gebhart/patrepeval huggingface dataset:
Comments on Rupture of Adsorbed Vesicles (2001)

We treat rupture of adsorbed vesicles by using elements of the fracture theory. This approach allows us to estimate the rupture rate constant and, in analogy with the conventional purely thermodynamical analysis, to introduce the critical value of the lipid−substrate interaction and the critical vesicle size for vesicle rupture. In our treatment, these values are however related to the kinetics and accordingly they are dependent (logarithmically) on the time scale of the experiment.
Component-Based and Service-Oriented Software Engineering: Key Concepts and Principles (2007)

Component-based software engineering (CBSE) and service-oriented software engineering (SOSE) are two of the most dominant engineering paradigms in current software community and industry. Although they have continued their development tracks in parallel and have different focus, both paradigms have similarities in many senses, which also have resulted in confusion in understanding and applying similar concepts or the same concepts designated differently. In this paper, we present a comparison analysis framework of CBSE and SOSE and analyze them from a variety of perspectives. We discuss as well the possibility of combining the strengths of the two paradigms to meet non-functional requirements. The contribution of this paper is to clarify the characteristics of CBSE and SOSE, shorten the gap between them and bring the two worlds together so that researchers and practitioners become aware of essential issues of both paradigms, which may serve as inputs for further utilizing them in a reasonable and complementary way.
Anaerobic and aerobic batch cultivations ofSaccharomyces cerevisiae mutants impaired in glycerol synthesis (2000)

Glycerol is formed as a by-product in production of ethanol and baker's yeast during fermentation of Saccharomyces cerevisiae under anaerobic and aerobic growth conditions, respectively. One physiological role of glycerol formation by yeast is to reoxidize NADH, formed in synthesis of biomass and secondary fermentation products, to NAD(+). The objective of this study was to evaluate whether introduction of a new pathway for reoxidation of NADH, in a yeast strain where glycerol synthesis had been impaired, would result in elimination of glycerol production and lead to increased yields of ethanol and biomass under anaerobic and aerobic growth conditions, respectively. This was done by deletion of GPD1 and GPD2, encoding two isoenzymes of glycerol 3-phosphate dehydrogenase, and expression of a cytoplasmic transhydrogenase from Azotobacter vinelandii, encoded by cth. In anaerobic batch fermentations of strain TN5 (gpd2-Delta1), formation of glycerol was significantly impaired, which resulted in reduction of the maximum specific growth rate from 0.41/h in the wild-type to 0.08/h. Deletion of GPD2 also resulted in a reduced biomass yield, but did not affect formation of the remaining products. The modest effect of the GPD1 deletion under anaerobic conditions on the maximum specific growth rate and product yields clearly showed that Gdh2p is the important factor in glycerol formation during anaerobic growth. Strain TN6 (gpd1-Delta1 gpd2-Delta1) was unable to grow under anaerobic conditions due to the inability of the strain to reoxidize NADH to NAD(+) by synthesis of glycerol. Also, strain TN23 (gpd1-Delta1 gpd2-Delta1 YEp24-PGKp-cth-PGKt) was unable to grow anaerobically, leading to the conclusion that the NAD(+) pool became limiting in biomass synthesis before the nucleotide levels favoured a transhydrogenase reaction that could convert NADH and NADP(+) to NADPH and NAD(+). Deletion of either GPD1 or GPD2 in the wild-type resulted in a dramatic reduction of the glycerol yields in the aerobic batch cultivations of strains TN4 (gpd1-Delta1) and TN5 (gpd2-Delta1) without serious effects on the maximum specific growth rates or the biomass yields. Deletion of both GPD1 and GPD2 in strain TN6 (gpd1-Delta1 gpd2-Delta1) resulted in a dramatic reduction in the maximum specific growth rate and in biomass formation. Expression of the cytoplasmic transhydrogenase in the double mutant, resulting in TN23, gave a further decrease in micromax from 0.17/h in strain TN6 to 0.09/h in strain TN23, since the transhydrogenase reaction was in the direction from NADPH and NADP(+) to NADH and NADP(+). Thus, it was not possible to introduce an alternative pathway for reoxidation of NADH in the cytoplasm by expression of the transhydrogenase from A. vinelandii in a S. cerevisiae strain with a double deletion in GPD1 and GPD2.
A Novel Single-Feed Circular Microstrip Antenna With Reconfigurable Polarization Capability (2008)

