gebhart/patrepeval huggingface dataset:
Correlation between Mortality and the Levels of Inter‐Alpha Inhibitors in the Plasma of Patients with Severe Sepsis (2003)

Inter-alpha inhibitor protein (IalphaIp) is an endogenous serine protease inhibitor in human plasma. Circulating IalphaIp levels were lower in 51 patients with severe sepsis than in healthy volunteers. Mean levels were 688+/-295 mg/L in patients with severe sepsis who survived (n=32), 486+/-193 mg/L in patients with sepsis who died (n=19), and 872+/-234 mg/L in control subjects (n=25). IalphaIp levels were lower in patients with shock versus those without (540+/-246 [n=33] vs. 746+/-290 [n=18] mg/L; P=.0102). IalphaIp levels were inversely correlated with 28-day mortality rates and Acute Physiology and Chronic Health Evaluation II scores and directly correlated with antithrombin III, protein C, and protein S levels. The administration of IalphaIp (30 mg/kg body weight intravenously) increased the 50% lethal dose in mice by 100-fold after an intravenous challenge of Escherichia coli. Thus, human IalphaIp may be a useful predictive marker and potential therapeutic agent in sepsis.
Dissolved Sediment Delivery by the Samaru Stream into Kubanni Reservoir of Ahmadu Bello University Zaria, Nigeria (2016)

This study analyzes the dissolved sediment delivery by Samaru stream, a tributary of Kubanni reservoir. The stream was monitored for 7 months, from 1 st of April to 10 th of October, 2014 which mainly marks the flow period of the year. The study analyzed the dissolved sediment concentration (DSC), discharge (Q), relationship between dissolved sediment discharge (DSD) and discharge (Q) and the estimate of the dissolved sediment yield for the year. The velocity and cross sectional area (AV) method was employed for the discharge measurement of the stream which gave a mean value of 0.2528 m 3 /s, and an annual total discharge value of 4,850,232 m 3 /yr. The lowest discharge of 0.057 m 3 /s was recorded in April and the highest discharge of 4.133 m 3 /s was recorded in August. DSC obtained varies from a minimum value of 20 mg/L to a maximum value of 120 mg/L with a mean value of 58.87 mg/L, and total sum of 4180 mg/L. DSD using the rating curve varied from a minimum value of 1.14 mg/s to a maximum value of 325.44 mg/s, and a total value of 3162 mg/s. DSD and Q were related and it gave a strong relationship because both values of r (0.866) and r 2 (0.749) are high. A total value of 174,000 kg/yr was estimated as the dissolved sediment yield of the stream with a Channel Sediment Yield (CSY) of 174 tons/yr. The amount is high and can be attributed to the anthropogenic activities upstream. It is therefore recommended that the Ahmadu Bello University should intensify on their efforts in creating awareness among the academic and neighboring Samaru community on conservative methods of reducing the rate of pollution of the reservoir. Keywords: Dissolved Sediment, Discharge, Samaru Stream, Kubanni Reservoir, Ahmadu Bello University.
Identification and Quantification of a New Family of Peptide Endocannabinoids (Pepcans) Showing Negative Allosteric Modulation at CB1 Receptors (2012)

