gebhart/patrepeval huggingface dataset:
Abscisic acid induces oscillations in guard-cell cytosolic free calcium that involve phosphoinositide-specific phospholipase C (1999)

Oscillations in cytosolic free Ca2+ concentration ([Ca2+]cyt) are an important component of Ca2+-based signal transduction pathways. This fact has led us to investigate whether oscillations in [Ca2+]cyt are involved in the response of stomatal guard cells to the plant hormone abscisic acid (ABA). We show that ABA induces oscillations in guard-cell [Ca2+]cyt. The pattern of the oscillations depended on the ABA concentration and correlated with the final stomatal aperture. We examined the mechanism by which ABA generates oscillations in guard-cell [Ca2+]cyt by using 1-(6-[17beta-3-methoxyestra-1,3, 5(10)-trien-17-yl]aminohexyl)-1H-pyrrole-2,5-dione (U-73122), an inhibitor of phosphoinositide-specific phospholipase C (PI-PLC)-dependent processes in animals. U-73122 inhibited the hydrolysis of phosphatidylinositol 4,5-bisphosphate by a recombinant PI-PLC, isolated from a guard-cell-enriched cDNA library, in a dose-dependent manner. This result confirms that U-73122 is an inhibitor of plant PI-PLC activity. U-73122 inhibited both ABA-induced oscillations in [Ca2+]cyt and stomatal closure. In contrast, U-73122 did not inhibit external Ca2+-induced oscillations in guard-cell [Ca2+]cyt and stomatal closure. Furthermore, there was no effect of the inactive analogue 1-(6-[17beta-3-methoxyestra-1,3, 5(10)-trien-17-yl]aminohexyl)-2,5-pyrrolidinedione on recombinant PI-PLC activity or ABA-induced and external Ca2+-induced oscillations in [Ca2+]cyt and stomatal closure. This lack of effect suggests that the effects of U-73122 in guard cells are the result of inhibition of PI-PLC and not a consequence of nonspecific effects. Taken together, our data suggest a role for PI-PLC in the generation of ABA-induced oscillations in [Ca2+]cyt and point toward the involvement of oscillations in [Ca2+]cyt in the maintenance of stomatal aperture by ABA.
Research and development of a new RF-assisted device for bloodless rapid transection of the liver: Computational modeling and in vivo experiments (2009)

A new RF-assisted device for bloodless, rapid liver resection was designed, built and tested. The results demonstrate the potential advantages of this device over others currently employed.
Neurobiology of the Caenorhabditis elegans Genome (1998)

Neurotransmitter receptors, neurotransmitter synthesis and release pathways, and heterotrimeric GTP-binding protein (G protein)-coupled second messenger pathways are highly conserved between Caenorhabditis elegans and mammals, but gap junctions and chemosensory receptors have independent origins in vertebrates and nematodes. Most ion channels are similar to vertebrate channels but there are no predicted voltage-activated sodium channels. The C. elegans genome encodes at least 80 potassium channels, 90 neurotransmitter-gated ion channels, 50 peptide receptors, and up to 1000 orphan receptors that may be chemoreceptors. For many gene families, C. elegans has both conventional members and divergent outliers with weak homology to known genes; these outliers may provide insights into previously unknown functions of conserved protein families.
The relationship between high-dose treatment and combination chemotherapy: the concept of summation dose intensity. (1998)