A single-feed circular microstrip antenna with reconfigurable polarization capability is proposed. This antenna has a simple structure, which consists of a radiating circular patch, five switches (PIN diode), three matching stubs, and a 50 microstrip feed line. It can be switched between 4 different states: two states (low-frequency and high-frequency) for linear polarization (LP), one state for left hand circular polarization (LHCP) and one for right hand circular polarization (RHCP) by controlling the bias voltage of two PIN diodes. At the same time, three switchable matching stubs are used for matching every polarization state. Simulation results and experimental results show that the proposed antenna demonstrates a low cross polarization level, good impedance bandwidth, and a very good axial ratio in the circularly polarized states.
A population‐based study of genotypic and phenotypic variability in children with spinal muscular atrophy (2009)

The childhood incidence of SMA in the Swedish population is around 1 in 12,000 live births and it is unlikely that there is any founder effect involved in SMA in western Sweden.
Interleukin-6 Interweaves the Bone Marrow Microenvironment, Bone Loss, and Multiple Myeloma (2019)

The immune system is strongly linked to the maintenance of healthy bone. Inflammatory cytokines, specifically, are crucial to skeletal homeostasis and any dysregulation can result in detrimental health complications. Interleukins, such as interleukin 6 (IL-6), act as osteoclast differentiation modulators and as such, must be carefully monitored and regulated. IL-6 encourages osteoclastogenesis when bound to progenitors and can cause excessive osteoclastic activity and osteolysis when overly abundant. Numerous bone diseases are tied to IL-6 overexpression, including rheumatoid arthritis, osteoporosis, and bone-metastatic cancers. In the latter, IL-6 can be released with growth factors into the bone marrow microenvironment (BMM) during osteolysis from bone matrix or from cancer cells and osteoblasts in an inflammatory response to cancer cells. Thus, IL-6 helps create an ideal microenvironment for oncogenesis and metastasis. Multiple myeloma (MM) is a blood cancer that homes to the BMM and is strongly tied to overexpression of IL-6 and bone loss. The roles of IL-6 in the progression of MM are discussed in this review, including roles in bone homing, cancer-associated bone loss, disease progression and drug resistance. MM disease progression often includes the development of drug-resistant clones, and patients commonly struggle with reoccurrence. As such, therapeutics that specifically target the microenvironment, rather than the cancer itself, are ideal and IL-6, and its myriad of downstream signaling partners, are model targets. Lastly, current and potential therapeutic interventions involving IL-6 and connected signaling molecules are discussed in this review.
Distinct in vivo expression patterns of survivin splice variants in renal cell carcinomas (2002)

Survivin, a novel member of the inhibitor of apoptosis protein (IAP) family, reduces the susceptibility of tumor cells to proapoptotic stimuli, thereby promoting tumor cell survival during tumor progression and treatment with anticancer drugs. Recently, we identified 2 novel alternative splice variants of survivin, survivin-2B and survivin-Delta Ex3, which differ in their antiapoptotic properties. Survivin-2B has lost its antiapoptotic potential and may act as a naturally occurring antagonist of antiapoptotic survivin and survivin-Delta Ex3. Because the in vivo expression of these splice variants in human cancer has not been analyzed so far, 57 renal cell carcinomas (RCCs) were explored using quantitative reverse transcriptase polymerase chain reaction. We found that all RCCs express survivin-Delta Ex3, survivin-2B and survivin, the latter being the dominant transcript. When we compared early and intermediate stages with late stages of clear cell RCCs, no significant changes in the expression levels of survivin and survivin-Delta Ex3 became evident. However, a significant decrease was observed for the mRNA ratio between survivin-2B and survivin in late tumor stages (p = 0.036). Chromophilic/papillary RCCs, which are known to be less aggressive than clear cell RCCs, did not show significantly lower expression levels of antiapoptotic survivin and survivin-Delta Ex3, compared with stage-adjusted clear cell RCCs. Our study demonstrates for the first time in vivo expression of functionally different survivin variants and suggests a role of these survivin splice variants in the progression and clinical behavior of human RCCs.
Agarose Derivatives of Uridine Diphosphate and N-Acetylglucosamine for the Purification of a Galactosyltransferase (1972)

