bluuebunny/crossref_metadata_2025 huggingface dataset:
Phosphorylated Hexa-Acyl Disaccharides Augment Host Resistance Against Common Nosocomial Pathogens
Authors: Hernandez Antonio , Luan Liming , Stothers Cody L. , Patil Naeem K. , Fults Jessica B. , Fensterheim Benjamin A. , Guo Yin , Wang Jingbin , Sherwood Edward R. , Bohannon Julia K.
Published: September 2019

Objectives:

To determine whether synthetic phosphorylated hexa-acyl disaccharides provide antimicrobial protection in clinically relevant models of bacterial infection.

Design:

Laboratory study.

Setting:

University laboratory.

Subjects:

BALB/c, C57BL/10J, and C57BL/10ScNJ mice.

Interventions:

Mice were treated with lactated Ringer’s (vehicle) solution, monophosphoryl lipid A, or phosphorylated hexa-acyl disaccharides at 48 and 24 hours prior to intraperitoneal Pseudomonas aeruginosa or IV Staphylococcus aureus infection. Leukocyte recruitment, cytokine production, and bacterial clearance were measured 6 hours after P. aeruginosa infection. In the systemic S. aureus infection model, one group of mice was monitored for 14-day survival and another for S. aureus tissue burden at 3 days postinfection. Duration of action for 3-deacyl 6-Acyl phosphorylated hexa-acyl disaccharide was determined at 3, 10, and 14 days using a model of intraperitoneal P. aeruginosa infection. Effect of 3-deacyl 6-Acyl phosphorylated hexa-acyl disaccharide on in vivo leukocyte phagocytosis and respiratory burst was examined. Leukocyte recruitment, cytokine production, and bacterial clearance were measured after P. aeruginosa infection in wild-type and toll-like receptor 4 knockout mice treated with 3-deacyl 6-Acyl phosphorylated hexa-acyl disaccharide or vehicle to assess receptor specificity.

Measurements and Main Results:

During intraperitoneal P. aeruginosa infection, phosphorylated hexa-acyl disaccharides significantly attenuated infection-induced hypothermia, augmented leukocyte recruitment and bacterial clearance, and decreased cytokine production. At 3 days post S. aureus infection, bacterial burden in lungs, spleen, and kidneys was significantly decreased in mice treated with monophosphoryl lipid A or phosphorylated hexa-acyl disaccharides, which was associated with improved survival. Leukocyte phagocytosis and respiratory burst functions were enhanced after treatment with monophosphoryl lipid A or phosphorylated hexa-acyl disaccharides. A time course study showed that monophosphoryl lipid A– and 3-deacyl 6-Acyl phosphorylated hexa-acyl disaccharide–mediated protection against P. aeruginosa lasts for up to 10 days. Partial loss of augmented innate antimicrobial responses was observed in toll-like receptor 4 knockout mice treated with 3-deacyl 6-Acyl phosphorylated hexa-acyl disaccharide.

Conclusions:

Phosphorylated hexa-acyl disaccharides significantly augment resistance against clinically relevant Gram-negative and Gram-positive infections via enhanced leukocyte recruitment, phagocytosis, and respiratory burst functions of innate leukocytes. Improved antimicrobial protection persists for up to 10 days and is partially mediated through toll-like receptor 4.
Comparison of 4 Commercial Immunoassays Used in Measuring the Concentration of Tacrolimus in Blood and Their Cross-Reactivity to Its Metabolites
Authors: Shigematsu Tomohiro , Suetsugu Kimitaka , Yamamoto Nanae , Tsuchiya Yuichi , Masuda Satohiro
Published: September 2019

Background:

Therapeutic drug monitoring of tacrolimus is necessary for appropriate dose adjustment for a successful immunosuppressive therapy. Several commercial immunoassays are available for tacrolimus measurements. This study aimed at simultaneously evaluating the analytical performances of 4 such immunoassays, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) as a standard. For the first time, cross-reactivity to tacrolimus metabolites was assessed at concentrations frequently observed in clinical settings, as opposed to the higher concentrations tested by assay manufacturers.

Methods:

An affinity column-mediated immunoassay (ACMIA), using upgraded flex reagents; released in 2015, a chemiluminescence immunoassay (CLIA), an electrochemiluminescence immunoassay (ECLIA), and a latex agglutination turbidimetric immunoassay (LTIA) were evaluated using frozen whole blood samples collected from transplantation patients. Cross-reactivities to 3 major tacrolimus metabolites (13-O-demethyl-tacrolimus [M-I], 31-O-demethyl-tacrolimus [M-II], and 15-O-demethyl-tacrolimus [M-III]) were evaluated.

