gebhart/patrepeval huggingface dataset:
Effects of macroscopic polarization in III-V nitride multiple quantum wells (1999)

Huge built-in electric fields have been predicted to exist in wurtzite III-V nitrides thin films and multilayers. Such fields originate from heterointerface discontinuities of the macroscopic bulk polarization of the nitrides. Here we discuss the background theory, the role of spontaneous polarization in this context, and the practical implications of built-in polarization fields in nitride nanostructures. To support our arguments, we present detailed self-consistent tight-binding simulations of typical nitride quantum well structures in which polarization effects are dominant.
Understanding the Thermodynamics of Direct Injection Spark Ignition (DISI) Combustion Systems: An Analytical and Experimental Investigation (1996)

&lt;div class="htmlview paragraph"&gt;Direct-injection spark-ignition (DISI) engines have been investigated for many years but only recently have shown promise as a next generation gasoline engine technology. Much of this new enthusiasm is due to advances in the fuel injection system, which is now capable of producing a well-controlled spray with small droplets. A physical understanding of new combustion systems utilizing this technology is just beginning to occur. This analytical and experimental investigation with a research single-cylinder combustion system shows the benefits of in-cylinder gasoline injection versus injection of fuel into the intake port. Charge cooling with direct injection is shown to improve volumetric efficiency and reduce the mixture temperature at the time of ignition allowing operation with a higher compression ratio which improves the thermodynamic cycle efficiency. Volumetric efficiency improved by 2-3%, wide-open-throttle (WOT) output improved by 5-10% and part-load fuel consumption improved by 4-5% versus a production PI engine with stoichiometric calibration. A further gain of 6-7% was recorded with lean, homogeneous air-fuel operation.&lt;/div&gt;
A temporal signal, independent of agr, is required for hla but not spa transcription in Staphylococcus aureus (1991)

Staphylococcus aureus exoprotein expression is controlled by a global regulon known as agr. This system activates transcription of some target genes and represses transcription of others. Target genes expressed postexponentially such as alpha-hemolysin (hla) are activated by agr; target genes expressed during exponential phase such as protein A (spa) are repressed by agr. A unique feature of the agr system is that this transcriptional regulation is mediated by a 517-nucleotide transcript, RNAIII. While it is clear that agr differentially regulates the expression of exponential and postexponential exoproteins, the precise role of agr in the temporal control of these events has not yet been explored. In this report, we examine the effects of expressing RNAIII, the agr regulator, under the control of the inducible beta-lactamase (bla) promoter at different times in the growth cycle. We confirm previous results showing that agr is required for postexponential-phase expression of hla and further show that a separate postexponential-phase signal independent of agr function is also needed for activation of hla transcription. We also show that in an agr mutant transcription of spa occurs throughout the growth cycle, is inhibited immediately upon induction of RNAIII, and is thus indifferent to the postexponential signal required for hla activation.
Misbehaviour of XIST RNA in Breast Cancer Cells (2009)

A role of X chromosome inactivation process in the development of breast cancer have been suggested. In particular, the relationship between the breast cancer predisposing gene BRCA1 and XIST, the main mediator of X chromosome inactivation, has been intensely investigated, but still remains controversial. We investigated this topic by assessing XIST behaviour in different groups of breast carcinomas and in a panel of breast cancer cell lines both BRCA1 mutant and wild type. In addition, we evaluated the occurrence of broader defects of heterochromatin in relation to BRCA1 status in breast cancer cells. We provide evidence that in breast cancer cells BRCA1 is involved in XIST regulation on the active X chromosome, but not in its localization as previously suggested, and that XIST can be unusually expressed by an active X and can decorate it. This indicates that the detection of XIST cloud in cancer cell is not synonymous of the presence of an inactive X chromosome. Moreover, we show that global heterochromatin defects observed in breast tumor cells are independent of BRCA1 status. Our observations sheds light on a possible previously uncharacterized mechanism of breast carcinogenesis mediated by XIST misbehaviour, particularly in BRCA1-related cancers. Moreover, the significant higher levels of XIST-RNA detected in BRCA1-associated respect to sporadic basal-like cancers, opens the possibility to use XIST expression as a marker to discriminate between the two groups of tumors.
Differential Expression Patterns of Claudins, Tight Junction Membrane Proteins, in Mouse Nephron Segments (2002)

