gebhart/patrepeval huggingface dataset:
Production of N-sulfated polysaccharides using yeast-expressed N-deacetylase/N-sulfotransferase-1 (NDST-1) (2004)

Heparan sulfate/heparin N-deacetylase/N-sulfotransferase-1 (NDST-1) is a critical enzyme involved in heparan sulfate/heparin biosynthesis. This dual-function enzyme modifies the GlcNAc-GlcA disaccharide repeating sugar backbone to make N-sulfated heparosan. N-sulfation is an absolute requirement for the subsequent epimerization and O-sulfation steps in heparan sulfate/heparin biosynthesis. We have expressed rat liver (r) NDST-1 in Saccharomyces cerevisiae as a soluble protein. The yeast-expressed enzyme has both N-deacetylase and N-sulfotransferase activities. N-acetyl heparosan, isolated from Escherichia coli K5 polysaccharide, de-N-sulfated heparin (DNSH) and completely desulfated N-acetylated heparan sulfate (CDSNAcHS) are all good substrates for the rNDST-1. However, N-desulfated, N-acetylated heparin (NDSNAcH) is a poor substrate. The rNDST-1 was partially purified on heparin Sepharose CL-6B. Purified rNDST-1 requires Mn(2+) for its enzymatic activity, can utilize PAPS regenerated in vitro by the PAPS cycle (PAP plus para-nitrophenylsulfate in the presence of arylsulfotransferase IV), and with the addition of exogenous PAPS is capable of producing 60-65% N-sulfated heparosan from E. coli K5 polysaccharide or Pasteurella multocida polysaccharide.
Architectural Transcription Factor HMGI(Y) Promotes Tumor Progression and Mesenchymal Transition of Human Epithelial Cells (2001)

Numerous studies have demonstrated that overexpression or aberrant expression of the HMGI(Y) family of architectural transcription factors is frequently associated with both neoplastic transformation of cells and metastatic tumor progression. Little is known, however, about the molecular roles played by the HMGI(Y) proteins in these events. Here we report that human breast epithelial cells harboring tetracycline-regulated HMGI(Y) transgenes acquire the ability to form both primary and metastatic tumors in nude mice only when the transgenes are actively expressed. Unexpectedly, the HMG-Y, rather than the HMG-I, isoform of these proteins is the most effective elicitor of both neoplastic transformation and metastatic progression in vivo. Furthermore, expression of either antisense or dominant-negative HMGI(Y) constructs inhibits both the rate of proliferation of tumor cells and their ability to grow anchorage independently in soft agar. Array analysis of transcription profiles demonstrates that the HMG-I and HMG-Y isoform proteins each modulate the expression of distinctive constellations of genes known to be involved in signal transduction, cell proliferation, tumor initiation, invasion, migration, induction of angiogenesis, and colonization. Immunohistochemical analyses of tumors formed in nude mice indicate that many have undergone an epithelial-mesenchymal transition in vivo. Together, these findings demonstrate that overexpression of the HMGI(Y) proteins, more specifically, the HMG-Y isoform protein, is causally associated with both neoplastic transformation and metastatic progression and suggest that induction of integrins and their signaling pathways may play significant molecular roles in these biological events.
APP Transgenic Mice Tg2576 Accumulate Aβ Peptides That Are Distinct from the Chemically Modified and Insoluble Peptides Deposited in Alzheimer's Disease Senile Plaques (2001)