Results:

Each immunoassay correlated well with LC-MS/MS, and the Pearson's correlation coefficients (R) were 0.974, 0.977, 0.978, and 0.902 for ACMIA, CLIA, ECLIA, and LTIA, respectively. Using Bland–Altman difference plots to compare the immunoassays with LC-MS/MS, the calculated average biases were −6.73%, 6.07%, 7.46%, and 12.27% for ACMIA, CLIA, ECLIA, and LTIA, respectively. The cross-reactivities of ACMIA to the tacrolimus metabolites M-II and M-III were 81% and 78%, respectively, when blood was spiked at 2 ng/mL, and 94% and 68%, respectively, when it was spiked at 5 ng/mL.

Conclusions:

Each immunoassay was useful, but had its own characteristics. ACMIA cross-reactivities to M-II and M-III were much higher than the respective 18% and 15% reported on its package insert, suggesting that cross-reactivity should be examined at clinically relevant concentrations.
A critical appraisal of vasomotor symptom assessment tools used in clinical trials evaluating hormone therapy compared to placebo
Authors: Christakis Marie K. , Strobino Donna M. , Shen Wen
Published: September 2019

Objective:

Vasomotor symptoms (VMS) have been consistently reported as the leading predictor of health-related quality of life (HRQOL) among menopausal women, and the strongest indication for treatment. The North American Menopause Society endorses the use of oral estrogen for the treatment of VMS based on a Cochrane meta-analysis. The Cochrane review concludes that oral hormone therapy reduces the frequency and severity of VMS. The objective of this review is to critically appraise the outcome measures used in these clinical trials to evaluate whether there is adequate evidence that oral hormone therapy improves HRQOL.

Methods:

Each trial in the 2004 Cochrane review of oral hormone therapy for the management of VMS was evaluated with respect to study design, outcome measures, and method of analysis.

Results:

Twenty-four randomized, double-blind, placebo-controlled clinical trials were appraised. Six trials were excluded from the Cochrane meta-analysis due to inadequate reporting of outcome measures. Of the remaining trials, 15 trials assessed only symptom frequency and/or severity. One trial used a subscale of the General Health Questionnaire. Two trials used the Greene Climacteric Scale, a validated outcome measure in menopausal women, to directly assess the impact of hormone therapy on HRQOL. Both studies showed an improvement in HRQOL in the hormone-treated group, although the sample size was small (n = 118) and the effect was modest.

Conclusion:

Although oral hormone therapy improves VMS scores, there is a paucity of evidence on whether it improves HRQOL in menopausal women. Future studies using validated, patient-reported outcome measures that directly assess HRQOL are needed.
Lipid profile differences during menopause: a review with meta-analysis
Authors: Ambikairajah Ananthan , Walsh Erin , Cherbuin Nicolas
Published: September 2019

Objectives:

The aim of the study was to determine lipid profile differences between premenopausal and postmenopausal women.

Methods:

The present review used a meta-analytic approach. Sixty-six studies were included, which provided a total sample of 114,655 women consisting of 68,394 that were premenopausal and 46,261 that were postmenopausal.

Results:

The main findings were that (1) lipoproteins were significantly higher in postmenopausal women compared to premenopausal women including triglycerides (0.27 mmol/L, 95% confidence interval, 0.22-0.31), total cholesterol (0.58, 0.50-0.65), low-density lipoprotein (0.45, 0.38-0.53), and total cholesterol to high-density lipoprotein levels (0.39, 0.16-0.62); (2) there was no difference in high-density lipoprotein levels between premenopausal and postmenopausal women (0.02, −0.00-0.04); and (3) the differences in lipid levels was partly attributable to the mean age difference between premenopausal and postmenopausal women.

Conclusions:

These findings are important as they provide precise estimates of lipid differences in women around menopause. Furthermore the results suggest that the unfavorable lipid profile that develops in postmenopausal women puts them at higher risk of cardiovascular disease such as heart disease and stroke if appropriate lifestyle/pharmacological interventions are not implemented.
FADS1 and FADS2 polymorphism are associated with changes in fatty acid concentrations after calorie-restricted Central European and Mediterranean diets
Authors: Muzsik Agata , Bajerska Joanna , Jeleń Henryk H. , Walkowiak Jarosław , Krzyżanowska-Jankowska Patrycja , Chmurzynska Agata
Published: September 2019

Objective:

In the present study, we tested whether calorie-restricted diets differing in their percentage of energy derived from monounsaturated fatty acids and carbohydrates can affect the metabolism of fatty acids (FAs) in postmenopausal women. Moreover, we examined whether polymorphisms ofFADS1andFADS2are associated with these changes.