As the first step in understanding the physiologic functions of claudins (tight junction integral membrane proteins) in nephrons, the expression of claudin-1 to -16 in mouse kidneys was examined by Northern blotting. Among these claudins, only claudin-6, -9, -13, and -14 were not detectable. Claudin-5 and -15 were detected only in endothelial cells. Polyclonal antibodies specific for claudin-7 and -12 were not available. Therefore, the distributions of claudin-1, -2, -3, -4, -8, -10, -11, and -16 in nephron segments were examined with immunofluorescence microscopy. For identification of individual segments, antibodies specific for segment markers were used. Immunofluorescence microscopic analyses of serial frozen sections of mouse kidneys with polyclonal antibodies for claudins and segment markers revealed that claudins demonstrated very complicated, segment-specific, expression patterns in nephrons, i.e., claudin-1 and -2 in Bowman's capsule, claudin-2, -10, and -11 in the proximal tubule, claudin-2 in the thin descending limb of Henle, claudin-3, -4, and -8 in the thin ascending limb of Henle, claudin-3, -10, -11, and -16 in the thick ascending limb of Henle, claudin-3 and -8 in the distal tubule, and claudin-3, -4, and -8 in the collecting duct. These segment-specific expression patterns of claudins are discussed, with special reference to the physiologic functions of tight junctions in nephrons.
Mapping site‐specific protein N‐glycosylations through liquid chromatography/mass spectrometry and targeted tandem mass spectrometry (2010)

Glycosylation is one of the most common posttranslational modifications (PTMs) of proteins, the characterization of which is commonly achieved through proteomic protocol, involving trypsin digestion followed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, it is often not possible to characterize all glycopeptides in a complex sample because of the high complexity of glycoproteomic samples, and the relative lower abundances of glycopeptides in comparison to the unmodified peptides. We present here a targeted MS/MS analysis approach, which utilizes a previously developed computational tool, GlyPID, to guide multiple experiments, thus permitting a complete characterization of all N-glycosylation sites of glycoproteins present in a complex sample. We have tested our approach using model glycoproteins analyzed by high-resolution LTQ-FT MS. The results demonstrate a potential use of our method for a high-throughput characterization of complex mixtures of glycosylated proteins.
An approach to remove albumin for the proteomic analysis of low abundance biomarkers in human serum (2003)

Proteomic technologies are being used to discover and identify disease-associated biomarkers. The application of these technologies in the search for potential diagnostic/prognostic biomarkers in the serum of patients has been limited by the presence of highly abundant albumin and immunoglobulins that constitute approximately 60-97% of the total serum proteins. The purpose of the study was to evaluate whether treatment of human serum with Affi-Gel Blue alone or in combination with Protein A (Aurum serum protein mini kit, Bio-Rad) before two-dimensional gel electrophoresis (2-DE) analysis removed high abundance proteins to allow the visualization of low abundant proteins. Serum samples were treated with either Affi-Gel Blue or Aurum kit and then subjected to 2-DE using 11 cm, pH 4-7 isoelectric focussing strips for the first dimension and 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis for second dimension. Protein spots were visualized using a fluorescent protein dye (SYPRO Ruby, Bio-Rad). Comparison between treatment methods showed significant removal of albumin by both Affi-Gel Blue and Aurum kit and considerable differences in the protein profile of the gels after each treatment. Direct comparison between treatments revealed twenty-eight protein spots unique to Affi-Gel Blue while only two spots were unique after Aurum kit treatment. Unique spots in Affi-Gel Blue and Aurum kit treated serum were not visualized in untreated serum. Sixteen hours of Affi-Gel Blue treatment resulted in enhanced visualization of fifty-three protein spots by two-fold, thirty-one by five-fold, twelve by ten-fold and six by twenty-fold. In parallel after Aurum kit treatment two-, five-, ten- and twenty-fold enhancements of thirty, thirteen, eight and five protein spots, respectively, were observed. The pattern of increased visualization of protein spots with both treatment methods was similar. In conclusion, treatment of serum samples with Affi-Gel Blue or Aurum kit before 2-DE analysis can be used to remove high abundance proteins in order to increase the detection sensitivity of proteins present in low abundance.
<title>Angular dependence of the intensity of backscattered light from human lenses with nuclear cataract: implications for measurement</title> (2000)

