gebhart/patrepeval huggingface dataset:
Impact of p85α Alterations in Cancer (2019)

The phosphatidylinositol 3-kinase (PI3K) pathway plays a central role in the regulation of cell signaling, proliferation, survival, migration and vesicle trafficking in normal cells and is frequently deregulated in many cancers. The p85α protein is the most characterized regulatory subunit of the class IA PI3Ks, best known for its regulation of the p110-PI3K catalytic subunit. In this review, we will discuss the impact of p85α mutations or alterations in expression levels on the proteins p85α is known to bind and regulate. We will focus on alterations within the N-terminal half of p85α that primarily regulate Rab5 and some members of the Rho-family of GTPases, as well as those that regulate PTEN (phosphatase and tensin homologue deleted on chromosome 10), the enzyme that directly counteracts PI3K signaling. We highlight recent data, mapping the interaction surfaces of the PTEN⁻p85α breakpoint cluster region homology (BH) domain, which sheds new light on key residues in both proteins. As a multifunctional protein that binds and regulates many different proteins, p85α mutations at different sites have different impacts in cancer and would necessarily require distinct treatment strategies to be effective.
Quorum Sensing Controls Adaptive Immunity through the Regulation of Multiple CRISPR-Cas Systems (2016)

Bacteria commonly exist in high cell density populations, making them prone to viral predation and horizontal gene transfer (HGT) through transformation and conjugation. To combat these invaders, bacteria possess an arsenal of defenses, such as CRISPR-Cas adaptive immunity. Many bacterial populations coordinate their behavior as cell density increases, using quorum sensing (QS) signaling. In this study, we demonstrate that QS regulation results in increased expression of the type I-E, I-F, and III-A CRISPR-Cas systems in Serratia cells in high-density populations. Strains unable to communicate via QS were less effective at defending against invaders targeted by any of the three CRISPR-Cas systems. Additionally, the acquisition of immunity by the type I-E and I-F systems was impaired in the absence of QS signaling. We propose that bacteria can use chemical communication to modulate the balance between community-level defense requirements in high cell density populations and host fitness costs of basal CRISPR-Cas activity.
Bioengineering Microgels and Hydrogel Microparticles for Sensing Biomolecular Targets (2017)

Hydrogels, and in particular microgels, are playing an increasingly important role in a diverse range of applications due to their hydrophilic, biocompatible, and highly flexible chemical characteristics. On this basis, solution-like environment, non-fouling nature, easy probe accessibility and target diffusion, effective inclusion of reporting moieties can be achieved, making them ideal substrates for bio-sensing applications. In fact, hydrogels are already successfully used in immunoassays as well as sensitive nucleic acid assays, also enabling hydrogel-based suspension arrays. In this review, we discuss key parameters of hydrogels in the form of micron-sized particles to be used in sensing applications, paying attention to the protein and oligonucleotides (i.e., miRNAs) targets as most representative kind of biomarkers.
Prognostic and Predictive Factors in Early-Stage Breast Cancer (2004)

Breast cancer is the most common malignancy among American women. Due to increased screening, the majority of patients present with early-stage breast cancer. The Oxford Overview Analysis demonstrates that adjuvant hormonal therapy and polychemotherapy reduce the risk of recurrence and death from breast cancer. Adjuvant systemic therapy, however, has associated risks and it would be useful to be able to optimally select patients most likely to benefit. The purpose of adjuvant systemic therapy is to eradicate distant micrometastatic deposits. It is essential therefore to be able to estimate an individual patient's risk of harboring clinically silent micrometastatic disease using established prognostic factors. It is also beneficial to be able to select the optimal adjuvant therapy for an individual patient based on established predictive factors. It is standard practice to administer systemic therapy to all patients with lymph node-positive disease. However, there are clearly differences among node-positive women that may warrant a more aggressive therapeutic approach. Furthermore, there are many node-negative women who would also benefit from adjuvant systemic therapy. Prognostic factors therefore must be differentiated from predictive factors. A prognostic factor is any measurement available at the time of surgery that correlates with disease-free or overall survival in the absence of systemic adjuvant therapy and, as a result, is able to correlate with the natural history of the disease. In contrast, a predictive factor is any measurement associated with response to a given therapy. Some factors, such as hormone receptors and HER2/neu overexpression, are both prognostic and predictive.
The active fraction of psyllium seed husk (2003)