Methods:

Postmenopausal women (the mean age: 60.5 ± 5.0 y) were randomized for 16 weeks to two different calorie-restricted diets: a Central European diet (CED) or a Mediterranean diet (MED).

Results:

After the intervention, levels of most FAs in red blood cells decreased in both groups. The delta values for the 20:1n-9 and the 20:2n-6 levels differed between the CED and the MED (−1.55 ± 4.02 μg/mL vs 0.39 ± 4.11 μg/mL and −0.62 ± 10.93 μg/mL vs 3.06 ± 8.75 μg/mL;P< 0.05). Women in the CED group with at least one minor allele ofFADSgenes had greater decreases of α-linolenic acid, dihomo-γ-linolenic acid, total n-6, and total PUFA (by approximately 70%, 40%, 35%, and 35%, respectively) than did women with the major alleles. After the intervention, the change in the lipid accumulation product index was −28.28 ± 27.84 and −32.00 ± 78.55 in the CED and the MED group, respectively.

Conclusions:

The effect of the dietary intervention on FA metabolism seems to depend mostly on calorie restriction, but not on type of diet.FADS1andFADS2gene polymorphisms can modify the response to the CED.
The metabotropic glutamate receptor 5 negative allosteric modulator fenobam: pharmacokinetics, side effects, and analgesic effects in healthy human subjects
Authors: Cavallone Laura F. , Montana Michael C. , Frey Karen , Kallogjeri Dorina , Wages James M. , Rodebaugh Thomas L. , Doshi Tina , Kharasch Evan D. , Gereau Robert W.
Published: September 2019

Metabotropic glutamate receptor 5 (mGlu5) has been shown to modulate nociception in animals, but no mGlu5 antagonists have been developed commercially as analgesics. The mGlu5 antagonist fenobam [N-(3-chlorophenyl)-N′-(4,5-dihydro-1-methyl-4-oxo-1H-imidazole-2-yl)urea] was originally evaluated for development as a nonbenzodiazepine anxiolytic. Fenobam is analgesic in numerous mouse pain models, acting exclusively through mGlu5 blockade. Furthermore, fenobam showed no signs of analgesic tolerance with up to 2 weeks of daily dosing in mice. Analgesic effects of fenobam in humans have not been reported. The purpose of this investigation was to evaluate fenobam pharmacokinetics and analgesic effects in humans. We first evaluated single-dose oral fenobam disposition in a parallel-group dose-escalation study in healthy volunteers. A second investigation tested the analgesic effects of fenobam in an established experimental human pain model of cutaneous sensitization using capsaicin cream and heat, in a double-blind placebo-controlled study. The primary outcome measure was the area of hyperalgesia and allodynia around the area applied with heat/capsaicin. Secondary outcome measures included nociception, measured as pain rating on a visual analog scale, heat pain detection threshold, and effects on cognition and mood. Fenobam plasma exposures showed considerable interindividual variability and were not linear with dose. Fenobam reduced sensitization vs placebo at a single timepoint (peak plasma concentration); we found no other difference between fenobam and placebo. Our results suggest highly variable fenobam disposition and minimal analgesic effects at the dose tested. We suggest that future studies testing analgesic effects of mGlu5 blockade are warranted, but such studies should use molecules with improved pharmacokinetic profiles.
Medication Nonadherence or Self-care? Understanding the Medication Decision-Making Process and Experiences of Older Adults With Heart Failure
Authors: Meraz Rebecca
Published: September 2019

Background

More than half of all patients with heart failure (HF) do not take medications as prescribed, resulting in negative health outcomes. Research has shown that medication adherence may be intentional rather than the ability to follow prescribed regimens, yet very little is known about medication-taking decisions in older patients with HF.

Objective

The purpose of this qualitative study was to gain insight into the decision-making processes and experiences of older patients with HF by exploring the different aspects in choosing to take or not take medications as prescribed in the community setting.

Methods

Using a narrative inquiry approach, the personal narratives of 11 adults 65 years or older who took at least 2 daily medications for HF were gathered using in-depth, semistructured interviews. The data in this study were organized and analyzed using Riessman's framework for narrative analysis.

Results

Participants made intentional decisions to take particular medications differently than prescribed. A worrisome symptom prompted a naturalistic decision-making process. When a medication interfered with attaining a personal goal, participants coped by individualizing their medication regimen. Participants did not consider taking a medication differently than prescribed as nonadherence but a necessary aspect of maintaining a personal level of health, which could be seen as self-care.