It is concluded that there is no angular dependence of back scattering of light from a nuclear cataract. This implicates that reading one meridian, e.g. the 90 degree, is enough for measurement of nuclear cataract with slit lamp microscopy with Scheimpflug projection. Altogether, ten patients with nuclear cataract were measured with the NIDEK EAS-1000 system in 6 meridians. There was a slight angular dependence fitting a second order polynomial with a maximum at 90 degrees. In total, three different concentrations of standard scattering solution were measured with the same system at the same meridians. Also for these measurements, there was a slight angular dependence fitting a second order polynomial with the maximum at 90 degrees. Thus, there is a system related factor that causes a slight change of intensity of back scattered light as function of meridian.
Assays of serum lipase: analytical and clinical considerations. (1986)

We evaluated three commercially available methods for determining lipase (EC 3.1.1.3) in serum--the Du Pont aca, Boehringer Mannheim Diagnostics (BMD), and Kodak Ektachem (EK) procedures--for their analytical properties and diagnostic efficiencies. Titrimetry was used as the comparative method. The BMD and EK methods showed better agreement with the titrimetric method, owing to the presence of the necessary cofactor, colipase, in their reagents. Colipase also increased the analytical sensitivity of the BMD and EK procedures as compared with the aca method. Determinations of serum lipase, by all methods, had a clinical sensitivity in excess of 80% for acute pancreatitis; the specificity of the lipase test was about 60%, or twice that of serum amylase. Serum lipase determinations with the current, simpler technology are superior to total amylase in the diagnosis of patients with acute pancreatitis. When a colipase-supplemented method is used, a serum lipase value greater than 10-fold the upper reference limit appears to be pathognomonic for acute pancreatitis or inflammation of organs close to the pancreas.
Clinical application of monoclonal antibody-drug conjugates for immunotargeting chemotherapy of colorectal carcinoma (1988)

Monoclonal antibody-drug conjugates were applied as a clinical trial for patients who, based on the experimental study, had colorectal cancer. Monoclonal antibody A7, from a mouse splenocyte immunized against human colon cancer, was used as a drug carrier for colon cancer. The anti-cancer drugs mitomycin C (MMC) and neocarzinostatin (NCS) were bound covalently to A7 to form the conjugates A7-MMC and A7-NCS. The in vitro cytotoxic effects of the conjugates on SW1116 cells were stronger than those on free MMC or NCS. The conjugate A7-NCS, when administered to nude mice, brought about the highest NCS tumor concentration, whereas normal immunoglobulin G (IgG)-NCS distributed evenly in all tissues. The conjugates showed a strong antitumor effect on colon cancer transplanted into nude mice. Forty-one patients with colorectal cancer, including ten patients with postoperative metastasis, were given A7-NCS. The immunoperoxidase and drug concentration studies of the resected specimens showed that NCS was localized specifically in cancer. Patients receiving the conjugate did not experience serious adverse effects. Of the eight patients with postoperative liver metastasis, three showed evidence of tumor reduction on computed tomography (CT) scan and three claimed pain relief. The conjugate did not benefit patients with multiple lung metastasis or peritoneal metastasis.
Microbial Reduction of Aromatic Carboxylic Acids (1993)

Several benzoic, cinnamic and phenylacetic acid derivatives were screened with 20 micro-organisms, mainly fungi, for the reduction of their carboxylic function. For all organisms several compounds were reduced in fairly good yields up to 80% to the corresponding alcohol. No general rule could be established, concerning the substitution pattern, as to which compounds were transformed to the alcohol. Generally the reactions were accomplished within 48-70 h. Only minor, if any, side products were detected. Dicarboxylic acids, such as phthalic or phenylglutaric acids and similar compounds could not be reduced by the microorganisms tested.
Enhancement of Wound Healing by Topical Treatment with Epidermal Growth Factor (1989)