Abstract The applicability of affinity chromatography for the purification of UDP-galactose: N-acetylglucosamine galactosyltransferase has been evaluated. Three different types of specific adsorbents have been synthesized by reaction of a ligand structurally related to portions of the substrates of the transferase with cyanogen bromide-treated agarose. The synthesis of the ligands, P1-(6-amino-1-hexyl)-P2-(5'-uridine)-pyrophosphate, 6-amino-1-hexyl-2-acetamido-2-deoxy-β-d-glucopyranoside and P1-(6-amino-1-hexyl)-P2-(β-d-galactopyranosyl)pyrophosphate is described. The galactosyltransferase from bovine milk has been found to bind to two of the adsorbents and some of the parameters influencing the binding have been evaluated. The affinity of the transferase for the UDP-hexanolamine-agarose adsorbent was enhanced by manganous ions whereas the affinity was decreased by EDTA, urea, borate, or magnesium ions. The affinity of the enzyme for N-acetylglucosamine hexanolamine-agarose was enhanced considerably by UDP or UMP and was decreased by borate, urea or N-acetylglucosamine. N-Acetylglucosamine-agarose also served as an acceptor substrate for the transferase. The galactosyl pyrophosphate-agarose was found to have a low capacity and specificity of binding for the galactosyltransferase. On the basis of the properties of the adsorbents, it has been possible to purify the galactosyltransferase from bovine milk to constant specific activity soley by affinity chromatography. The enzyme from the whey of bovine milk was first adsorbed on UDP-agarose and the eluate from this adsorbent then chromatographed on either N-acetylglucosamine-agarose or α-lactalbumin-agarose. The properties of the transferase are very similar to those reported earlier although at least three species of enzyme differing slightly in molecular weight have been found. The three species are glycoproteins and their amino acid compositions are very similar. The UDP-agarose adsorbent may be useful for purification of other UDP-glycosyltransferases as shown in preliminary studies with rabbit muscle glycogen synthetase. It is also possible that other nucleotide-agarose or glycosyl-agarose adsorbents may be used together for the purification of many nucleotide-sugar transferases.
Analysis of Toxicity in Escherichia coli from the Expression of Human Purinergic Receptor $P2X_4$ (2011)

In general, expression of membrane protein in Escherichia coli is very toxic to the host organism, but the mechanism for the toxicity is not clear yet. Expression of human purinergic receptor P2X4 was found to be extremely toxic to the host E. coli. We examined this toxicity by isolation and analysis of less toxic mutant proteins. We could isolate 30 less toxic mutants of P2X4 after hydroxylamine mutagenesis. Western blot showed that all of them produced proteins smaller than the wild type P2X4. DNA sequencing of two largest mutant proteins showed that they were lost its second transmembrane domain. Localization analysis of these mutant proteins showed that they are not in cytoplasmic membrane, but in inclusion bodies. These data showed that inactive truncated P2X4 is not toxic to E. coli and membrane integration and functionality of P2X4 may be needed to show host toxicity.
Prevalence of CD44+/CD24−/low Cells in Breast Cancer May Not Be Associated with Clinical Outcome but May Favor Distant Metastasis (2005)

Our findings suggest that the prevalence of CD44(+)/CD24(-/low) tumor cells in breast cancer may not be associated with clinical outcome and survival but may favor distant metastasis.
Interaction of Partially Structured States of Acidic Fibroblast Growth Factor with Phospholipid Membranes (1995)

Although acidic fibroblast growth factor (aFGF) lacks a conventional signal sequence, it is often found complexed to sulfated proteoglycans on the external surface of cells. The protein also forms a "molten globule"-like state at neutral pH and physiological temperatures as well as at acidic pH in the presence of physiological ionic strength or moderate quantities of polyanions. These states display a marked tendency to aggregate. Such observations suggest that related partially structured states might be involved in the membrane translocation of aFGF. To explore this hypothesis, we examined the interaction of this growth factor with lipid vesicles as well as the effect of such surfaces on the structure of the protein. We find that these states interact with negatively charged but not neutral phospholipid unilammelar vesicles at acidic pH, inducing bilayer disruption. The rate of leakage of a liposome-entrapped fluorescent probe is proportional to the logarithm of the aFGF concentration, suggesting competition between protein self-association and membrane binding. Liposome leakage can be also induced at neutral pH by partial unfolding of aFGF at or above physiological temperature in contrast to most control proteins. The importance of partially folded hydrophobic surfaces in aFGF self-association and membrane binding is further suggested by the fact that thermally unfolded aFGF does not aggregate, in contrast to states observed at intermediate temperatures or transiently during unfolding at high temperatures. In contrast to heparin, a polyanion which stabilizes the native structure of aFGF, negatively charged phospholipid membranes appear to enhance the disruption of aFGF tertiary structure at submicellar concentrations of sodium dodecyl sulfate but stabilize the remaining secondary structure.(ABSTRACT TRUNCATED AT 250 WORDS)
New strategies and emerging technologies for massively parallel sequencing: applications in medical research (2009)