Conclusions

The older patient with HF should be carefully assessed for nonadherence. The development of interventions that are patient specific, target medications with the greatest potential for nonadherence, and use easy-to-access resources may promote decisions for medication adherence. More research is needed to develop interventions that promote decisions for medication adherence.
Palpable Purpura on the Legs and Buttocks
Authors: Patel Dharmik , Martin Kari L.
Published: September 2019

This is a case of a young girl with palpable purpura on the legs and buttocks who was seen using telecommunication technology. Store-and-forward teledermatology increases overall access to dermatology care by sending protected medical information electronically to off-site medical providers (Roman & Jacob, 2014). The following case of palpable purpura is presented in the standardized teledermatological reader format.
The Relation Between Tinnitus and a Neurovascular Conflict of the Cochleovestibular Nerve on Magnetic Resonance Imaging
Authors: Peters Thomas T. A. , van den Berge Minke J. C. , Free Rolien H. , van der Vliet Anton M. , Knoppel Hanna , van Dijk Pim , Hofman Rutger
Published: September 2019

Introduction:

Magnetic resonance (MR) imaging is often used in diagnostic evaluation of tinnitus patients. Incidental findings like a neurovascular conflict (NVC) in the cerebellopontine angle are often found; however, the diagnostic value of this finding remains unclear. The aim of this study is to investigate whether the type or degree of compression of the vestibulocochlear nerve is of diagnostic value in patients with a NVC.

Methods:

A retrospective study was performed in 111 tinnitus patients with available MR imaging between 2013 and 2015. Clinical and audiometric variables were gathered and MR imaging was reevaluated by two neuroradiologists. NVCs were analyzed using a grading system based on previous research by Sirikci et al.

Results:

In total, 220 ears were available for assessment. In patients with unilateral tinnitus a loop compression and an indentation of the cochleovestibular nerve were more frequent than in patients with bilateral tinnitus. However, there was no significant difference in distribution of the type of compression between tinnitus and nontinnitus ears. Patient with unilateral tinnitus had a significantly higher degree of hearing loss in the symptomatic ear, compared with the asymptomatic ear and with the bilateral tinnitus group. Also, it was found that the degree of hearing loss did not differ between the various types of compression.

Conclusion:

This study did not find a diagnostic value of specific types of compression in patients with a NVC. Although the distribution of NVC classification was different in patients with unilateral and bilateral tinnitus, there was no definite relation between the type of NVC and the presence of ipsilateral tinnitus. Also, the degree of hearing loss was not related to specific types of NVC.
Insulin Therapy: Future Perspectives
Authors: Cernea Simona , Raz Itamar
Published: September 2019

Background:

Insufficient insulin secretion is a core pathogenetic mechanism of diabetes mellitus and therefore, insulin therapy remains the cornerstone of management. Over the past 100 years, much progress has been made in the development of insulin therapy, including elaboration of novel insulin formulations and delivery methods.

Areas of Uncertainty:

Despite significant advances, there are still many barriers, challenges, and uncertainties involving insulin therapy. With newer pharmacological and technological approaches, there are many potential drawbacks to be addressed, such as immunogenicity, biocompatibility, degradation/clearance of delivery materials, stability, precision of dosing, reproducibility, predictability of performance, and safety over time, etc. In addition, the new formulations/delivery systems should be cost-effective and accessible.

Data Sources:

A literature search of original and review articles, editorials, and meta-analyses in Medline/PubMed and Google Scholar has been performed. ClinicalTrials.gov website was searched for ongoing relevant clinical trials.

Therapeutic Advances:

New insulin formulations (ultralong basal and ultrarapid analogues) were designed to obtain a prolonged, flatter profile, with less hypoglycemia and improvement of postprandial glucose control, respectively. The next generation of insulin therapy is probably best represented by the “smart” (glucose-responsive) insulins, which deliver it according to an endogenous glucose-sensing feedback mechanism. Another area of continuous advances includes insulin delivery systems with new jet injectors, smart pens, patch pumps, and other needle-free devices for subcutaneous administrations. Many alternative routes of insulin delivery (pulmonary, nasal, buccal, oral, and transdermal) have also been explored, with some reaching clinical use. The digitalization of diabetes care has made considerable progress in the past several years and will most probably make even more so in the near future.

Conclusions:

The improved insulin formulations, newer delivery methods/routes, and digital technologies are rapidly becoming effective and have great potential to improve metabolic control as well as other outcomes, including quality of life of persons living with diabetes mellitus.
Performance of an Automated Screening Algorithm for Early Detection of Pediatric Severe Sepsis*
Authors: Eisenberg Matthew , Madden Kate , Christianson Jeffrey R. , Melendez Elliot , Harper Marvin B.
Published: September 2019

Objectives:

To create and evaluate a continuous automated alert system embedded in the electronic health record for the detection of severe sepsis among pediatric inpatient and emergency department patients.

