bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genotyping of the Common Haptoglobin Hp 1/2 Polymorphism Based on PCR
Authors: Koch Werner , Latz Wolfgang , Eichinger Marianne , Roguin Ariel , Levy Andrew P , Schömig Albert , Kastrati Adnan 
Published: January 2020

Abstract
Background: A genetically defined molecular heterogeneity of haptoglobin, characterized by the major phenotypic forms Hp 1-1, Hp 2-1, and Hp 2-2, has been associated with distinct clinical manifestations. To enable the use of DNA samples for the study of this polymorphism, we established a haptoglobin genotyping method based on PCR.
Methods: Taking advantage of the selectivity of PCR, we amplified DNA segments specifically representing haptoglobin alleles Hp 1 and Hp 2 from genomic DNA. The products were analyzed by agarose gel electrophoresis. Haptoglobin phenotyping of plasma samples was performed by polyacrylamide gel electrophoresis and peroxidase staining.
Results: Exploiting the known size difference between Hp 1 and Hp 2, we amplified allele-specific DNA molecules with one pair of oligonucleotide primers. As an alternative, we used separate primer pairs to generate amplification products indicative of alleles Hp 1 and Hp 2. Because of the primer design, genotype determination was not compromised by sequence variations specifying haptoglobin allele subtypes S and F. For the same reason, the sequence similarity between the haptoglobin gene and the haptoglobin-related gene did not interfere with the accuracy of genotyping. Analysis with restriction enzymes demonstrated the authenticity of the allele-specific DNA products. Haptoglobin DNA genotyping and protein phenotyping, performed in parallel, yielded fully corresponding results. In a group of 249 individuals, the haptoglobin genotype distribution was as follows: 14.5% Hp 1-1, 48.2% Hp 2-1, and 37.3% Hp 2-2.
Conclusion: The new method can be used for genotyping of a common haptoglobin polymorphism.
Expanding Tiny Earth to genomics: a bioinformatics approach for an undergraduate class to characterize antagonistic strains
Authors: Basalla Joseph , Harris Ryan , Burgess Elizabeth , Zeedyk Nicholas , Wildschutte Hans 
Published: January 2020

ABSTRACT
The evolution of multidrug resistant pathogens and the diminishing supply of effective antibiotics are global crisis. Tiny Earth (TE) is undergraduate curriculum that encourage students to pursue science careers by engagement in authentic drug discovery research. Through the TE program, students identify environmental strains that inhibit other bacteria. Although these isolates may produce antibiotics based on the antagonistic phenotype, understanding the activity in regard to genome content remains elusive. Previously, we developed a transposon mutagenesis module for use with TE to identify genes involved in antibiotic production. Here, we extend this approach to a second semester undergraduate course to understand the origin of antagonism and genome diversity. Using a bioinformatics strategy, we identified gene clusters involved in activity, and with annotated genomes in hand, students were able to characterize strain diversity. Genomes were analyzed using different computational tools, including average nucleotide identity for species identification and whole genome comparisons. Because the focus of TE involves the evolution of drug resistance, predicted products in strains were identified and verified using a drug susceptibility assay. An application of this curriculum by TE members would assist in efforts with antibiotic discovery.
Metabolites Associated with Walking Ability Among the Oldest Old from the CHS All Stars Study
Authors: Marron Megan M , Wendell Stacy G , Boudreau Robert M , Clish Clary B , Santanasto Adam J , Tseng George C , Zmuda Joseph M , Newman Anne B 
Published: January 2020

