and catabolism of fatty acids, the mechanism of action of antimony may relate to alteration of glycosomal structure or function. (2) Purine analogues can be utilized by the salvage pathway of purine biosynthesis in amastigotes to a greater extent than in mammalian cells, and allopurinol and allopurinol ribonucleoside are metabolized into presumably toxic nucleotides by these means. (3) Amastigote sterol biosynthesis is akin to that of such fungi as Candida in that the major demethylated sterol is of the ergostane series and in that ketoconazole inhibits its synthesis. Preliminary clinical studies suggest that the purines and the sterol inhibitors may have clinical utility as oral agents against cutaneous leishmaniasis. Possible treatment strategies for the classic and experimental agents have been proposed.
Monocyte-regulated IFN-gamma production in human T cells involves CD2 signaling. (1993)

Cooperation between monocytes and T lymphocytes is essential for several aspects of immunologic activation. We have utilized PHA and IL-2-activated human T cells to characterize the role of monocytes in the regulation of T cell-derived IFN-gamma production. The limited IFN-gamma production by isolated T cells in this culture system was increased more than 10-fold when monocytes were added. No influence of monocytes was observed on TNF production or T cell proliferation. Maximal level of IFN-gamma in the cell culture supernatants was obtained when monocytes were added within 12 h after activation of the T cells with IL-2 and PHA. Addition of monocytes 48 h after activation resulted in marginal production of IFN-gamma, suggesting that T cells are sensitive to the monocyte-related signal during a short time period after activation. Cell-to-cell contact between the T cells and accessory cells was found to be necessary for enhanced IFN-gamma production because separation of the cells with a semipermeable membrane abolished the effect. mAb blocking experiments suggested the involvement of the CD2/LFA-3 but not the LFA-1/ICAM-1 pathway in monocyte regulation of T cell synthesis of IFN-gamma. Chinese hamster ovary (CHO) cells transfected with LFA-3 (CHO-LFA-3) and HLA-DR4/LFA-3 (CHO-DR4/LFA-3) strongly enhanced T cell IFN-gamma production, whereas untransfected CHO cells, CHO cells transfected with ICAM-1 (CHO-DR4/ICAM-1), and HLA-DR4 (CHO-DR4) did not support IFN-gamma production. PCR analysis and in situ hybridization demonstrated enhanced IFN-gamma mRNA levels in T cells stimulated in the presence of CHO-DR4/LFA-3 compared with untransfected CHO cells, indicating that the CD2/LFA-3 pathway regulates IFN-gamma production at the mRNA level. CHO-LFA-3 and CHO-DR4/ICAM-1 cells mediated strong adhesion to T cells, whereas untransfected CHO cells and CHO-DR4 cells failed to mediate adhesion. This suggests that the ability of CHO-LFA-3 but not CHO-DR4/ICAM-1 cells to induce IFN-gamma production was attributed to signal transduction rather than cell adhesion only.
The Effects of Intravitreal Ophthalmic Medications on Intraocular Pressure (2009)

Ophthalmic medications are often given as intravitreal injection. Antimicrobials, antivirals, corticosteroids and anti- vascular endothelial growth factor agents are the main classes which can be administered through intravitreal injections. Possible complications of intravitreal injection include intraocular pressure changes, especially intraocular pressure elevations. This review discusses both injection-related intraocular pressure elevations which can occur immediately after injection of any kind of medication and drug specific-related intraocular pressure changes which may be detected days or even months after the injection.
Symbol rate and modulation level-controlled adaptive modulation/TDMA/TDD system for high-bit-rate wireless data transmission (1998)

This paper proposes a time-division multiple-access/time-division duplex (TDMA/TDD)-based symbol rate and modulation level-controlled adaptive modulation system for high-bit-rate data transmission. The proposed system controls both the symbol rate and modulation level for the next transmission time slot according to the estimated carrier power to noise spectral density ratio (C/N/sub 0/) and delay spread for the time slot to achieve higher bit rate and higher transmission quality as well as higher delay-spread immunity. It is demonstrated by computer simulation and laboratory experiments that the proposed system can achieve a higher average bit rate with higher transmission quality in comparison with the fixed-rate quaternary phase-shift keying (QPSK) system and modulation level-controlled adaptive modulation system in both flat Rayleigh and frequency-selective fading environments. The simulated and experimental results also show that the proposed adaptive modulation techniques can be applied to 1-2-Mb/s indoor and outdoor microcellular systems with its delay spread of up to 250 ns and its terminal mobility of up to pedestrian speed without employing any special antifrequency-selective fading techniques, such as the adaptive equalizer and space diversity.
Vasoactive intestinal peptide: cardiovascular effects (2001)

Vasoactive intestinal peptide (VIP) is present in the peripheral and the central nervous systems where it functions as a nonadrenergic, noncholinergic neurotransmitter or neuromodulator. Significant concentrations of VIP are present in the gastrointestinal tract, heart, lungs, thyroid, kidney, urinary bladder, genital organs and the brain. On a molar basis, VIP is 50-100 times more potent than acetylcholine as a vasodilator. VIP release in the body is stimulated by high frequency (10-20 Hz) nerve stimulation and by cholinergic agonists, serotonin, dopaminergic agonists, prostaglandins (PGE, PGD), and nerve growth factor. The VIP peptide combines with its receptor and dose-dependently activates adenylyl cyclase. The vasodilatory effect of VIP in different vascular tissues or species also may be due to increases in nitric oxide, cyclic GMP, and other signaling agents. In the heart, VIP immunoreactive nerve fibers are present not only in the epicardial coronary arteries and veins, but also the sinoatrial node, atrium, interatrial septum, atrioventricular node, intracardiac ganglia, and ventricles (right ventricle >> left ventricle). In the coronary arterial walls, VIP may contribute to the regulation of normal coronary vasomotor tone. In research animals and in humans, VIP, administered into the coronary artery or intravenously, increases the epicardial coronary artery cross-sectional area, decreases coronary vascular resistance, and significantly increases coronary artery blood flow. High frequency parasympathetic (vagal) nerve stimulation also releases endogenous VIP in the coronary vessels and heart and significantly increases coronary artery blood flow. In addition, the release of VIP in the heart is increased during coronary artery occlusion and during reperfusion where VIP may promote local blood flow and may have a free-radical scavenging effect. VIP also has a primary positive inotropic effect on cardiac muscle that is enhanced by its ability to facilitate ventricular-vascular coupling by reducing mean arterial pressure by 10-15%. In concentrations of 10(-8)-10(-5) mol, VIP augments developed isometric force and increases atrial and ventricular contractility. The presence of VIP-immunoreactive nerve fibers in and around the sinus and the atrioventricular nodes of mammals strongly suggests that this peptide can affect the heart rate. In this regard, endogenously released or exogenous VIP can significantly increase the heart rate and has a more potent effect on heart rate than does norepinephrine. The presence and significant cardiovascular effects of VIP in the heart suggests that this peptide is important in the regulation of coronary blood flow, cardiac contraction, and heart rate. Current investigations are defining the physiological role of VIP in the regulation of cardiovascular function.