A series of experiments and evaluations of fractions isolated from psyllium seed husk (PSH) were used to test the overall hypothesis that a gel-forming component of PSH is not fermented and that it is this component that is responsible for the laxative and cholesterol-lowering properties of PSH. A gel is isolated from human stools collected during a controlled diet study when PSH is consumed but not when the control diet only is consumed. Evaluations of three fractions isolated from PSH suggest that gel-forming fraction B, which is about 55% of PSH, is poorly fermented and is the component that increases stool moisture and faecal bile acid excretion, the latter leading to lower blood cholesterol levels. Fraction C, representing < 15% of PSH, is viscous, but is rapidly fermented. Fraction A is alkali-insoluble material that is not fermented. In concentrations comparable with their presence in PSH, fractions A and C do not alter moisture and bile acid output. The active fraction of PSH is a highly-branched arabinoxylan consisting of a xylose backbone and arabinose- and xylose-containing side chains. In contrast to arabinoxylans in cereal grains that are extensively fermented, PSH possesses a structural feature, as yet unidentified, that hinders its fermentation by typical colonic microflora.
Fibrinogen deficiency is compatible with the development of atherosclerosis in mice. (1998)

A critical role of the coagulation system in the development of atherosclerosis has been frequently postulated based on a variety of indirect observations, including the expression of procoagulants and fibrinolytic factors within atherosclerotic vessels, the presence of substantial amounts of fibrin(ogen) and fibrin degradation products within intimal lesions, the cellular infiltration and assimilation of mural thrombi into developing plaques, and the identification of high plasma fibrinogen (Fib) levels as an independent risk factor for the development of ischemic heart disease. To directly examine the role of fibrin(ogen) in atherogenesis, Fib-deficient mice were crossed to atherosclerosis-prone apolipoprotein E (apo E)-deficient mice. Both apo E-/- and apo E-/-/Fib-/- mice developed lesions throughout the entire aortic tree, ranging in appearance from simple fatty streaks to complex fibrous plaques. Furthermore, remarkably little difference in lesion size and complexity was observed within the aortae of age- and gender-matched apo E-/- and apo E-/-/Fib-/- mice. These results indicate that the contribution of fibrin(ogen) to intimal mass and local cell adhesion, migration, and proliferation is not strictly required for the development of advanced atherosclerotic disease in mice with a severe defect in lipid metabolism.
Mechanisms of heparanase inhibition by the heparan sulfate mimetic PG545 and three structural analogues (2013)

The tetrasaccharide heparan sulfate (HS) mimetic PG545, a clinical anti-cancer candidate, is an inhibitor of the HS-degrading enzyme heparanase. The kinetics of heparanase inhibition by PG545 and three structural analogues were investigated to understand their modes of inhibition. The cholestanol aglycon of PG545 significantly increased affinity for heparanase and also modified the inhibition mode. For the tetrasaccharides, competitive inhibition was modified to parabolic competition by the addition of the cholestanol aglycon. For the trisaccharides, partial competitive inhibition was modified to parabolic competition. A schematic model to explain these findings is presented.
Detection of Anti-Arboviral Immunoglobulin G by Using a Monoclonal Antibody-Based Capture Enzyme-Linked Immunosorbent Assay (2000)