AbstractBackgroundLow walking ability is highly prevalent with advancing age and predicts major health outcomes. Metabolomics may help to better characterize differences in walking ability among older adults, providing insight into potentially altered molecular processes underlying age-related decline in functioning. We sought to identify metabolites and metabolic pathways associated with high versus low walking ability among 120 participants ages 79–95 from the CHS All Stars study.MethodsUsing a nested case–control design, 60 randomly selected participants with low walking ability were matched one-to-one on age, gender, race, and fasting time with 60 participants with high walking ability. High versus low walking ability was defined as being in the best versus worst tertiles for both gait speed (≥0.9 vs &lt;0.7 m/s) and the Walking Ability Index (7–9 vs 0–1). Using liquid chromatography-mass spectrometry, 569 metabolites were identified in overnight-fasting plasma.ResultsNinety-six metabolites were associated with walking ability, where 24% were triacylglycerols. Triacylglycerols that were higher among those with high walking ability consisted mostly of polyunsaturated fatty acids, whereas triacylglycerols that were lower among those with high walking ability consisted mostly of saturated or monounsaturated fatty acids. Body composition partly explained associations between some metabolites and walking ability. Proline and arginine metabolism was a top pathway associated with walking ability.ConclusionThese results may partly reflect pathways of modifiable risk factors, including excess dietary lipids and lack of physical activity, contributing to obesity and further alterations in metabolic pathways that lead to age-related decline in walking ability in this older adult cohort.
An approximate fast-mapping approach to the surface NMR forward problem
Authors: Grombacher Denys , Kass Mason Andrew , Auken Esben , Larsen Jakob Juul 
Published: January 2020

SUMMARY
A surface nuclear magnetic resonance (NMR) forward model based on the full-Bloch equation improves the accuracy of the forward response given an arbitrary excitation pulse and a wider range of relaxation conditions. However, the full-Bloch solution imposes a significant slowdown in inversion times compared to the traditional forward model. We present a fast-mapping approach capable of dramatic increases in inversion speeds with minimal sacrifices in forward response accuracy. We show that the look-up tables used to calculate the transverse magnetization and the full surface NMR forward response are smoothly varying functions of the underlying T2* and T2 values. We exploit this smoothness to form a polynomial representation of the look-up tables and surface NMR forward responses, where a fast-mapping approximation of each are reduced to a simple matrix multiplication. Accurate approximations with less than 1 per cent error can be produced using 21 coefficient representations of the look-up tables for each B1 value and for the signal expected from a particular depth layer for a particular pulse moment. In essence, the proposed fast-mapping approach front-loads all expensive calculations and stores the results in a compressed form as a coefficient matrix containing less than a half a million elements. This allows all subsequent inversions to be performed at greatly improved speeds.
The centre in British politics since 1906
Authors: Nuttall Jeremy 
Published: January 2020

Abstract
The modern British ideological centre has been neglected and its impact underestimated. This article highlights the persistence of the centre’s moderating influence and its progressive, indeed at times radical, contribution. This ideological dynamism emanated from centrists’ synthesis of objectives often considered to conflict. Notably, centrists sought social justice alongside individual aspiration, albeit that this cross-ideological marriage was partial and incomplete. The article also examines the relationship between the centre and the people – presently portrayed as one of popular disconnection from an aloof elite. Yet, centrists have received considerable electoral sustenance from voters, and in turn demonstrated an appreciation of the contradictory ‘mix’ in many people, conservatism and progressivism in complex co-existence. Centrist history points to the contemporary political challenge as being one of raising the sights of a collective national ‘us’, rather than demonizing a variously targeted ‘other’.
P095 AMISELIMOD SAFETY PROFILE FOR CROHN’S DISEASE, STRATIFIED BY PREVIOUS TREATMENT WITH ANTI-TNF AGENTS
Authors: D’Haens Geert R A M , Slatkin Neal , Israel Robert , Heimanson Zeev 
Published: January 2020

Abstract

Background
Anti-TNF agents are an established treatment modality for ulcerative colitis (UC); however, as many as 30% of patients do not respond to anti-TNF agents, and almost 50% of responders lose clinical benefits after a year of treatment. Furthermore, numerous safety concerns are associated with long-term use of anti-TNF agents. An alternative treatment in development for autoimmune-mediated diseases, including Crohn’s disease (CD) and UC, are sphingosine 1-phosphate receptor modulators such as amiselimod (AMS).

Methods
The safety and efficacy of oral AMS 0.4 mg/d in adults with moderate to severe active CD over 14 wks were evaluated in a multicenter, randomized, double-blind, parallel-group, placebo (PBO)-controlled (DBPC), phase 2a clinical trial, followed by an open-label extension (OLE) study with AMS for up to 36 wks. Patients had previously used anti-TNF-α agents, immunosuppressants, or corticosteroids. Safety data (adverse events [AEs]) were stratified by patients with and without prior anti-TNF treatment.