Experimental studies in animals have demonstrated that the topical application of epidermal growth factor accelerates the rate of epidermal regeneration of partial-thickness wounds and second-degree burns. We conducted a prospective, randomized, double-blind clinical trial using skin-graft-donor sites to determine whether epidermal growth factor would accelerate the rate of epidermal regeneration in humans. Paired donor sites were created in 12 patients who required skin grafting for either burns or reconstructive surgery. One donor site from each patient was treated topically with silver sulfadiazine cream, and one was treated with silver sulfadiazine cream containing epidermal growth factor (10 μg per milliliter). The donor sites were photographed daily, and healing was measured with the use of planimetric analysis. The donor sites treated with silver sulfadiazine containing epidermal growth factor had an accelerated rate of epidermal regeneration in all 12 patients as compared with that in the paired donor sites treated with silver sulfadiazine alone. Treatment with epidermal growth factor significantly decreased the average length of time to 25 percent and 50 percent healing by approximately one day and that to 75 percent and 100 percent healing by approximately 1.5 days (P<0.02). Histologic evaluation of punch-biopsy specimens taken from the centers of donor sites three days after the onset of healing supported these results. We conclude that epidermal growth factor accelerates the rate of healing of partial-thickness skin wounds. Further studies are required to determine the clinical importance of this finding. (N Engl J Med 1989; 321:76–9.)
T7 RNA polymerase-directed transcripts are processed in yeast and link 3??? end formation to mRNA nuclear export (2002)

We have characterized transcripts synthesized in vivo by bacteriophage T7 RNA polymerase to investigate yeast mRNA processing. T7 transcripts are not capped, consistent with capping being tightly coupled to RNA polymerase II (pol II) transcription. In contrast to higher eukaryotic non-pol II transcripts, yeast T7 transcripts are spliced as well as cleaved and polyadenylated. However, T7 and pol II transcripts are affected differently in cleavage and polyadenylation mutant strains, indicating that pol II may have a role in yeast 3' end formation. T7 transcripts with 3' ends directed by a polyadenylation signal are exported from the nucleus, and this export is dependent on the canonical cleavage and polyadenylation machinery. Importantly, transcripts with T7 terminator-directed 3' ends are unadenylated and predominantly nuclear in wild-type cells. Our results suggest that transcription by pol II is required for neither the nuclear export of an in vivo-transcribed mRNA nor for the retention of transcripts with aberrant 3' ends. Moreover, proper 3' end formation may be necessary and sufficient to promote mRNA export in yeast.
A Monoclonal Antibody Reactive with a 40-kDa Molecule on Fetal Thymocytes and Tumor Cells Blocks Proliferation and Stimulates Aggregation and Apoptosis (1999)

E710.2.3 is a murine thymic lymphoma cell line with an immature phenotype (CD4-CD8-) that proliferates in response to thymocytes or PMA when cultured at low density and proliferates spontaneously when grown at high density. To identify functional molecules on this cell line, we screened for mAbs that could block its proliferation. A hamster mAb, DMF10.62.3, inhibited the spontaneous, thymocyte-induced, and PMA-stimulated proliferation of E710.2.3 in vitro and induced these cells to undergo apoptosis. The mAb also caused homotypic aggregation of E710.2.3, which was inhibited by cytochalasin B, trifluoperazine, a combination of sodium azide and 2-deoxyglucose, EDTA, incubation at 4 degrees C, or treatment with paraformaldehyde. The DMF10 62.3 mAb stained a number of immortalized murine and human cell lines and, where tested, blocked their proliferation and caused death to varying extents by apoptosis. The molecule recognized by the mAb DMF10.62.3 was expressed on day 14 fetal thymus Thy1.2-positive cells. However, it was not detected on adult murine thymocytes, splenocytes, or bone marrow cells or on splenic LPS-activated B cells or Con A-activated T cells. The Ab immunoprecipitated a 40-kDa molecule from E710.2.3 that was not glycosylphosphatidylinositol linked. The data suggest that the molecule recognized by DMF62.3 is a novel cell surface molecule that may be involved in cell proliferation and/or cell death.
A phase retrieval algorithm for shifting illumination (2004)