Design:

Retrospective cohort study. The main outcome was the algorithm’s appropriate detection of severe sepsis. Episodes of severe sepsis were identified by chart review of encounters with clinical interventions consistent with sepsis treatment, use of a diagnosis code for sepsis, or deaths. The algorithm was initially tested based upon criteria of the International Pediatric Sepsis Consensus Conference; we present iterative changes which were made to increase the positive predictive value and generate an improved algorithm for clinical use.

Setting:

A quaternary care, freestanding children’s hospital with 404 inpatient beds, 70 ICU beds, and approximately 60,000 emergency department visits per year

Patients:

All patients less than 18 years presenting to the emergency department or admitted to an inpatient floor or ICU (excluding neonatal intensive care) between August 1, 2016, and December 28, 2016.

Intervention:

Creation of a pediatric sepsis screening algorithm.

Measurements and Main Results:

There were 288 (1.0%) episodes of severe sepsis among 29,010 encounters. The final version of the algorithm alerted in 9.0% (CI, 8.7–9.3%) of the encounters with sensitivity 72% (CI, 67–77%) for an episode of severe sepsis; specificity 91.8% (CI, 91.5–92.1%); positive predictive value 8.1% (CI, 7.0–9.2%); negative predictive value 99.7% (CI, 99.6–99.8%). Positive predictive value was highest in the ICUs (10.4%) and emergency department (9.6%).

Conclusions:

A continuous, automated electronic health record-based sepsis screening algorithm identified severe sepsis among children in the inpatient and emergency department settings and can be deployed to support early detection, although performance varied significantly by hospital location.
Rituximab Versus Cyclophosphamide for Central Nervous System Involvement of Antineutrophil Cytoplasmic Antibody–Associated Vasculitis
Authors: Krishna Rachana , De Giacomi Federica , Kumar Neeraj , Kalina Peter , Specks Ulrich , Baqir Misbah
Published: September 2019

Objective

To compare the effectiveness of rituximab (RTX) with cyclophosphamide (CYC) in patients who have central nervous system (CNS) involvement in antineutrophil cytoplasmic antibody–associated vasculitis (AAV).

Methods

A computer-assisted search was conducted to identify all adults who received a diagnosis of AAV with CNS involvement from January 1, 1997, through July 1, 2017, at our institution.

Results

Of the 17 patients identified, 11 had received RTX, and 6 had received CYC. Age at diagnosis of CNS involvement was similar in both groups. In the RTX group, 91% of the patients were women; in the CYC group, 33% were women (p = 0.03). At the time of CNS presentation, orbital involvement had occurred in 6 patients in the RTX group and in none of the patients in the CYC group. Initial remission of induction was achieved in all patients (100%) in the CYC group and in 10 patients (91%) in the RTX group. Two patients had no response to RTX: 1 patient when RTX was used for remission induction at the time of diagnosis and the second patient when RTX was used for remission induction after relapse. The median follow-up was 38 months (range, 9–127 months). Central nervous system relapse occurred in 4 patients in the RTX group and in 1 patient in the CYC group. Of the 4 patients in the RTX group with relapse, 3 had marked ocular involvement. Both nonresponder patients in the RTX group had ocular involvement.

Conclusion

Rituximab is as effective as CYC in remission induction in patients with CNS involvement in AAV.
Healthy ageing men have normal reproductive function but display germline-specific molecular changes
Authors: Laurentino S. , Cremers J.-F. , Horsthemke B. , Tüttelmann F. , Czeloth K. , Zitzmann M. , Pohl E. , Rahmann S. , Schröder C. , Berres S. , Redmann K. , Krallmann C. , Schlatt S. , Kliesch S. , Gromoll J.
Published: September 2019

Children of older fathers have higher risk for certain diseases. Nevertheless, how ageing specifically affects male germ cells is so far not completely understood. In a cohort of 197 healthy men (18-84 years), we found that semen and reproductive parameters remained normal over six decades. Along with an age-dependent increase in telomere length in sperm (r=0.41, p>0.001), we found accelerated DNA fragmentation, more prominent after the sixth decate of life, and with around 60% of men older than 66 showing abnormal levels of DNA breaks. At the epigenetic level, by whole genome bisulfite sequencing we identified 236 sperm-specific differentially methylated regions between the youngest and oldest group, affecting mostly regions associated with homeobox genes and nervous system development. Therefore, we propose that during ageing, male germ cells are affected by an intrinsic and specific ageing process, distinguishable from the soma. These age-dependent changes might have consequences for fertility and offspring of older men.
From rare Copy Number Variations to biological processes in ADHD
Authors: Harich Benjamin , van der Voet Monique , Klein Marieke , Čížek Pavel , Fenckova Michaela , Schenck Annette , Franke Barbara
Published: September 2019

Aim

Attention-deficit/hyperactivity disorder (ADHD) is a highly heritable psychiatric disorder. The objective of this study was to define ADHD-associated candidate genes, and their associated molecular modules and biological themes, based on the analysis of rare genetic variants.