The amyloid (Abeta) peptides generated in Hsiao's APP Tg2576 transgenic (Tg) mice are physically and chemically distinct from those characteristic of Alzheimer's disease (AD). Transgenic mouse Abeta peptides were purified using sequential size-exclusion and reverse-phase chromatographic systems and subjected to amino acid sequencing and mass spectrometry analyses. The mouse Abeta peptides lacked the extensive N-terminal degradations, posttranslational modifications, and cross-linkages abundant in the stable Abeta peptide deposits observed in AD. Truncated Abeta molecules appear to be generated in vivo by hydrolysis at multiple sites rather than by post-mortem C-terminal degradation. In contrast to AD amyloid cores, the Tg mice peptides were soluble in Tris-SDS-EDTA solutions, revealing both monomeric and SDS-stable oligomeric species of Abeta. In contrast to our report on Novartis Pharma APP23 Tg mice [Kuo et al. (2001) J. Biol. Chem. 276, 12991], which maintain high levels of soluble Abeta early on with later development of extensive vascular amyloid, Tg2576 mice exhibited an age-related elevation of soluble Abeta with relatively limited vascular amyloid deposition. The transgenic mouse levels of carboxy-terminal (CT) APP fragments were nearly 10-fold greater than those of human brains, and this condition may contribute to the unique pathology observed in these animals. Immunization of transgenic mice may act to prevent the pathological effects of betaAPP overproduction by binding CT molecules or halting their processing to toxic forms, in addition to having any effects on Abeta itself. Thus, differences in disease evolution and biochemistry must be considered when using transgenic animals to evaluate drugs or therapeutic interventions intended to reduce the Abeta burden in Alzheimer's disease.
Hericium erinaceus Mycelium Exerts Neuroprotective Effect in Parkinson’s Disease-in vitro and in vivo Models (2020)

Hericium erinaceus (H.E.) is a well-known edible and folk medicinal fungi in Japan, China and other Asian countries without harmful effects. It has been recognized that this unique mushroom is capable of keeping the brain healthy, supporting the immune system to help prevent gastric cancer and other diseases, boosting mood and concentration, decreasing inflammatory processes in the body. But more scientific researchers are needed to confirm its nutritional and medicinal effects. In the present study, we investigated the effects of Hericium erinaceus mycelium (H.E. mycelium) against 1-methyl-4-phenylpyridinium(MPP+)-induced neurotoxicity in PC12 cells and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinsonian mice. In the cell viability results, treatment with H.E.mycelium increased the cell viability in MPP+-treated cells and induced antioxidant activity in PC12 cells. H.E. mycelium also reduced MPTP-induced loss of dopamine concentration level and tyrosine hydroxylase (TH) positive cells in mice. Our results suggest that H.E.mycelium performs significant protection of dopaminergic neuron under severe conditions and is very effective in the treatment of damaged neuron in the brain to recover in the case of Parkinson's disease.
Near-infrared sensitivity enhancement of a back-illuminated complementary metal oxide semiconductor image sensor with a pyramid surface for diffraction structure (2017)

We demonstrated the near-infrared (NIR) sensitivity enhancement of back-illuminated complementary metal oxide semiconductor image sensors (BI-CIS) with a pyramid surface for diffraction (PSD) structures on crystalline silicon and deep trench isolation (DTI). The incident light diffracted on the PSD because of the strong diffraction within the substrate, resulting in a quantum efficiency of more than 30% at 850 nm. By using a special treatment process and DTI structures, without increasing the dark current, the amount of crosstalk to adjacent pixels was decreased, providing resolution equal to that of a flat structure. Testing of the prototype devices revealed that we succeeded in developing unique BI-CIS with high NIR sensitivity.
Human retroviruses and AIDS 1997 (1997)

This compendium is the result of an effort to compile, organize, and rapidly publish as much relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses as possible. The scope of the compendium and database is best summarized by the four parts that it comprises: (1) Nucleic Acid Alignments, (2) Amino Acid Alignments, (3) Reviews and Analyses, and (4) Related Sequences. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. This year we are not including floppy diskettes as the entire compendium is available both at our Web site and at our ftp site. If you need floppy diskettes please contact either Bette Korber (btk@t10.lanl.gov) or Kersti Rock (karm@t10.lanl.gov) by email or fax ((505) 665-4453). While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. The exception to this are reviews submitted by experts in areas deemed of particular and basic importance to research involving AIDS viral sequence information. These are included in Part III, and are contributed by scientists with particular expertise in the area of interest. In addition to the general descriptions below of the parts of the compendium, the user should read the individual introductions for each part.
Vital dye analysis of cranial neural crest cell migration in the mouse embryo (1992)