The most important variables for the clinical use of antitumor agents (AAs) are dose and combination chemotherapy. The objectives of this study were to analyze the relationship between these two variables and to propose a unified conceptual framework for the construct and interpretation of clinical trials. Definitions and variables with respect to dose include potency, therapeutic index, standard dose, efficacy, relative efficacy, dose-limiting toxicity (DLT), dose rate, dose density, dose intensity, and fractional dose intensity. Our overarching concept, that is, summation dose intensity (SDI), was calculated in several ways, depending upon the nature of the data, and included the relative efficacy method, the unit regimen method, and the high dose method. The SDI concept was then applied to disease categories and strategies to determine its usefulness and effectiveness in integrating dose and combinations. The tumors and settings were: mustargen-vincristine-procarbazine-prednisone in Hodgkin's disease, combination chemotherapy for acute lymphocytic leukemia in children, metastatic breast cancer including dose and combinations, selected other solid tumors, alternating chemotherapy, and high dose studies in the leukemias and lymphomas. SDI was effective in integrating and quantifying dose and combination chemotherapy. For classical AAs, the implication of SDI for the construct and analysis of clinical trials was emphasized. In addition to new drug development, emphasis should be given to reducing or eliminating DLTs, such as those of the marrow, now and, in the future, those of the gastrointestinal tract toxicity and other DLTs. The above was derived from and applies to the classical AAs. Whether they will apply to, with appropriate adjustment, agents with significantly different dose-response curves, such as biotherapeutics and hormonal agents, remains to be determined.
pH Transitions in Ion‐Exchange Systems: Role in the Development of a Cation‐Exchange Process for a Recombinant Protein (2002)

Unexpected transient changes in effluent pH can occur during ion-exchange chromatography. Such changes can occur even if a column that is equilibrated with a buffer receives another solution in the same buffer and of the same pH but of a different salt concentration. An attempt is made to understand the basis for this phenomenon and apply it to the process purification of a recombinant protein on a strong cation-exchange resin. Incomplete column equilibration was eliminated as a possible cause of these effects. Various buffering species and various salt ions were studied at different solution concentrations to investigate pH transitions on strong cation-exchange resins. A further comparison was made between cation-exchange resins with different backbone chemistries. On the basis of these studies, a mechanism is proposed for these phenomena based on competitive equilibria between ions from the buffer salts and H(+)/OH(-) ions. In addition to the equilibria between these ions and the functional groups on the resins, charged groups on the resin backbone were also found to contribute to transient pH changes. The results from this study were applied to the cation-exchange step for a recombinant protein that was sensitive to pH excursions to help maintain activity of the protein during the purification process.
Living with Water Stress: Evolution of Osmolyte Systems (1982)

Striking convergent evolution is found in the properties of the organic osmotic solute (osmolyte) systems observed in bacteria, plants, and animals. Polyhydric alcohols, free amino acids and their derivatives, and combinations of urea and methylamines are the three types of osmolyte systems found in all water-stressed organisms except the halobacteria. The selective advantages of the organic osmolyte systems are, first, a compatibility with macromolecular structure and function at high or variable (or both) osmolyte concentrations, and, second, greatly reduced needs for modifying proteins to function in concentrated intracellular solutions. Osmolyte compatibility is proposed to result from the absence of osmolyte interactions with substrates and cofactors, and the nonperturbing or favorable effects of osmolytes on macromolecular-solvent interactions.
Amphotropic Murine Leukemia Retrovirus Is Not an Acute Pathogen for Primates (1990)

The in vivo fate of amphotropic murine leukemia retrovirus was studied in five rhesus monkeys. Retrovirus infused intravenously into 3 normal animals and 1 immunosuppressed animal was cleared rapidly from the circulation and subsequent viremia has not been detected (mean follow-up of 27.4 months). A fifth monkey was immunosuppressed and transplanted with virus-producing autologous fibroblasts in addition to an intraperitoneal injection of virus. This animal was viremic for 2 days and its lymph node cells and peripheral blood mononuclear cells were shown to be producing virus for up to 22 days post-inoculation, but subsequently has been negative after 17.0 months of analysis. In the 5 animals studied (combined mean follow-up of 25.7 months), clinical illness has not been identified at any time. Therefore, murine amphotropic retroviruses do not appear to pose an acute health risk.
Refractive Variation during Autorefraction: Multivariate Distribution of Refractive Status (1995)