A variety of techniques that specifically target human gene sequences for differential capture from a genomic sample, coupled with next-generation, massively parallel DNA sequencing instruments, is rapidly supplanting the combination of polymerase chain reaction and capillary sequencing to discover coding variants in medically relevant samples. These studies are most appropriate for the sample numbers necessary to identify both common and rare single nucleotide variants, as well as small insertion or deletion events, which may cause complex inherited diseases. The same massively parallel sequencers are simultaneously being used for whole-genome resequencing and comprehensive, genome-wide variant discovery in studies of somatic diseases such as cancer. Viral and microbial researchers are using next-generation sequences to identify unknown etiologic agents in human diseases, to study the viral and microbial species that occupy surfaces of the human body, and to inform the clinical management of chronic infectious diseases such as human immunodeficiency virus (HIV). Taken together, these approaches are dramatically accelerating the pace of human disease research and are already impacting patient care.
Possible common biomarkers from FTIR microspectroscopy of cervical cancer and melanoma (2004)

Detection of malignancy at early stages is crucial in cancer prevention and management. Fourier transform infrared (FTIR) spectroscopy has shown promise as a non-invasive method with diagnostic potential in cancer detection. Studies were conducted with formalin-fixed biopsies of melanoma and cervical cancer by FTIR microspectroscopy (FTIR-MSP) to detect common biomarkers, which occurred in both types of cancer distinguishing them from the respective non-malignant tissues. Both types of cancer are diagnosed on skin surfaces. The spectra were analysed for changes in levels of biomolecules such as RNA, DNA, phosphates and carbohydrate (glycogen). Whereas carbohydrate levels showed a good diagnostic potential for detection of cervical cancer, this was not the case for melanoma. However, variation of the RNA/DNA ratio as measured at I(1121)/I(1020) showed similar trends between non-malignant and malignant tissues in both types of cancer. The ratio was higher for malignant tissues in both types of cancer.
Demethylation of RB Regulator MYPT1 by Histone Demethylase LSD1 Promotes Cell Cycle Progression in Cancer Cells (2010)

Histone demethylase LSD1 (also known as KDM1 and AOF2) is active in various cancer cells, but its biological significance in human carcinogenesis is unexplored. In this study, we explored hypothesized interactions between LSD1 and MYPT1, a known regulator of RB1 phosphorylation. We found that MYPT1 was methylated in vitro and in vivo by histone lysine methyltransferase SETD7 and demethylated by LSD1, identifying Lys 442 of MYPT1 as a target for methylation/demethylation by these enzymes. LSD1 silencing increased MYPT1 protein levels, decreasing the steady state level of phosphorylated RB1 (Ser 807/811) and reducing E2F activity. MYPT1 methylation status influenced the affinity of MYPT1 for the ubiquitin-proteasome pathway of protein turnover. MYPT1 was unstable in murine cells deficient in SETD7, supporting the concept that MYPT1 protein stability is physiologically regulated by methylation status. LSD1 overexpression could activate RB1 phosphorylation by inducing a destabilization of MYPT1 protein. Taken together, our results comprise a novel cell cycle regulatory mechanism mediated by methylation/demethylation dynamics, and they reveal the significance of LSD1 overexpression in human carcinogenesis.
Genetics and Cytology of the ms6 Male-Sterile Soybean (1989)