Monoclonal antibody (MAb)-based capture enzyme-linked immunosorbent assays (ELISAs) for the detection of anti-arboviral immunoglobulin G (IgG ELISAs) were developed for a comprehensive array of medically important arboviruses from the Alphavirus, Flavivirus, and Bunyavirus genera. Tests were optimized and standardized so that maximum homology could be maintained among working parameters for the different viral agents, enabling a wide range of viruses to be easily tested for at one time. MAbs were screened for suitability as capture vehicles for antigens from the three genera. The final test configuration utilized group-reactive MAbs eastern equine encephalitis virus 1A4B-6, dengue 2 virus 4G2, and La Crosse encephalitis virus 10G5.4 to capture the specific inactivated viral antigens. Serum IgG was detected by using alkaline phosphatase-conjugated anti-human IgG (Fc portion). A dilution of 1:400 was chosen as the universal screening serum dilution, with endpoint titrations of serum samples testing positive eliminating occasional false-positive results. IgG ELISA results correlated with those of the standard plaque-reduction neutralization assays. As expected, some test cross-reactivity was encountered within the individual genera, and tests were interpreted within the context of these reactions. The tests were standardized for laboratory diagnosis of arboviral infections, with the intent that they be used in tandem with the corresponding IgM antibody-capture ELISAs.
A Skin-selective Homing Mechanism for Human Immune Surveillance T Cells (2004)

Effective immune surveillance is essential for maintaining protection and homeostasis of peripheral tissues. However, mechanisms controlling memory T cell migration to peripheral tissues such as the skin are poorly understood. Here, we show that the majority of human T cells in healthy skin express the chemokine receptor CCR8 and respond to its selective ligand I-309/CCL1. These CCR8(+) T cells are absent in small intestine and colon tissue, and are extremely rare in peripheral blood, suggesting healthy skin as their physiological target site. Cutaneous CCR8(+) T cells are preactivated and secrete proinflammatory cytokines such as tumor necrosis factor-alpha and interferon-gamma, but lack markers of cytolytic T cells. Secretion of interleukin (IL)-4, IL-10, and transforming growth factor-beta was low to undetectable, arguing against a strict association of CCR8 expression with either T helper cell 2 or regulatory T cell subsets. Potential precursors of skin surveillance T cells in peripheral blood may correspond to the minor subset of CCR8(+)CD25(-) T cells. Importantly, CCL1 is constitutively expressed at strategic cutaneous locations, including dermal microvessels and epidermal antigen-presenting cells. For the first time, these findings define a chemokine system for homeostatic T cell traffic in normal human skin.
Right-handed triplex formed between peptide nucleic acid PNA-T8 and poly(dA) shown by linear and circular dichroism spectroscopy (1993)

The binding of an eightmer of peptide nucleic acid, H-T8-Lys-NH2 (=PNA-T8), to a polynucleotide, poly(dA), was studied by flow linear dichroism (LD) and circular dichroism (CD) spectroscopy. Whereas the single stranded DNA, due to its high flexibility, does not display any measurable LD signal when subjected to shear flow, the complex with PNA does. A titration shows that saturation occurs at a stoichiometry of two PNA thymine bases per DNA adenine base, indicating the formation of a triplex PNA2-DNA complex. The persistence length of the adduct remains small up to relatively high stoichiometries (above 1:1 T:A) indicating that no significant amounts of PNA:DNA duplex are formed. Instead triplex stretches seem to form surrounded by flexible parts of single stranded poly(dA). Upon approaching the stoichiometry 2:1 of T:A the LD increases dramatically demonstrating that the stiffness of the PNA-DNA triplex arises from base-base contacts preventing bending of the chain. It is also inferred that the main stiffness of duplex DNA very probably has a similar origin and is not primarily a result of the increased phosphate-phosphate repulsion. Circular dichroism spectra support the conclusion that a triplex is formed as the only PNA-DNA complex and that it is a right-handed helix. The wavelength dependence of the reduced linear dichroism shows that the inclination of the bases from perpendicularity relative to the helix axis is small. The base conformation of the poly(dA)[PNA-T8]2 triplex is very similar to that of the conventional poly(dA)[poly(dT)]2 triplex.
Comparison of an atmospheric pressure, radio-frequency discharge operating in the α and γ modes (2005)

The α and γ modes of an atmospheric pressure, radio-frequency plasma have been investigated. The plasma source consisted of two parallel electrodes that were fed with helium and 0.4 vol% nitrogen. The transition from α to γ was accompanied by a 40% drop in voltage, a 12% decrease in current and a surge in power density from 25 to 2083 W cm−3. Optical emission confirmed that sheath breakdown occurred at the transition point. The maximum light intensity shifted from a position 0.25 mm above the electrodes to right against the metal surfaces. The average density of ground-state nitrogen atoms produced in the atmospheric plasma was determined from the temporal decay of N2(B) emission in the afterglow. It was found that 5.2% and 15.2% of the N2 fed were dissociated into atoms when the plasma was operated in the α and γ modes, respectively. The lower efficiency of the γ discharge may be attributed to the non-uniform distribution of the discharge between the electrodes.
A comparison of the quantitative anatomy of the bronchi in normal subjects, in status asthmaticus, in chronic bronchitis, and in emphysema (1969)