The spatial and temporal aspects of cranial neural crest cell migration in the mouse are poorly understood because of technical limitations. No reliable cell markers are available and vital staining of embryos in culture has had limited success because they develop normally for only 24 hours. Here, we circumvent these problems by combining vital dye labelling with exo utero embryological techniques. To define better the nature of cranial neural crest cell migration in the mouse embryo, premigratory cranial neural crest cells were labelled by injecting DiI into the amniotic cavity on embryonic day 8. Embryos, allowed to develop an additional 1 to 5 days exo utero in the mother before analysis, showed distinct and characteristic patterns of cranial neural crest cell migration at the different axial levels. Neural crest cells arising at the level of the forebrain migrated ventrally in a contiguous stream through the mesenchyme between the eye and the diencephalon. In the region of the midbrain, the cells migrated ventrolaterally as dispersed cells through the mesenchyme bordered by the lateral surface of the mesencephalon and the ectoderm. At the level of the hindbrain, neural crest cells migrated ventrolaterally in three subectodermal streams that were segmentally distributed. Each stream extended from the dorsal portion of the neural tube into the distal portion of the adjacent branchial arch. The order in which cranial neural crest cells populate their derivatives was determined by labelling embryos at different stages of development. Cranial neural crest cells populated their derivatives in a ventral-to-dorsal order, similar to the pattern observed at trunk levels. In order to confirm and extend the findings obtained with exo utero embryos, DiI (1,1-dioctadecyl-3,3,3',3'-tetramethylindo-carbocyanine perchlorate) was applied focally to the neural folds of embryos, which were then cultured for 24 hours. Because the culture technique permitted increased control of the timing and location of the DiI injection, it was possible to determine the duration of cranial neural crest cell emigration from the neural tube. Cranial neural crest cell emigration from the neural folds was completed by the 11-somite stage in the region of the rostral hindbrain, the 14-somite stage in the regions of the midbrain and caudal hindbrain and not until the 16-somite stage in the region of the forebrain. At each level, the time between the earliest and latest neural crest cells to emigrate from the neural tube appeared to be 9 hours.(ABSTRACT TRUNCATED AT 400 WORDS)
Endoplasmic Reticulum Calcium Pumps and Cancer Cell Differentiation (2012)

The endoplasmic reticulum (ER) is a major intracellular calcium storage pool and a multifunctional organelle that accomplishes several calcium-dependent functions involved in many homeostatic and signaling mechanisms. Calcium is accumulated in the ER by Sarco/Endoplasmic Reticulum Calcium ATPase (SERCA)-type calcium pumps. SERCA activity can determine ER calcium content available for intra-ER functions and for calcium release into the cytosol, and can shape the spatiotemporal characteristics of calcium signals. SERCA function therefore constitutes an important nodal point in the regulation of cellular calcium homeostasis and signaling, and can exert important effects on cell growth, differentiation and survival. In several cell types such as cells of hematopoietic origin, mammary, gastric and colonic epithelium, SERCA2 and SERCA3-type calcium pumps are simultaneously expressed, and SERCA3 expression levels undergo significant changes during cell differentiation, activation or immortalization. In addition, SERCA3 expression is decreased or lost in several tumor types when compared to the corresponding normal tissue. These observations indicate that ER calcium homeostasis is remodeled during cell differentiation, and may present defects due to decreased SERCA3 expression in tumors. Modulation of the state of differentiation of the ER reflected by SERCA3 expression constitutes an interesting new aspect of cell differentiation and tumor biology.
Heparin, Protamine, and Ionized Calcium In Vitro and In Vivo (1985)

The possibility that hypotension associated with protamine or heparin might be related to changes in levels of serum ionized calcium values was determined by in vitro and in vivo studies in dogs. In vitro protamine did not decrease serum calcium levels, but heparin did in a dose-dependent fashion. The reduction ranged from 7% with 10 units/ml of heparin to 20% with 100 units/ml of heparin. Ionized calcium concentrations initially decreased by heparin were restored toward control levels by our increasing the dose of protamine, indicating that the electrostatic attraction between protamine and heparin molecules is stronger than that between heparin and ionized calcium. Despite significant reductions in blood pressure and heart rate, clinical doses of protamine did not decrease ionized calcium in vivo. Although the results of the in vitro study suggested that heparin-induced hypocalcemia might occur in vivo, in vivo heparin caused neither a decrease in ionized calcium nor hypotension. The reduction of ionized calcium by heparin might have been rapidly compensated for in vivo. The results indicate that hypotension due to protamine or heparin is unlikely to be related to changes in serum ionized calcium levels.
Cultivation factors and population size control the uptake of nitrogen by the microalgae Chlorella vulgaris when interacting with the microalgae growth-promoting bacterium Azospirillum brasilense (2005)