The α-hemoglobin-derived dodecapeptide RVD-hemopressin (RVDPVNFKLLSH) has been proposed to be an endogenous agonist for the cannabinoid receptor type 1 (CB(1)). To study this peptide, we have raised mAbs against its C-terminal part. Using an immunoaffinity mass spectrometry approach, a whole family of N-terminally extended peptides in addition to RVD-Hpα were identified in rodent brain extracts and human and mouse plasma. We designated these peptides Pepcan-12 (RVDPVNFKLLSH) to Pepcan-23 (SALSDLHAHKLRVDPVNFKLLSH), referring to peptide length. The most abundant Pepcans found in the brain were tested for CB(1) receptor binding. In the classical radioligand displacement assay, Pepcan-12 was the most efficacious ligand but only partially displaced both [(3)H]CP55,940 and [(3)H]WIN55,212-2. The data were fitted with the allosteric ternary complex model, revealing a cooperativity factor value α < 1, thus indicating a negative allosteric modulation. Dissociation kinetic studies of [(3)H]CP55,940 in the absence and presence of Pepcan-12 confirmed these results by showing increased dissociation rate constants induced by Pepcan-12. A fluorescently labeled Pepcan-12 analog was synthesized to investigate the binding to CB(1) receptors. Competition binding studies revealed K(i) values of several Pepcans in the nanomolar range. Accordingly, using competitive ELISA, we found low nanomolar concentrations of Pepcans in human plasma and ∼100 pmol/g in mouse brain. Surprisingly, Pepcan-12 exhibited potent negative allosteric modulation of the orthosteric agonist-induced cAMP accumulation, [(35)S]GTPγS binding, and CB(1) receptor internalization. Pepcans are the first endogenous allosteric modulators identified for CB(1) receptors. Given their abundance in the brain, Pepcans could play an important physiological role in modulating endocannabinoid signaling.
Insertional Tagging, Cloning, and Expression of the Hypoxanthine-Xanthine-Guanine Phosphoribosyltransferase Gene (1996)

A nonhomologous integration vector was used to identify the Toxoplasma gondii hypoxanthine-xanthine-guanine phosphoribosyl transferase (HXGPRT) gene by insertional mutagenesis. Parasite mutants resistant to 6-thioxanthine arose at a frequency of approximately3 x 10(-7). Genomic DNA flanking the insertion sites was retrieved by marker rescue and used to identify molecular clones exhibiting unambiguous homology to H(X)GPRT genes from other species. Sequence analysis of vector/genome junction sites reveals that integration of the linearized vector occurred with minimal rearrangement of either vector or target sequences, although the addition of filler DNA and small duplications or deletions of genomic sequences at the transgene termini was observed. Two differentially spliced classes of cDNA clones were identified, both of which complement hpt and gpt mutations in Escherichia coli. Kinetic analysis of purified recombinant enzyme revealed no significant differences between the two isoforms. Internally deleted clones spanning the genomic locus were used to create "knock-out" parasites, which lack all detectable HXGPRT activity. Complete activity could be restored to these knock-out mutants by transient transformation with either genomic DNA or cDNA-derived minigenes encoding both enzyme isoforms. Stable HXGPRT+ transformants were isolated under selection with mycophenolic acid, demonstrating the feasibility of HXGPRT as both a positive and negative selectable marker for stable transformation of T. gondii.
[Differentiation of neuroblastoma cells caused by cytochalasin B]. (1983)

The action of cytochalasin B (CB) on the differentiation of cultured neuroblastoma cells has been studied. CB treatment (1.8 micrograms/ml for 3 days) blocked cytokinesis, leading to the multinucleation of neuroblastoma cells. The replacement of medium with CB by standard medium without CB led to the improvement of cell spreading on the substrate and to the appearance of 43.7 +/- 4.1% of morphologically differentiated cells. 4.7 +/- 0.6% of differentiated cells formed in CB-untreated control cultures. Thus, incubation with CB followed by the agent removal from the medium induced the differentiation of neuroblastoma cells. A possible role of multinucleation in this process is discussed.
Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope. (1996)

In vitro selection of nucleic acid binding species (aptamers) is superficially similar to the immune response. Both processes produce biopolymers that can recognize targets with high affinity and specificity. While antibodies are known to recognize the sequence and conformation of protein surface features (epitopes), very little is known about the precise interactions between aptamers and their epitopes. Therefore, aptamers that could recognize a particular epitope, a peptide fragment of human immunodeficiency virus type I Rev, were selected from a random sequence RNA pool. Several of the selected RNAs could bind the free peptide more tightly than a natural RNA ligand, the Rev-binding element. In accord with the hypothesis that protein and nucleic acid binding cusps are functionally similar, interactions between aptamers and the peptide target could be disrupted by sequence substitutions. Moreover, the aptamers appeared to be able to bind peptides with different solution conformations, implying an induced fit mechanism for binding. Just as anti-peptide antibodies can sometimes recognize the corresponding epitope when presented in a protein, the anti-peptide aptamers were found to specifically bind to Rev.
Nutritional Intake of Vitamins K1 (Phylloquinone) and K2 (Menaquinone) in The Netherlands (1999)