Methods

We combined data from 11 published copy number variation (CNV) studies in 6176 individuals with ADHD and 25026 controls and prioritized genes by applying an integrative strategy based on criteria including recurrence in ADHD individuals, absence in controls, complete coverage in copy number gains, and presence in the minimal region common to overlapping CNVs, as well as on protein-protein interactions and information from cross-species genotype-phenotype annotation.

Results

We localized 2241 eligible genes in the 1532 reported CNVs, of which we classified 432 as high-priority ADHD candidate genes. The high-priority ADHD candidate genes were significantly co-expressed in the brain. A network of 66 genes was supported by ADHD-relevant phenotypes in the cross-species database. In addition, four significantly interconnected protein modules were found among the high-priority ADHD genes. A total of 26 genes were observed across all applied bioinformatic methods. Look-up in the latest genome-wide association study for ADHD showed that among those 26,POLR3CandRBFOX1were also supported by common genetic variants.

Conclusions

Integration of a stringent filtering procedure in CNV studies with suitable bioinformatics approaches can identify ADHD candidate genes at increased levels of credibility. Our pipeline provides additional insight in the molecular mechanisms underlying ADHD and allows prioritization of genes for functional validation in validated model organisms.
Cytosine methylation affects the mutability of neighbouring nucleotides in human, Arabidopsis, and rice
Authors: Kusmartsev Vassili , Warnecke Tobias
Published: September 2019

Methylated cytosines deaminate at higher rates than unmethylated cytosines and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans,Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighbouring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3nt) of methylated cytosines mutate less frequently. In contrast, methylation is associated with increased neighbourhood mutation risk inA. thalianaand rice. The difference in mutation risk associated with methylation is less pronounced further away from the focal CpG, is modulated by regional GC content, and enhanced in heterochromatic regions. Our results are consistent with a model where elevated risk at neighbouring bases is linked to lesion formation at the focal cytosine and subsequent long-patch repair. Our results provide evidence that cytosine methylation has a broader mutational footprints than commonly assumed. They also illustrate that methylation is not intrinsically associated with higher mutation risk for surrounding bases, but that mutagenic effects reflect evolved species-specific and lesion-specific predispositions to elicit error-prone long-patch DNA repair.
Transmission Chains or Independent Solvers? A Comparative Study of Two Collective Problem-Solving Methods
Authors: Yahosseini Kyanoush Seyed , Moussaïd Mehdi
Published: September 2019

Groups can be very successful problem-solvers. This collective achievement crucially depends on how the group is structured, that is, how information flows between members and how individual contributions are merged. Numerous methods have been proposed, which can be divided into two major categories: those that involve an exchange of information between the group members, and those that do not. Here we compare two instances of such methods for solving complex problems: (1) transmission chains, where individuals tackle the problem one after the other, each one building on the solution of the predecessor and (2) groups of independent solvers, where individuals tackle the problem independently, and the best solution found in the group is selected afterwards.

By means of numerical simulations and experimental observations, we show that the best performing method is determined by the interplay between two key factors: the skills of the individuals and the difficulty of the problem. We find that transmission chains are superior either when the problem is rather easy, or when the group is composed of rather unskilled individuals. On the contrary, groups of independent solvers are preferable for harder problems or for groups of rather skillful individuals. Finally, we deepen the comparison by studying the impact of the group size and diversity. Our research stresses that efficient collective problem-solving requires a good matching between the nature of the problem and the structure of the group.
Development of CAR-T Cell Therapy for B-ALL Using a Point-of-Care Approach
Authors: de Macedo Abdo Luiza , Barros Luciana Rodrigues Carvalho , Viegas Mariana Saldanha , Marques Luisa Vieira Codeço , de Sousa Ferreira Priscila , Chicaybam Leonardo , Bonamino Martín Hernán
Published: September 2019