The refractive variation of a sample of 106 university students (63 females and 43 males) studying optometry was examined by means of autorefraction. Stereo-pair scatter plots in Euclidean three-dimensional h-space are used to illustrate the nature of the spread or distribution of data measurements found in particular subjects. A wide variety of different distributions were observed ranging from tightly to loosely clustered arrangements of measurements. Some aspects of departure from multivariate normality, including outliers (atypical measurements in a sample) and polymodal or multimodal distributions, are demonstrated. Outliers appear to be possible anywhere in the space of the scatter plots, although outliers may be more common in the region of h-space corresponding to transitory increases in accommodation. Multimodal distributions may be indicative of changes in ocular fixation during autorefraction or may reflect accommodative or other anomalies. Other departures from multivariate normality such as kurtosis and skewness are also of importance when attempting to form an understanding of variation of refractive state. Measurements made on an artificial or test eye showed very tight clusters in h-space. This suggests that the autorefractor itself contributes little to the variation observed during autorefraction of an eye.
An Expeditious Synthesis of 2-Aryl- and 2-Alkylquinazolin-4(3H)-ones (1991)

2-Aryl- and alkylquinazolin-4(3H)-ones are readily accessible by reaction of the lithium 2-(diethylaminocarbonyl)anilide with appropriate aryl and alkyl nitriles.
Impact of mobility on distributed computations (1993)

The integration of mobile/portable computers within existing static networks introduces a new set of issues to distributed computations. A mobile host can connect to the network from different locations at different times; distributed algorithms therefore, cannot rely on the assumption that a participant maintains a fixed and universally known location in the network at all times. Mobile hosts communicate with the rest of the network via a wireless broadcast medium and portable computers such as laptops and palmtops, often operate in a "disconnected" or "doze" mode to conserve battery power. These unique physical features of a mobile computing environment need to be considered as well, while designing distributed algorithms for such systems.
Bayesian Networks in Fault Diagnosis (2017)

Fault diagnosis is useful in helping technicians detect, isolate, and identify faults, and troubleshoot. Bayesian network (BN) is a probabilistic graphical model that effectively deals with various uncertainty problems. This model is increasingly utilized in fault diagnosis. This paper presents bibliographical review on use of BNs in fault diagnosis in the last decades with focus on engineering systems. This work also presents general procedure of fault diagnosis modeling with BNs; processes include BN structure modeling, BN parameter modeling, BN inference, fault identification, validation, and verification. The paper provides series of classification schemes for BNs for fault diagnosis, BNs combined with other techniques, and domain of fault diagnosis with BN. This study finally explores current gaps and challenges and several directions for future research.
Microcontact printing and pattern transfer using trichlorosilanes on oxide substrates (1996)

Microcontact printing was used to pattern silicon, aluminum, and titanium substrates using octadecyltrichlorosilane as the ink and an elastomer as the stamp. Patterns were transferred into the substrates using both dry and wet etching. The Al and Ti were etched using an electron cyclotron resonance (ECR) plasma source at low ion energies and low pressure. Silicon was etched in HF to remove the native oxide, followed by KOH. Microcontact printing using OTS ink is a convenient and easy way to pattern both semiconductor and metal surfaces without the extended use of photolithography.
Rapid Fabrication of Complex 3D Extracellular Microenvironments by Dynamic Optical Projection Stereolithography (2012)

The topographic features of the extracelluar matrix (ECM) lay the foundation for cellular behavior. A novel biofabrication method using a digital-mirror device (DMD), called dynamic optical projection stereolithography (DOPsL) is demonstrated. This robust and versatile platform can generate complex biomimetic scaffolds within seconds. Such 3D scaffolds have promising potentials for studying cell interactions with microenvironments in vitro and in vivo.
The Matrix: Computer Networks and Conferencing Systems Worldwide (1989)

From the Publisher:
This complete, central source lets you tap into the worldwide information sharing network of engineers, scientists, and researchers - no matter where you live or work. It's a hands-on encyclopedic directory of specific networks and conferencing systems that encompasses millions of users across every continent!
Acute unilateral ischemic renal injury induces progressive renal inflammation, lipid accumulation, histone modification, and “end-stage” kidney disease (2011)