Vitamin K plays a key role in the hepatic synthesis of blood clotting factors. Recently, other tissues (bone, vessel wall) were shown to produce vitamin K-dependent proteins not involved in blood coagulation. Multiple forms of vitamin K have been found in human food: phylloquinone (K1) and various menaquinones. A recommended dietary allowance (RDA) has only been defined for K1, and its value is exclusively based on blood clotting data. We have prepared a provisional table of menaquinones in food, which has been used to calculate the total vitamin K intake in a well-defined cohort of the Dutch population. It is concluded that K1 is the major form of nutritional vitamin K, that total vitamin K intake is higher than in other populations described and that the correlation between vitamin K intake and serum concentration is poor. It is suggested that present RDA values be reconsidered and intakes comparable with those in the highest quartile of our study population are recommended.
Anti-Inflammatory Role of the Murine Formyl-Peptide Receptor 2: Ligand-Specific Effects on Leukocyte Responses and Experimental Inflammation (2010)

The human formyl-peptide receptor (FPR)-2 is a G protein-coupled receptor that transduces signals from lipoxin A(4), annexin A1, and serum amyloid A (SAA) to regulate inflammation. In this study, we report the creation of a novel mouse colony in which the murine FprL1 FPR2 homologue, Fpr2, has been deleted and describe its use to explore the biology of this receptor. Deletion of murine fpr2 was verified by Southern blot analysis and PCR, and the functional absence of the G protein-coupled receptor was confirmed by radioligand binding assays. In vitro, Fpr2(-/-) macrophages had a diminished response to formyl-Met-Leu-Phe itself and did not respond to SAA-induced chemotaxis. ERK phosphorylation triggered by SAA was unchanged, but that induced by the annexin A1-derived peptide Ac2-26 or other Fpr2 ligands, such as W-peptide and compound 43, was attenuated markedly. In vivo, the antimigratory properties of compound 43, lipoxin A(4), annexin A1, and dexamethasone were reduced notably in Fpr2(-/-) mice compared with those in wild-type littermates. In contrast, SAA stimulated neutrophil recruitment, but the promigratory effect was lost following Fpr2 deletion. Inflammation was more marked in Fpr2(-/-) mice, with a pronounced increase in cell adherence and emigration in the mesenteric microcirculation after an ischemia-reperfusion insult and an augmented acute response to carrageenan-induced paw edema, compared with that in wild-type controls. Finally, Fpr2(-/-) mice exhibited higher sensitivity to arthrogenic serum and were completely unable to resolve this chronic pathology. We conclude that Fpr2 is an anti-inflammatory receptor that serves varied regulatory functions during the host defense response. These data support the development of Fpr2 agonists as novel anti-inflammatory therapeutics.
BOLD fMRI activation induced by vagus nerve stimulation in seizure patients (2003)

BOLD fMRI can detect activation associated with vagus nerve stimulation. There may be a relation between thalamic activation and a favourable clinical outcome.
Handheld Miniature Ion Trap Mass Spectrometers (2009)

For field applications, "miniature" and "rapid" have become almost synonymous, yet these small mass spectrometers are not useful if performance is too severely compromised. (To listen to a podcast about this feature, please go to the Analytical Chemistry website at pubs.acs.org/journal/ancham .).
Beyond the increasing complexity of the immunomodulatory HLA-G molecule (2008)

Human leukocyte antigen G (HLA-G) is a nonclassic major histocompatibility complex (MHC) class I molecule that functions as an immunomodulatory molecule capable of protecting fetal tissues from the maternal immune system. The relevance of HLA-G in other contexts was investigated soon afterward. Numerous studies have sought (and some have shown) the relevance of HLA-G in pathologic conditions, such as transplantation, autoimmunity, and cancer and hematologic malignancies. One of the main goals of the current research on HLA-G is now to use it in the clinic, either for diagnosis or as a therapeutic tool/target. For this, precise knowledge on the nature and functions of HLA-G is critical. We highlight here what we consider are recent key basic findings on the immunomodulatory function of HLA-G. These strengthen the case for considering HLA-G as clinically relevant.
Use of BONSAI decision trees for the identification of potential MHC Class I peptide epitope motifs (1998)