Recently approved by the FDA and European Medicines Agency, CAR-T cell therapy is a new treatment option for B-cell malignancies. Currently, CAR-T cells are manufactured in centralized facilities and face bottlenecks like complex scaling up, high costs and logistic operations. These difficulties are mainly related to the use of viral vectors and the requirement to expand CAR-T cells to reach the therapeutic dose. In this paper, by using Sleeping Beauty-mediated genetic modification delivered by electroporation, we show that CAR-T cells can be generated and used without the need for ex vivo activation and expansion, consistent with a point-of-care (POC) approach. Our results show that minimally manipulated CAR-T cells are effective in vivo against RS4;11 leukemia cells engrafted in NSG mice even when inoculated after only 4 hours of gene transfer. In an effort to better characterize the infused CAR-T cells, we show that 19BBz T lymphocytes infused after 24h of electroporation (where CAR expression is already detectable) can improve the overall survival and reduce tumor burden in organs of mice engrafted with RS4;11 or Nalm-6 B cell leukemia. A side-by-side comparison of POC approach with a conventional 8-day expansion protocol using Transact beads demonstrated that both approaches have equivalent antitumor activity in vivo. Our data suggests that POC approach is a viable alternative for the generation and use of CAR-T cells, overcoming the limitations of current manufacturing protocols. Its use has the potential to expand CAR immunotherapy to a higher number of patients, especially in the context of low-income countries.
Saccade vigor partly reflects the subjective economic value of the visual stimulus
Authors: Yoon Tehrim , Jaleel Afareen , Ahmed Alaa A. , Shadmehr Reza
Published: September 2019

Decisions are made based on the subjective value that the brain assigns to options. However, subjective value is a mathematical construct that cannot be measured directly, but rather inferred from choices. Recent results have demonstrated that reaction time and velocity of movements are modulated by reward, raising the possibility that there is a link between how the brain evaluates an option, and how it controls movements toward that option. Here, we asked people to choose among risky options represented by abstract stimuli, some associated with gain, others with loss. From their choices in decision trials we estimated the subjective value that they assigned to each stimulus. In probe trials, they were presented with a single stimulus at center and made a saccade to a peripheral location. We found that the reaction time and peak velocity of that saccade varied roughly linearly from loss to gain with the subjective value of the stimulus. Naturally, participants differed in how much they valued a given stimulus. Remarkably, those who valued a stimulus more, as evidenced by their choices in decision trials, tended to move with greater vigor in response to that stimulus in probe trials. Thus, saccade vigor partly reflected the subjective value that the brain assigned the stimulus. However, the influence of subjective value on vigor was only a modest predictor of preference: vigor in probe trials allowed us to predict choice in decision trials with roughly 60% accuracy.

New and Noteworthy

We found that saccade vigor tends to vary monotonically with subjective value: smallest for stimuli that predict a loss, and highest for stimuli that predict a gain. Notably, between-subject differences in valuation could be gleaned from the between-subject differences in their patterns of vigor. However, the influence of subjective value on vigor was modest, allowing partial ability to infer subjective value for the purpose of predicting choice in decision trials.
Increased cell size, structural complexity and migration of cancer cells acquiring fibroblast organelles by cell-projection pumping
Authors: Zoellner Hans , Chami Belal , Kelly Elizabeth , Moore Malcolm A.S.
Published: September 2019

We recently described a hydrodynamic mechanism for cytoplasmic transfer between cells, termed cell-projection pumping (CPP). Earlier image analysis related altered SAOS-2 osteosarcoma cell morphology, to what we now recognize as CPP uptake of fibroblast cytoplasm. We here examine SAOS-2 phenotype following co-culture with human dermal fibroblasts (HDF) in which organelles were pre-labelled with a fluorescent lipophilic marker. Fluorescence activated cell sorting (FACS) analysis was performed of HDF and SAOS-2, cultured either alone or together. FACS forward scatter is proportionate to cell size, and increased for SAOS-2 with high levels of HDF fluorescence uptake (p < 0.004). FACS side scatter is proportionate to internal cell complexity, and increased in SAOS-2 with increasing uptake of HDF fluorescence (p < 0.004), consistent with uptake of HDF organelles. Scratch migration assays revealed that HDF migrated more quickly than SAOS-2 in both isolated cell culture, and following co-culture (p < 0.004). Notably, SAOS-2 with high levels of HDF labelling migrated faster compared with SAOS-2 with low HDF labelling (p < 0.008). A slight and unconvincing reduction in SAOS-2 proliferation was seen (p < 0.02). Similar results were obtained in single additional experiments with A673 and H312 cancer cells. Forward and side scatter results suggest organellar transfer by CPP increases cancer cell morphological diversity. This may contribute to histological pleomorphism relevant to cancer diagnosis and prognosis. Also, increased migration of sub-populations of cancer cells with high CPP organellar uptake, may contribute to invasion and metastasis in-vivo. We thus suggest relevance of CPP to cancer diagnosis and progression.
A Functionally Conserved Mechanism of Modulation via a Vestibule Site in Pentameric Ligand-Gated Ion Channels
Authors: Brams Marijke , Govaerts Cedric , Kambara Kumiko , Price Kerry , Spurny Radovan , Gharpure Anant , Pardon Els , Evans Genevieve L. , Bertrand Daniel , Lummis Sarah C. R. , Hibbs Ryan E. , Steyaert Jan , Ulens Chris
Published: September 2019