Growth of and the capacity to take up nitrogen in the freshwater microalgae Chlorella vulgaris were studied while varying the concentrations of ammonium and nitrate, the pH and the source of carbon in a synthetic wastewater growth medium when co-immobilized in alginate beads with the microalgae growth-promoting bacterium Azospirillum brasilense. Analyses of 29 independent experiments showed that co-immobilization of the microalgae with A. brasilense could result in two independent phenomena directly affected by cultivation factors, such as nitrogen species, pH and presence of a carbon source. First, growth of the microalgal population increased without an increase in the capacity of the single cells to take up nitrogen, or second, the capacity of cells to take up nitrogen increased without an increase of the total microalgal population. These phenomena were dependent on the population density of the microalgae, which was in turn affected by cultivation factors. This supports the conclusion that the size of the microalgal population controls the uptake of nitrogen in C. vulgaris cells - the higher the population (regardless the experimental parameters), the less nitrogen each cell takes up.
Potentiation of fludarabine cytotoxicity on non-Hodgkin's lymphoma by pentoxifylline and rituximab. (2000)

This study proves the hypothesis that Rituximab and pentoxifylline may provide a clinical approach to hinder the outgrowth of drug refractory tumor cells and achieve a longer period of remission.
Scalable routing strategies for ad hoc wireless networks (1999)

We consider a large population of mobile stations that are interconnected by a multihop wireless network. The applications of this wireless infrastructure range from ad hoc networking (e.g., collaborative, distributed computing) to disaster recovery (e.g., fire, flood, earthquake), law enforcement (e.g., crowd control, search-and-rescue), and military (automated battlefield). Key characteristics of this system are the large number of users, their mobility, and the need to operate without the support of a fixed (wired or wireless) infrastructure. The last feature sets this system apart from existing cellular systems and in fact makes its design much more challenging. In this environment, we investigate routing strategies that scale well to large populations and can handle mobility. In addition, we address the need to support multimedia communications, with low latency requirements for interactive traffic and quality-of-service (QoS) support for real-time streams (voice/video). In the wireless routing area, several schemes have already been proposed and implemented (e.g., hierarchical routing, on-demand routing, etc.). We introduce two new schemes-fisheye state routing (FSR) and hierarchical state routing (HSR)-which offer some competitive advantages over the existing schemes. We compare the performance of existing and proposed schemes via simulation.
Studies on the Transfer of Steroid Hormones Across the Blood-Cerebrospinal Fluid Barrier in the Rhesus Monkey (1976)

Indwelling canulae were placed in the lateral ventricles of the brains of six adult male rhesus monkeys, and the movement of estradiol-17β (E2), testosterone (T), and 5α-dihydrotestosterone (DHT) across the blood-cerebrospinal fluid (CSF) barrier was measured. Serial samples of blood and CSF were collected every 30 minutes during a 6 hour infusion of the tritiated steroids, and the quantity of free steroid in the blood and CSF was determined by recrystallization to constant specific activity. During the course of the 6-hour infusion, the average CSF concentration of steroid, expressed as dpm/ml, was about 3.5% of the concurrent plasma level of E2, 1.6% of the concurrent plasma level of T, and 0.08% of the concurrent plasma level of DHT. It is proposed that these differences in steroid transfer can be attributed to differential binding of these steroids to testosterone-estrogen-binding globulin (TeBG) in plasma. {Endocrinology99: 400, 1976)
Case 5 (2013)

This is a case from the Arthritis section of Emergency Radiology Cases. The specific content of each case and its diagnosis are necessarily hidden from this abstract. Each case contains case history, followed immediately by the diagnosis, which is supported with findings, differential diagnosis, teaching points, management, and further reading suggestions.
Phosphatidylinositol 3 kinase contributes to the transformation of hematopoietic cells by the D816V c-Kit mutant (2001)