Recognition of short peptides of 8 to 10 mer bound to MHC class I molecules by cytotoxic T lymphocytes forms the basis of cellular immunity. While the sequence motifs necessary for binding of intracellular peptides to MHC have been well studied, little is known about sequence motifs that may cause preferential affinity to the T cell receptor and/or preferential recognition and response by T cells. Here we demonstrate that computational learning systems can be useful to elucidate sequence motifs that affect T cell activation. Knowledge of T cell activation motifs could be useful for targeted vaccine design or immunotherapy. With the BONSAI computational learning algorithm, using a database of previously reported MHC bound peptides that had positive or negative T cell responses, we were able to identify sequence motif rules that explain 70% of positive T cell responses and 84% of negative T cell responses.
A comparative study of efficiencies of fibre optic and prism TIRF sensors (1992)

A comparative study of the respective performances of total internal reflection fluorescence (TIRF) prisms and fibre optic sensors in terms of their detection capabilities is presented. Theoretical models based on geometrical considerations described the excitation and collection efficiencies of the two optical systems. The models are shown to be in excellent agreement with the experimental TIRF obtained from the adsorption of albumin onto prism or fibre surfaces. Improvements in system performance, based on optimization of the optical configurations, have been evaluated. The studies demonstrate that, in terms of the requirements of biosensor devices, in which compactness and high efficiencies are paramount, fibre optic systems are superior to prism systems.
Demographic Differences Between Sheltered Homeless Families and Housed Poor Families: Implications for Policy and Practice (1995)

This study compares homeless families with a representative sample of low income family households in St. Louis city and county to determine how they differ on key demographic variables. The research addresses methodological problems in prior research by comparing the findings of this study's random sample to the findings of four previous comparison studies. Findings from this study's random comparison sample are presented. Homeless families are significantly younger, never married, female-headed families of color. Housed and homeless families are not significantly different in the number of children or in the educational level of the head of household but housed families are larger and have greater income. This suggests the presence of another adult earner in poor, housed families. Research implications include addressing sampling biases in comparative research through longitudinal studies. Policy and practice recommendations center on providing social and economic supports to homeless families to increase the number of supportive adults in the home.
Suppression of the Immune Response by a Soluble Complement Receptor of B Lymphocytes (1991)

The CD19-CR2 complex of B lymphocytes contains proteins that participate in two host-defense systems, the immune and complement systems. The ligand for the subunit of the immune system, CD19, is not known, but the complement receptor subunit, CR2 (CD21), binds activation fragments of the C3 component of the complement system and may mediate immunopotentiating effects of complement. A recombinant, soluble CR2 was prepared by fusing the C3-binding region of the receptor to immunoglobulin G1 (IgG1). The (CR2)2-IgG1 chimera competed with cellular CR2 for C3 binding and suppressed the antibody response to a T cell-dependent antigen when administered to mice at the time of immunization. This inhibitory effect of (CR2)2-IgG1 demonstrates the B cell-activating function of the CD19-CR2 complex and suggests a new method for humoral immunosuppression.
Human Immunodeficiency Virus: Scientific Challenges Impeding Candidate Vaccines (2003)

Most initial work with HIV vaccines was directed at developing vaccines that elicited neutralizing antibodies. These neutralizing antibodies have been narrow in the focus of their action and specific almost entirely to the strain of the innoculating virus. Additionally, controversy has been reported about both the design of assay systems to measure the neutralization of such isolates and interpretation of the results. Researchers are now looking for a "broad-spectrum" vaccine; however, the high variability of the HIV envelope glycoprotein and its rapid rate of mutation creates an elusive target. Safety concerns have reduced interest in live attenuated virus or whole killed virus vaccines. Some novel approaches being taken include increasing cytotoxic T-lymphocyte responses, induction of immune responses in mucosal tissue surfaces, peptide-based vaccines, oligomeric envelope protein-based vaccine regimens, recombinant Tat protein vaccines, natural killer T-cell (NKT) ligand serving as adjuvant, and fusion of SIV gag with the extracellular domain of CTLA-4 as adjuvant. Most of the HIV vaccines currently in development are the products of recombinant DNA technology.
Estrogen receptor interaction with estrogen response elements (2001)