There is an emerging concept in clinical nephrology that acute kidney injury (AKI) can initiate chronic kidney disease (CKD). However, potential mechanisms by which this may occur remain elusive. Hence, this study tested the hypotheses that 1) AKI triggers progressive activation of selected proinflammatory genes, 2) there is a relative failure of compensatory anti-inflammatory gene expression, 3) proinflammatory lipid accumulation occurs, 4) these changes correspond with "gene-activating" histone acetylation, and 5) in concert, progressive renal disease results. CD-1 mice were subjected to 30 min of unilateral renal ischemia. Assessments were made 1 day, 1 wk, or 3 wk later. Results were contrasted to those observed in uninjured contralateral kidneys or in kidneys from normal mice. Progressive renal injury occurred throughout the 3-wk postischemic period, as denoted by stepwise increases in neutrophil gelatinase-associated lipocalin gene induction and ongoing histologic damage. By 3 wk postischemia, progressive renal disease was observed (massive tubular dropout; 2/3rds reduction in renal weight). These changes corresponded with progressive increases in proinflammatory cytokine/chemokine gene expression (MCP-1, TNF-α, TGF-β1), a relative failure of anti-inflammatory enzyme/cytokine (heme oxygenase-1; IL-10) upregulation, and progressive renal lipid (cholesterol/triglyceride) loading. Stepwise increases in collagen III mRNA and collagen deposition (Sirius red staining) indicated a progressive profibrotic response. Postischemic dexamethasone treatment significantly preserved renal mass, indicating functional significance of the observed proinflammatory state. Progressive gene-activating H3 acetylation was observed by ELISA, rising from 5% at baseline to 75% at 3 wk. This was confirmed by chromatin immunoprecipitation assay of target genes. In sum, these results provide experimental support for the clinical concept that AKI can trigger CKD, this is partially mediated by progressive postischemic inflammation, ongoing lipid accumulation results (potentially evoking "lipotoxicity"), and increasing histone acetylation at proinflammatory/profibrotic genes may contribute to this self-sustaining injury-promoting state.
Purification and structural analysis of a type III antifreeze protein from the european eelpout Zoarces viviparus. (2007)

It has recently been reported that the eelpout Zoarces viviparus synthesizes a family of antifreeze proteins (AFP) similar in sequence to type III AFPs. A method has been set up to separate these antifreeze proteins from blood serum of this teleost species. A total of nine proteins with antifreeze activity have been isolated, several to a purity suited for NMR experiments. One of the proteins, Zvafp13, has been subject to partial structure determination by NMR. 1D- and 2D-H NMR analyses were carried out. In the 1D-experiments it was observed that the protein contained 28 slow-exchanging amides, suggesting a compact structure. The 2D-experiments were utilized to assign observed signals to specific amino acids. From TOCSY- and NOESY-experiments 35 out of a total of 66 amino acids were assigned. The amide exchange pattern, protein primary sequence, chemical shifts and NOE-cross-peaks between amides and -protons in the -sheets suggest that Zvafp13 structurally resembles the recombinant type III AFP rQAE m1.1.
Parallels between Pathogens and Gluten Peptides in Celiac Sprue (2008)

Pathogens are exogenous agents capable of causing disease in susceptible organisms. In celiac sprue, a disease triggered by partially hydrolyzed gluten peptides in the small intestine, the offending immunotoxins cannot replicate, but otherwise have many hallmarks of classical pathogens. First, dietary gluten and its peptide metabolites are ubiquitous components of the modern diet, yet only a small, genetically susceptible fraction of the human population contracts celiac sprue. Second, immunotoxic gluten peptides have certain unusual structural features that allow them to survive the harsh proteolytic conditions of the gastrointestinal tract and thereby interact extensively with the mucosal lining of the small intestine. Third, they invade across epithelial barriers intact to access the underlying gut-associated lymphoid tissue. Fourth, they possess recognition sequences for selective modification by an endogenous enzyme, transglutaminase 2, allowing for in situ activation to a more immunotoxic form via host subversion. Fifth, they precipitate a T cell-mediated immune reaction comprising both innate and adaptive responses that causes chronic inflammation of the small intestine. Sixth, complete elimination of immunotoxic gluten peptides from the celiac diet results in remission, whereas reintroduction of gluten in the diet causes relapse. Therefore, in analogy with antibiotics, orally administered proteases that reduce the host's exposure to the immunotoxin by accelerating gluten peptide destruction have considerable therapeutic potential. Last but not least, notwithstanding the power of in vitro methods to reconstitute the essence of the immune response to gluten in a celiac patient, animal models for the disease, while elusive, are likely to yield fundamentally new systems-level insights.
Effect of water on piezoelectric, dielectric, and elastic properties of bone (1982)