Stem cell factor (SCF) binds the receptor tyrosine kinase c-Kit and is critical for normal hematopoiesis. Substitution of valine for aspartic acid 816 (D816V) constitutively actives human c-Kit, and this mutation is found in patients with mastocytosis, leukemia, and germ cell tumors. Immortalized murine progenitor cells (MIHCs) transduced with wild-type c-Kit proliferate in response to SCF, whereas cells expressing D816V c-Kit (MIHC-D816V) are factor-independent and tumorigenic. However, the mechanisms mediating transformation by D816V c-Kit are unknown. The objective of this study was to identify signaling components that contribute to D816V c-Kit-mediated transformation. SCF stimulates association of p85PI3K with phosphorylated tyrosine 721 of wild-type c-Kit. Phosphatidylinositol 3 kinase (PI3K) subsequently contributes to the activation of Akt and Jnks. In contrast, these studies demonstrated that the D816V c-Kit mutant was constitutively associated with phosphorylated p85PI3K, and, downstream of PI3K, Jnk 1 and Jnk 2 were activated but Akt was not. Interestingly, Erks 1 and 2 were not constitutively activated by D816V c-Kit. Thus, D816V c-Kit maintains the activity of PI3K but not of all signaling pathways activated by wild-type c-Kit. Further, all pathways downstream of PI3K are not constitutively active in MIHC-D816V cells. Studies with a PI3K inhibitor and D816V/Y721F c-Kit, a mutant incapable of recruiting PI3K, indicate that constitutive activation of PI3K through direct recruitment by D816V c-Kit plays a role in factor-independent growth of MIHC and is critical for tumorigenicity.
Near-Infrared Raman Spectroscopy of Liquids and Solids with a Fiber-Optic Sampler, Diode Laser, and CCD Detector (1990)

Fluorescence interference often present in conventional Raman techniques may be considerably reduced by moving from a visible laser source to one in the near-infrared (NIR) region. Fourier transform Raman spectroscopy (FT-Raman) performed at 1064 nm dramatically reduces fluorescence background and extends the utility of Raman spectroscopy to a wider range of samples. However, FT-Raman exhibits a lower signal-to-noise ratio (S/N) than visible Raman because of reduced scattering (due to the v4 factor) and higher noise associated with detectors useful in the range above 1064 nm. An alternative procedure for NIR Raman involves a 783-or 830-nm GaAlAs diode laser, a charge-coupled device (CCD) detector, and a single-grating spectrograph. Excellent reduction of fluorescence background has been achieved, yet Raman spectra are obtained at wavelengths within the quantum efficiency range of the CCD detector. Because the CCD detector is shot-noise limited, a much higher S/N is attained in comparison with FT-Raman, permitting the use of low laser power and weakly scattering samples. The approach is similar to other CCD Raman spectrometers based on He-Ne11 or NIR dye lasers, and exhibits a trade-off between quantum efficiency and fluorescence reduction since the laser wavelength is extended into the NIR.
Ultrafast heterodyne-detected transient-grating spectroscopy using diffractive optics (1998)

We present a method for implementing optical heterodyne detection using a diffractive optic for time-resolved transient-grating experiments. This technique does not require active phase locking of pulse pairs to achieve interferometric stability. The phase stability, intrinsic time resolution, and signal amplification are demonstrated experimentally through Raman scattering in carbon disulfide.
Subcutaneous Heparin Compared with Continuous Intravenous Heparin Administration in the Initial Treatment of Deep Vein Thrombosis (1992)

The results of our meta-analysis indicated that heparin administered subcutaneously twice daily in the initial treatment of deep vein thrombosis is more effective and at least as safe as continuous intravenous heparin administration. Administration of heparin subcutaneously may simplify patient treatment and could facilitate home treatment.
Physical models for moving shadow and object detection in video (2004)

Current moving object detection systems typically detect shadows cast by the moving object as part of the moving object. In this paper, the problem of separating moving cast shadows from the moving objects in an outdoor environment is addressed. Unlike previous work, we present an approach that does not rely on any geometrical assumptions such as camera location and ground surface/object geometry. The approach is based on a new spatio-temporal albedo test and dichromatic reflection model and accounts for both the sun and the sky illuminations. Results are presented for several video sequences representing a variety of ground materials when the shadows are cast on different surface types. These results show that our approach is robust to widely different background and foreground materials, and illuminations.