Genetic studies of a new male-sterile, female-fertile soybean [Glycine max(L.) Merr.] found in an F breeding line showed that the allele involved was not allelic to any previously identified male sterility loci (ms1, ms2, ms3, ms4, or ms5). On the basis of allelism tests, we assigned the gene symbol ms6 to this mutant The heterozygote T295H is maintained in the Soybean Genetic Type Collection. Close linkage (2.48% ± 0.1% to 3.15% ± 0.1%) was found between ms6 and the w1 locus in linkage group 8. In addition, the ms6 allele expressed a pleiotroplc effect resulting in smaller flower size. Cytological studies showed that tapetal abnormalities in the anthers of sterile plants were correlated with sterility, whereas female gametophytes were properly formed. Close linkage of the ms6 allele with the w1 locus, the pleiotropic effect of the ms6 allele on flower size, and normal female reproduction are unique characteristics of this genetic male-sterile, female-fertile mutant. The ms6 mutant may be suitable for application to genetic problems and breeding schemes in soybean.
A scheme for classifying integration types in CIM (1992)

Abstract. A two-dimensional classification scheme for manufacturing integration is proposed. The first dimension focuses on where in the manufacturing operations the integration is occurring, while the second dimension focuses on what type of integration is occurring. This scheme will provide system designers with: the ability to document and thus efficiently transfer and implement solution technologies or ‘know-how’ for each class of integration; the ability to identify which integration classes are most desirable or beneficial to a specific company; and the basis for setting up a CIM implementation plan or programme.
Analysis of Thermal Induction Plasmas between Coaxial Cylinders (1972)

A previously derived approximate solution of the one-dimensional energy-balance equation for steady thermal induction plasmas is applied to the case of an annular plasma contained between coaxial cylinders. It is assumed that heat conduction is the only loss mechanism and that both walls are at zero temperature. Charted material is presented to facilitate determination of heat loads to either wall and calculation of temperature distributions across the gap. Results for an atmospheric-pressure argon discharge are compared with both exact numerical calculations and with experimental data. With the former, agreement is fair to good; with the latter it is poor. The disagreement is shown to be caused by electron diffusion which leads to overpopulation near the walls and suggests erroneously high temperatures when Saha equilibrium is assumed. The experimental temperature profiles are reproduced with excellent accuracy from a diffusion profile for the electrons which takes into account the nonuniformity of the induced electric field.
An Alternate Core 2 β1,6- N -Acetylglucosaminyltransferase Selectively Contributes to P-Selectin Ligand Formation in Activated CD8 T Cells (2005)

Core 2 beta1,6-N-acetylglucosaminyltransferase (C2GlcNAcT) synthesizes essential core 2 O-glycans on selectin ligands, which mediate cell-cell adhesion required for lymphocyte trafficking. Although gene-deletion studies have implicated C2GlcNAcT-I in controlling selectin ligand-mediated cell trafficking, little is known about the role of the two other core 2 isoenzymes, C2GlcNAcT-II and C2GlcNAcT-III. We show that C2GlcNAcT-I-independent P-selectin ligand formation occurs in activated C2GlcNAcT-I(null) CD8 T cells. These CD8 T cells were capable of rolling under shear flow on immobilized P-selectin in a P-selectin glycoprotein ligand 1-dependent manner. RT-PCR analysis identified significant levels of C2GlcNAcT-III RNA, identifying this enzyme as a possible source of core 2 enzyme activity. Up-regulation of P-selectin ligand correlated with altered cell surface binding of the core 2-sensitive mAb 1B11, indicating that CD43 and CD45 are also physiological targets for this alternate C2GlcNAcT enzyme. Furthermore, C2GlcNAcT-I-independent P-selectin ligand induction was observed in an in vivo model. HY(tg) CD8 T cells from C2GlcNAcT-I(null) donors transferred into male recipients expressed P-selectin ligand in response to male Ag, although at reduced levels compared with wild-type HY(tg) CD8 T cells. Our data demonstrate that multiple C2GlcNAcT enzymes can contribute to P-selectin ligand formation and may cooperate with C2GlcNAcT-I in the control of CD8 T cell trafficking.
Nucleotide Sequence of a Complementary DNA Clone Encoding Stearoyl-Acyl Carrier Protein Desaturase from Castor Bean, Ricinus communis (1991)

Stearoyl-ACP' desaturase (EC 1.14.99.6) catalyzes the ini- tial desaturation in the biosynthesis of unsaturated fatty acids in plants and plays a role in the regulation of fatty acid 'Abbreviation: ACP, acyl carrier protein.