Results
Of the 78 patients randomized 1:1 to receive AMS (n=40) or PBO (n=38), 78% (n=61) completed the DBPC treatment phase. Of those patients continuing into the OLE, 26 patients (AMS/AMS [n=14]; PBO/AMS [n=12]) completed it. Oral AMS 0.4 mg for 12 wks did not have a significant effect on clinical disease activity in CD. Patients previously treated with anti-TNF agents had more serious AEs (SAEs) (27% AMS [n=22]; 4% PBO [n=25]) than did patients without prior anti-TNF treatment (0 AMS and 0 PBO patients). Relative numbers of treatment-emergent AEs (TEAEs) were similar between groups receiving prior anti-TNF agents (68% AMS [n=22]; 68% PBO [n=25]) and no prior treatment (65% AMS [n=17]; 31% PBO [n=13]). There was a trend toward more mild TEAEs and less severe AEs in patients not previously treated with anti-TNF agents compared to those previously treated. Conversely, in the OLE, patients not previously treated with anti-TNF agents had more AEs (100% AMS/AMS [n=11]; 67% PBO/AMS [n=9]) than those with prior treatment (60% AMS/AMS [n=10]; 87% PBO/AMS [n=16]). All of these TEAEs were mild or moderate. In the OLE, only 1 patient receiving AMS/AMS with no prior anti-TNF treatment had an SAE versus no patients with prior treatment.

Conclusions
Previous treatment with anti-TNF agents did not significantly affect the TEAEs associated with AMS. While SAEs appeared to be more common in previously treated patients in the DBPC, patients had fewer AEs during the OLE. This analysis suggests that previous treatment with anti-TNF agents should be considered when assessing the AE profile of AMS in future trials.
P152 EVALUATING THE EFFICACY OF GLUTAMATE CARBOXYPEPTIDASE II (GCPII) INHIBITORS IN “WILD-TYPE” MICE: LESSONS LEARNED FROM THE DEDICATOR OF CYTOKINESIS 2 MUTANT MOUSE
Authors: Peters Diane , Norris Lauren , Slusher Barbara 
Published: January 2020

Abstract

Background
Glutamate carboxypeptidase II (GCPII) is highly upregulated in human IBD and is a therapeutic target under active investigation by our laboratory. We recently published that a spontaneously occurring loss-of-function mutation in dedicator of cytokinesis 2 (Dock2Hsd) that was present in commercially-purchased “wild-type” C57Bl6/NHsd mice increased their sensitivity to DSS-colitis and caused them to closely resemble human IBD with respect to GCPII. The DSS-exposed Dock2Hsd mice had significantly elevated colon GCPII activities and were sensitive to treatment with the GCPII inhibitor, 2-PMPA. We hypothesized that if colitis of the same severity were to be induced in Dock2WT mice, that they would also exhibit heightened colon GCPII activity and would be equally sensitive to 2-PMPA treatment.

Methods
DSS-colitis was induced in weight-, age- and gender-matched C57Bl/6NHsd mice (Dock2Hsd and Dock2WT). Increasing concentrations of DSS were utilized (2.5%-4.0%) and disease activity index was monitored daily. Mice received once daily treatment with vehicle or GCPII inhibitor 2-PMPA (IP).

Results
With increased DSS concentrations (4%), a severe colitis could be established in the Dock2WT mice which closely resembled the disease seen in Dock2Hsd mice induced with 2.5% DSS. Interestingly, despite similarity in DAI scores and disease progression, the GCPII activity in colons of Dock2WT mice (4% DSS) remained significantly lower than that of Dock2Hsd mice (2.5% DSS) (p&lt;0.001, t-test). Further, while 2-PMPA was effective in both groups, higher systemic doses were required in the IBD-resistant Dock2WT mice.

Conclusions
Following identification that the spontaneously occurring mutation Dock2Hsd influences murine DSS-colitis sensitivity and alters the activity of our therapeutic target protein, GCPII, in the colon, we sought to re-establish our DSS model using Dock2WT mice. While we were successfully able to recapitulate disease severity in the Dock2WT mice by increasing the DSS concentration from 2.5% to 4%, the underlying disease biology was not conserved. Despite having comparable DAI scores at study termination, Dock2WT mice had decreased GCPII activity in their colons relative to Dock2Hsd mice and were less sensitive to inhibition with the GCPII inhibitor, 2-PMPA. These data caution that target protein expression must be verified even with subtle changes to experimental method when utilizing the DSS-colitis model.
P157 FBXO3-FBXL2 AXIS MODULATORS AS A NOVEL CLASS OF ORAL SMALL MOLECULE COMPOUNDS FOR THE TREATMENT OF CROHN’S DISEASE
Authors: Angeli Franca , Wyborski Russell , Chen Bill , Mallampalli Rama , Lark Michael 
Published: January 2020