We propose a method of iterative phase retrieval that uses measured intensities in the diffraction plane to solve the phase problem in a way that bypasses the problem of lens aberration, leading to greatly improved spatial resolution. This method is stable, easy to implement experimentally, and can be used to view a large area of the specimen when that is desired.
Lnk negatively regulates self-renewal of hematopoietic stem cells by modifying thrombopoietin-mediated signal transduction (2007)

One of the central tasks of stem cell biology is to understand the molecular mechanisms that control self-renewal in stem cells. Several cytokines are implicated as crucial regulators of hematopoietic stem cells (HSCs), but little is known about intracellular signaling for HSC self-renewal. To address this issue, we attempted to clarify how self-renewal potential is enhanced in HSCs without the adaptor molecule Lnk, as in Lnk-deficient mice HSCs are expanded in number >10-fold because of their increased self-renewal potential. We show that Lnk negatively regulates self-renewal of HSCs by modifying thrombopoietin (TPO)-mediated signal transduction. Single-cell cultures showed that Lnk-deficient HSCs are hypersensitive to TPO. Competitive repopulation revealed that long-term repopulating activity increases in Lnk-deficient HSCs, but not in WT HSCs, when these cells are cultured in the presence of TPO with or without stem cell factor. Single-cell transplantation of each of the paired daughter cells indicated that a combination of stem cell factor and TPO efficiently induces symmetrical self-renewal division in Lnk-deficient HSCs but not in WT HSCs. Newly developed single-cell immunostaining demonstrated significant enhancement of both p38 MAPK inactivation and STAT5 and Akt activation in Lnk-deficient HSCs after stimulation with TPO. Our results suggest that a balance in positive and negative signals downstream from the TPO signal plays a role in the regulation of the probability of self-renewal in HSCs. In general, likewise, the fate of stem cells may be determined by combinational changes in multiple signal transduction pathways.
AIDS Pathogenesis: A Finite Immune Response to Blame? (1996)

Some rare individuals infected with the HIV virus do not develop AIDS, and their immune systems remain healthy indefinitely. In a report in this issue of Science , Wolinsky et al . describe several indices of immune system function in six of these long-term survivors. In their Perspective, Miedema and Klein discuss what these exceptional cases reveal about the more usual course of events for infected individuals—collapse of the immune system and development of AIDS.
The Information Theoretical Significance of Spatial and Temporal Masking in Video Signals (1989)

We discuss the significance of masking effects for source coding of video signals without visible impairments. A new nonlinear spatiotemporal model of human threshold vision is proposed. Linearization yields the space-time-varying w-model. The model predicts both spatial and temporal masking effects accurately. Maximum bit-rate savings by irrelevancy reduction according to the w-model are evaluated for natural test pictures on the basis of the Shannon Lower Bound of rate distortion theory. Maximum bit-rate savings due to masking are below 0.5 bit/sample in the average. Typically 1/3 of the masking gain is due to spatial masking, the rest is due to the presence of dark and bright areas in the picture, where the visibility of noise is reduced. Gains due to temporal masking are significant only in the first 100 ms after a scene cut.
Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between product and template (2007)

Glycerol nucleic acid (GNA) is an interesting alternative base-pairing system based on an acyclic, glycerol-phosphate backbone repeat unit. The question of whether DNA polymerases can catalyze efficient template-dependent synthesis using GNA as the template is of particular interest because GNA is unable to form a stable duplex with DNA. In the present study, we screened a variety of DNA polymerases for GNA-dependent DNA synthesis. We find that Bst DNA polymerase can catalyze full-length DNA synthesis on a dodecamer GNA template. The efficiency of DNA synthesis is increased by replacing adenine with diaminopurine in both the GNA template and the DNA monomers and by the presence of manganese ions. We suggest that the BstDNA polymerase maintains a short, transient region of base-pairing between the DNA product strand and the GNA template, but that stable duplex formation between product and template strands is not required for template-dependent polymerization.