The estrogen receptor (ER) is a ligand-activated enhancer protein that is a member of the steroid/nuclear receptor superfamily. Two genes encode mammalian ER: ERalpha and ERbeta. ER binds to specific DNA sequences called estrogen response elements (EREs) with high affinity and transactivates gene expression in response to estradiol (E(2)). The purpose of this review is to summarize how natural and synthetic variations in the ERE sequence impact the affinity of ER-ERE binding and E(2)-induced transcriptional activity. Surprisingly, although the consensus ERE sequence was delineated in 1989, there are only seven natural EREs for which both ERalpha binding affinity and transcriptional activation have been examined. Even less information is available regarding how variations in ERE sequence impact ERbeta binding and transcriptional activity. Review of data from our own laboratory and those in the literature indicate that ERalpha binding affinity does not relate linearly with E(2)-induced transcriptional activation. We suggest that the reasons for this discord include cellular amounts of coactivators and adaptor proteins that play roles both in ER binding and transcriptional activation; phosphorylation of ER and other proteins involved in transcriptional activation; and sequence-specific and protein-induced alterations in chromatin architecture.
Human beta 2-adrenergic receptors expressed in Escherichia coli membranes retain their pharmacological properties. (1988)

The coding region of the gene for the human beta 2-adrenergic receptor gene was fused to the beta-galactosidase gene of the lambda gt11 expression vector. The Y1089 Escherichia coli strain was lysogenized with this modified vector and transcription of the fusion gene was induced. Expression of this transcription unit was shown by the appearance in the bacteria of proteins of molecular weight higher than that of native beta-galactosidase, which are immunoreactive with anti-beta-galactosidase antibodies. Production of beta 2-adrenergic receptors was shown by the presence, on intact bacteria, of binding sites for catecholamine agonists and antagonists possessing a typical beta 2-adrenergic pharmacological profile. Binding and photoaffinity labeling studies performed on intact E. coli and its membrane fractions showed that these binding sites are located in the inner membrane of the bacteria. Expression of pharmacologically active human beta 2-adrenergic receptors in E. coli further supports the similar transmembrane organization proposed for bacteriorhodopsin and eukaryotic membrane-embedded receptors coupled to guanine nucleotide-binding regulatory proteins. Moreover, this system should facilitate future analyses of the ligand-binding properties within this family of membrane receptors.
MUC5AC and MUC5B Mucins Increase in Cystic Fibrosis Airway Secretions during Pulmonary Exacerbation (2007)

During a CF exacerbation, concentration of secreted mucin increased to the amount found in mucus from normal subjects, suggesting that the capacity to secrete mucin in response to an infection or inflammatory stimulus is preserved in CF airways. This might help to protect the airway from injury.
Neuroendocrine regulation of food intake (1999)

Maintenance of appropriate stores of metabolic fuels depends on carefully matching caloric intake to caloric expenditure. Achieving such 'energy balance' is a product of complex interactions of peripheral hormones with effector systems in the central nervous system (CNS) that regulate food intake and energy expenditure. Leptin is a hormone that is made in the adipocytes, circulates in the blood and interacts with receptors in the CNS. These receptors can be found in two different types of systems. One effector system is termed 'anabolic' and is activated by low levels of leptin during negative energy balance. This system (exemplified by the hypothalamic neuropeptide Y system) increases food intake and decreases energy expenditure to facilitate the regaining of lost energy stores. The other effector system is termed 'catabolic' and is activated by high levels of leptin during positive energy balance. This system (exemplified by the hypothalamic melanocortin and corticotrophin-releasing hormone systems) decreases food intake and increases energy expenditure to facilitate the loss of excess energy stores. Further understanding of these systems is necessary to develop adequate treatments for disorders of energy balance, such as obesity and wasting.