Abstract

Background
Ubiquitination is a common post-translational modification, tagging proteins for degradation. The ubiquitin proteasome system is activated in Crohn’s Disease (CD), and modulation of its components might be a novel strategy for therapeutic intervention to control inflammation. The conjugation of ubiquitin to a target protein is orchestrated by a series of enzymatic reactions, the last step being catalyzed by a selective ubiquitin E3 ligase. Among ubiquitin E3 ligases, Fbxl2 serves as a sentinel gatekeeper to limit inflammation by targeting and enhancing the degradation of tumor necrosis factor receptor associated factors (TRAF) proteins, which link cell surface signals (through NFkB signaling) to cytokine secretion. In addition, Fbxl2 controls the ubiquitination of the inflammasome, NOD-like receptor protein 3 (NLRP3), which mediates the release of interleukin (IL)1β and IL18 (Fig.1). Fbxl2 protein itself is ubiquitinated and degraded by another protein, called Fbxo3. Inhibition of Fbxo3 results in increased Fbxl2 levels and decreased TRAF and NLRP3. Individuals with a natural occurring polymorphism within Fbxo3V221Ihave decreased lipopolysaccharide(LPS)-induced cytokine (TNFα, IL1β & IL6) production, Fbxo3 and TRAF levels and increased Fbxl2, providing human genetic target validation for Fbxo3-Fbxl2 axis modulation in inflammatory conditions. BC1261 is a first-in-class, selective, orally available Fbxo3 inhibitor in clinical development for the treatment of CD.

Methods and Results
In vitro data demonstrated that BC1261 binds to Fbxo3, prevents Fbxo3/Fbxl2 association and produces a concentration-dependent inhibition of LPS-induced release of TNFα and IL1β from human peripheral blood mononuclear cells. In an acute DSS-mouse model, administration of BC-1261 via drinking water ad libitum (30 μg/ml) or by daily intraperitoneal (IP) injection (150 μg) for 5 days resulted in the attenuation of the shortening of colonic length, tissue damage (Fig2.A), and TNFα and IL6 tissue levels (Fig.2B). In a repeated DSS-mouse model, BC-1261 (10 mg/kg bid) given orally for 19 days was comparable to the positive control (anti-p40) in the DAI composite (Fig2.C), stool consistency (Fig2.D), and histopathology score in the proximal colon (Fig2.E). BC-1261 also lead to clinically relevant reductions on endoscopy score (Fig2.F).

Conclusion
BC1261, a Fbxo3 inhibitor, was efficacious in both acute and chronic preclinical models of colitis. Taken together, these results suggest the potential utility of selective Fbxo3-Fbxl2 modulation in the treatment of CD.
P068 MIRIKIZUMAB TREATMENT IMPROVES BOWEL MOVEMENT URGENCY IN PATIENTS WITH MODERATELY TO SEVERELY ACTIVE ULCERATIVE COLITIS
Authors: Dubinsky Marla , Lee Scott D , Panaccione Remo , Abreu Maria , Vermeire Séverine , Lissoos Trevor , Morris Nathan , Arora Vipin , Dong Yan , Naegeli April , Sands Bruce 
Published: January 2020

Abstract

Background
Mirikizumab (miri; LY3074828) is a humanized monoclonal antibody directed against the p19 subunit of IL-23, which demonstrated efficacy and was well-tolerated in a phase 2 randomized clinical trial (NCT02589665) in patients with ulcerative colitis (UC). Bowel movement urgency is one of the most bothersome symptoms experienced by patients with UC with an often-overlooked impact of their quality of life (QoL). Here we show the effect of miri on patient-reported urgency.