The quantitative anatomy of the bronchi has been studied in sudden deaths in normal subjects, in deaths from status asthmaticus and chronic bronchitis, and in patients with emphysema. In the normal bronchi the observed range of values for the percentage volume of mucous glands was between 7·6 and 16·7. In the status asthmaticus group the mucous gland volume was greatly increased and in no case was there an overlap with the normal subjects. In the 19 cases of chronic bronchitis, two cases had values of 15·2 and 15·4% respectively, but all the others had values higher than the normal range and, in two instances, values of over 40% were obtained. The values obtained for mucous gland volume in the bronchi in emphysema were variable, approximately half being within the normal range. The bronchial smooth muscle accounted for 4·6±2·2% of the volume of the normal bronchial wall. The values obtained in chronic bronchitis and emphysema did not differ significantly from this but in those dying of status asthmaticus there was a very significant increase with a mean value of 11·9±3·36.
Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study The SWISS-PROT accession numbers for the N-terminal amino acid sequences reported in this paper are: P00691 for AmyE; P54507 for CotN; O07921 for Csn; P09124 for Gap; P26901 for KatA; P39116 for Pel; P39824 for PenP; P54375 for SodA; P29141 for Vpr; Q07833 for WapA; P54423 for WprA; P54327 for XkdG; Q45071 for XynD; P94421 for YclQ; O31803 for YcnM; O05512 for YdhT; O34952 for YflE; O06487 for YfnI; O31737 for YlqB; P96740 for YwtD; P42110 for YxaK; P94356 for YxkC. (2000)

To analyse the proteome of Bacillus subtilis extracellular proteins, extracellular protein samples were prepared from culture media (minimal medium containing 0.4% glucose) of parental B. subtilis 168, a secA-temperature sensitive mutant and an ffh conditional mutant, and examined by two-dimensional gel electrophoresis. Approximately 100 to 110 spots were visualized in a gel of B. subtilis 168 extracellular proteins. Over 90% and 80% of these disappeared in the absence of SecA and Ffh, respectively. Thirty-eight obvious spots on the gel of the B. subtilis 168 preparation were selected and compared with spots obtained under SecA- or Ffh-deficient conditions. The appearance of 36 of these 38 spots depended on SecA and Ffh. Nineteen additional extracellular proteins were detected in cultures maintained in cellobiose, maltose and soluble starch. Among 23 proteins of which the N-terminal amino acid sequences were determined, 17 were extracellular proteins having signal peptides in their precursor form. Two membrane proteins, Yfnl and YflE, were cleaved behind 226Ala-Tyr-Ala228 and 213Ala-Leu-Ala215, respectively, and of which products seemed to be liberated into the culture medium. The production of Yfnl and YflE were also dependent on SecA and Ffh. These results indicate that most extracellular proteins target to and translocate across the cytoplasmic membrane by co-operation between the signal-recognition particle and Sec protein-secretion pathways. In contrast, a spot for Hag appeared independent from SecA and Ffh. Intracellular proteins Gap, SodA and KatA were identified in the extracellular protein samples. On the basis of these results and computer searches, it was predicted that B. subtilis produces 150 to 180 proteins extracellularly.
Vasopressin increases milk flow and milk fat concentration in the goat (2003)

We conclude that vasopressin increases milk flow and milk fat concentration and suggest that vasopressin, like oxytocin, acts on the myoepithelial cells.
Fulminant hepatic failure in murine hepatitis virus strain 3 infection: tissue-specific expression of a novel fgl2 prothrombinase (1997)