Abstract The complex piezoelectric constant ( d = d ′ − id ″), elastic constant ( c = c ′ + ic ″), and dielectric constant (ε = ε′ − i ε″) were measured at a frequency of 10 Hz over the temperature range from −150 to 50°C and for a range of hydration up to 0.26 g/g for decalcified bone and up to 0.084 g/g for bone. For decalcified bone, ε′ and ε″ increased with increasing hydration with a deflection at the critical hydration h c = 0.08 g/g; d ′ at −150°C increased below h c but decreased above h c with increasing hydration; c ′ increased below −60°C but decreased above −60°C with increasing hydration; and the peak temperatures of ε″, d ″, and c ″ below −50°C agree with each other and decreased with increasing hydration with a deflection at h c . For bone, similar hydration and temperature dependences were observed for ε and c . However, the dependence of d on hydration and temperature was different from that of decalcified bone, reflecting a two‐phase structure consisting of collagen fibers and mineral hydroxyapatite. The critical hydration for bone was 0.04 g/g.
Efficiency Issues for Ray Tracing (1998)

Abstract Ray casting is the bottleneck of many rendering algorithms. Although much work has been done on making ray casting more efficient, most published work is high level. This paper discusses efficiency at a slightly lower level, presenting optimizations for bounding-volume hierarchies that many people use but are rarely described in the lite rature. A set of guid elines for optimization are presented that avoid some of the common pitfalls. Finally, the effects of the optimizations are shown for a set of models.
Cell cultures of neuroblasts from rat olfactory epithelium that show odorant responses. (1989)

We have developed procedures that permit isolation and propagation of clonal cell cultures from the olfactory epithelium of the 5- to 7-day-old rat that appear to represent the neuroblasts that repopulate the sensory neurons in the olfactory epithelium throughout life. The cell lines we report here synthesize neuron-specific enolase, which is a neuron marker, 43-kDa growth-associated protein, a protein associated with neuronal growth cones, and carnosine, a possible olfactory neurotransmitter. In two of the cell lines we have found dose-dependent cAMP accumulation following exposure to submicromolar concentrations of chemical odorants in the medium. These two cell lines show different patterns of odorant specificity when tested against a panel of six chemicals commonly used as test odorants. We anticipate that these and similarly derived cell lines will prove valuable in studying aspects of neurogenesis and olfaction.
Gene Expression Profile of Glioblastoma Multiforme Invasive Phenotype Points to New Therapeutic Targets (2005)

The invasive phenotype of glioblastoma multiforme (GBM) is a hallmark of malignant process, yet molecular mechanisms that dictate this locally invasive behavior remain poorly understood. Gene expression profiles of human glioma cells were assessed from laser capture-microdissected GBM cells collected from paired patient tumor cores and white matter-invading cell populations. Changes in gene expression in invading GBM cells were validated by quantitative reverse transcription polymerase chain reaction (QRT-PCR) and immunohistochemistry in an independent sample set. QRT-PCR confirmed the differential expression in 19 of 21 genes tested. Immunohistochemical analyses of autotaxin (ATX), ephrin B3, B-cell lymphoma-w (BCLW), and protein tyrosine kinase 2 beta showed them to be expressed in invasive glioma cells. The known GBM markers, insulin-like growth factor binding protein 2 and vimentin, were robustly expressed in the tumor core. A glioma invasion tissue microarray confirmed the expression of ATX and BCLW in invasive cells of tumors of various grades. GBM phenotypic and genotypic heterogeneity is well documented. In this study, we show an additional layer of complexity: transcriptional differences between cells of tumor core and invasive cells located in the brain parenchyma. Gene products supporting invasion may be novel targets for manipulation of brain tumor behavior with consequences on treatment outcome.