Methods
Patients were randomized 1:1:1:1 to receive intravenous placebo (PBO), miri 50mg or 200mg with possibility of exposure-based dose increases, or fixed miri 600mg every 4 weeks (Q4W), with efficacy assessment at Week 12. Patients who achieved clinical response to miri at Week 12 (decrease in 9-point Mayo score ≥ 2 points and ≥ 35% from baseline, and either a decrease in rectal bleeding (RB) subscore ≥1 or RB subscore of 0 or 1) were re-randomized 1:1 to double-blind maintenance treatment with miri 200mg subcutaneously (SC) every 4 (Q4W) or 12 (Q12W) weeks and were treated through Week 52. Patients reported daily symptoms, including absence or presence of bowel movement urgency. Logistic regression analysis was conducted to evaluate the treatment differences in absence of urgency among patients who had urgency at baseline for the first 12 weeks, with absence of urgency defined as no urgency symptom for three consecutive days prior to each scheduled visit. The proportion of patients with no urgency was calculated for the maintenance period among patients who had urgency at baseline and reached clinical response at Week 12, irrespective of urgency status at Week 12. Patients who had missing urgency data were imputed as having experienced urgency.

Results
At Week 12 patients in the 200mg and 600mg miri groups showed significantly higher rates of achieving absence of urgency compared to the PBO group (PBO: 10/55, 18.2% [CI: 8.0–28.4]; miri 50mg: 18/59, 30.5% [CI: 18.8–42.3]; 200mg: 22/56, 39.3% [CI: 26.5, 52.1], p=0.016; 600mg: 22/51, 43.1% [CI: 29.5, 56.7], p=0.006, Figure 1). Induction clinical responders who continued onto the maintenance period sustained this improvement in urgency with minimal variation (Figure 2).

Conclusion
In patients who reported bowel movement urgency at baseline, mirikizumab treatment resulted in significantly higher proportions of patients with no bowel movement urgency compared to placebo at Week 12, with numerical improvement observed as early as Week 4 and statistically significant improvement by Week 8. The reduction in bowel movement urgency was sustained through Week 52.
P056 DISCRIMINATORY ROLE OF ANTI-MICROBIAL ANTIBODIES IN DIAGNOSIS OF CROHN’S DISEASE AGAINST NORMAL AND OTHER MIMICS
Authors: Zhang Peilin , Minardi Lawrence , Kuenstner J Todd , Zekan Steve , Kruzelock Rusty 
Published: January 2020

Abstract
Anti-microbial antibodies have been found useful for diagnosis of Crohn’s disease (CD) and Sjogren’s syndrome (Sjo). These antibodies are also elevated in other autoimmune disease such as rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and multiple sclerosis (MS). The prevalence of these antibodies in the normal healthy population is unknown. We set to survey the normal population for these anti-microbial antibodies in comparison with Crohn’s disease and others. Totally 288 blood samples from the donor units of the leukocyte-reduced red blood cells from the American Red Cross were examined for the presence of anti-microbial antibodies using direct ELISA assays established in our laboratory using the recombinant microbial protein antigens. Our results showed that the prevalence of RPOB antibody in the normal blood donor population is 2.4% (7 positive of 288 samples). The prevalence of EF-G antibody is 4.2% (12 positive of 288 samples), ATP5a 5.2% (15 positive), Hsp65 2.8% (8 positive), EF-Tu 5.6% (16 positive), and NMPC 4.2% (12 positive). Meanwhile, in 109 patients with Crohn’s disease and 28 patients with Sjogren’s syndrome, these anti-bacterial antibodies are significantly increased (p&lt;0.001) (Figure 1). The anti-microbial antibodies were also elevated in ulcerative colitis (UC) and rheumatoid arthritis (RA). ROC curve analysis showed excellent sensitivity and specificity (Figure 2). These results indicate that the specific anti-microbial antibodies within the normal general population are uncommon, but frequent in chronic disease states. The presence of anti-microbial antibodies in patients but not in normal controls can serve as biomarkers for chronic diseases such as Crohn’s disease and Sjogren’s, and their presence indicates abnormal B-cell/plasma cell function in response to the commensal/pathogenic microbes. Since the antigens were derived from the common microbes present in normal population, the antimicrobial antibodies in patients with diseases but not in the normal population suggest a deficient clearance of the microbes from the circulation by the innate immunity system in chronic diseases. These results also raise questions of bacterial vaccination using whole bacterial extracts as these anti-bacterial antibodies appear pathogenic rather than protective, offering fresh thinking in designing bacterial vaccines as preventive or therapeutic measures in chronic diseases such as Crohn’s disease and Sjogren’s Disease.