Activation of the immune coagulation system has been implicated in the pathogenesis of fulminant liver failure caused by murine hepatitis virus strain 3 (MHV-3). The recent discovery of the fgl2 gene, which encodes for MHV-3-induced prothrombinase (fgl2 prothrombinase), allows for fundamental studies to determine the molecular basis for fulminant liver failure. Transcription of the fgl2 gene and translation of the protein it encodes were examined in the liver and other organs of susceptible mice following MHV-3 infection. No constitutive expression of the fgl2 gene or the fgl2 prothrombinase was detected. Within 12 to 24 h of MHV-3 infection, however, fgl2 gene transcripts were detected in large amounts in the liver, spleen, and lungs, all of which are rich in reticuloendothelial cells, but were only focally present in small amounts in the kidney and brain. There was sequential detection of fgl2 prothrombinase in the liver, where it was localized specifically to the endothelium of intrahepatic veins and hepatic sinusoids; this was allowed by fibrin deposition, which resulted in confluent hepatocellular necrosis. These results provide further evidence for the role of the selective expression of this novel fgl2 prothrombinase in the pathogenesis of MHV-3-induced fulminant liver failure.
Wnt / &#946;-Catenin Signaling Pathway as Novel Cancer Drug Targets (2004)

Wnt proteins are a large family of secreted glycoproteins. Wnt proteins bind to the Frizzled receptors and LRP5/6 co-receptors, and through stabilizing the critical mediator beta-catenin, initiate a complex signaling cascade that plays an important role in regulating cell proliferation and differentiation. Deregulation of the canonical Wnt/beta-catenin signaling pathway, mostly by inactivating mutations of the APC tumor suppressor, or oncogenic mutations of beta-catenin, has been implicated in colorectal tumorigenesis. Although oncogenic mutations of beta-catenin have only been discovered in a small fraction of non-colon cancers, elevated levels of beta-catenin protein, a hallmark of activated canonical Wnt pathway, have been observed in most common forms of human malignancies, indicating that activation of this pathway may play an important role in tumor development. Over the past 15 years, our understanding of this signaling pathway has significantly improved with the identification of key regulatory proteins and the important downstream targets of beta-catenin/Tcf transactivation complex. Given the fact that Wnt/beta-catenin signaling is tightly regulated at multiple cellular levels, the pathway itself offers ample targeting nodal points for cancer drug development. In this review, we discuss some of the strategies that are being used or can be explored to target key components of the Wnt/beta-catenin signaling pathway in rational cancer drug discovery.
Preservation of Bovine Spermatozoa in Yolk-Citrate Diluent and Field Results from its Use (1941)

Summary 1. An M/15 solution of sodium citrate mixed in equal amounts with fresh, egg yolk produced a diluent which dispersed the fat globules and other material in the yolk so that when semen was diluted with it the individual spermatozoa could be readily seen upon microscopic examination. 2. The yolk-citrate diluent and the yolk-phosphate diluent were apparently equal as preservatives of the motility of spermatozoa which were stored in them under standard conditions for two and four days. 3. The yolk-citrate diluent was superior to the yolk-phosphate diluent for the preservation of motility when semen was stored six days or more. 4. In actual insemination tests with semen stored up to 5 days no significant difference in fertility was found between the semen stored in the yolk-citrate and the yolk-phosphate diluents. 5. The results of the fertility studies tend to bear out the results of laboratory storage studies on the maintenance of motility under standard conditions.
A domain-independent system for sketch recognition (2003)

Freehand sketching is a natural and powerful means of interpersonal communication. But to date, it still cannot be supported effectively by human-computer interface. In this paper, we describe a domain-independent system for sketch recognition. Our system allows users to draw sketches as naturally as how they do on paper, and it recognizes the drawing through imprecise stroke approximation which is implemented in a unified and incremental procedure. This method can handle smooth curves and hybrid shapes as gracefully as it does to polylines. With a feature-area verification mechanism and the intelligent adjustment in the post-process, the system can produce user-intended results. Moreover, the output is organized in a hierarchical structure which includes syntactic and semantic information as well as raw data. Our system mainly utilizes low-level geometric features and does not rely on any domain-specific knowledge. Therefore, it will serve as a general and solid foundation for future high-level applications.