Pentameric ligand-gated ion channels (pLGICs) belong to a class of ion channels involved in fast synaptic signaling in the central and peripheral nervous systems. Molecules acting as allosteric modulators target binding sites that are remote from the neurotransmitter binding site, but functionally affect coupling of ligand binding to channel opening. Here, we investigated an allosteric binding site in the ion channel vestibule, which has converged from a series of studies on prokaryote and eukaryote channel homologs. We discovered single domain antibodies, called nanobodies, which are functionally active as allosteric modulators, and solved co-crystal structures of the prokaryote channel ELIC bound either to a positive (PAM) or a negative (NAM) allosteric modulator. We extrapolate the functional importance of the vestibule binding site to eukaryote ion channels, suggesting a conserved mechanism of allosteric modulation. This work identifies key elements of allosteric binding sites and extends drug design possibilities in pLGICs using nanobodies.
Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community
Authors: Fritts Ryan K , Bird Jordan T , Behringer Megan G , Lipzen Anna , Martin Joel , Lynch Michael , McKinlay James B
Published: September 2019

Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered mutualistic cross-feeding between N2-fixingRhodopseudomonas palustrisand fermentativeEscherichia coli. EngineeredR. palustrisexcreted essential nitrogen as NH4+toE. coliwhileE. coliexcreted essential carbon as fermentation products toR. palustris. Here, we enriched for nascent cross-feeding in cocultures with wild-typeR. palustris, not known to excrete NH4+. Emergent NH4+cross-feeding was driven by adaptation ofE. colialone. A missense mutation inE. coliNtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+transporter. This activity likely allowedE. colito subsist on the small amount of leaked NH4+and better reciprocate through elevated excretion of organic acids from a largerE. colipopulation. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge.
A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth
Authors: Kamrad Stephan , Grossbach Jan , Rodríguez-López Maria , Townsend StJohn , Mülleder Michael , Cappelletti Valentina , Stojanovski Gorjan , Picotti Paola , Beyer Andreas , Ralser Markus , Bähler Jürg
Published: September 2019

Cells balance glycolysis with respiration to support their energetic and biosynthetic needs in different environmental or physiological contexts. With abundant glucose, many cells prefer to grow by aerobic glycolysis, or fermentation in yeast. Using 161 natural isolates of fission yeast, we investigated the genetic basis and phenotypic effects of the fermentation-respiration balance. The laboratory and a few other strains were more dependent on respiration. This trait was associated with a missense variant in a highly conserved region of Pyk1. Pyk1 is the single pyruvate kinase in fission yeast, while most organisms possess isoforms with different activity. This variant reduced Pyk1 activity and glycolytic flux. Replacing the ‘low-activity’pyk1allele in the laboratory strain with the common ‘high-activity’ allele was sufficient to increase fermentation and decrease respiration. This metabolic reprogramming triggered systems-level adaptations in the transcriptome and proteome, and in cellular phenotypes, including increased growth and chronological lifespan, but decreased resistance to oxidative stress. Thus, low Pyk1 activity provided no growth advantage but stress tolerance, despite increased respiration. The genetic tuning of glycolytic flux by a single-nucleotide change might reflect an adaptive trade-off in a species lacking pyruvate-kinase isoforms.
Effect of Changing Heart Rate on the Ocular Pulse and Dynamic Biomechanical Behavior of the Optic Nerve Head
Authors: Jin Yuejiao , Wang Xiaofei , Irnadiastputri Sylvi Febriana Rachmawati , Mohan Rosmin Elsa , Aung Tin , Perera Shamira A. , Boote Craig , Jonas Jost B. , Schmetterer Leopold , Girard Michaël J.A.
Published: September 2019

Purpose

To study the effect of changing heart rate on the ocular pulse and the dynamic biomechanical behaviour of the optic nerve head (ONH) using a comprehensive mathematical model.

Methods

In a finite element model of a healthy eye, a biphasic choroid consisted of a solid phase with connective tissues and a fluid phase with blood, and the lamina cribrosa (LC) was viscoelastic as characterized by a stress-relaxation test. We applied arterial pressures at 18 ocular entry sites (posterior ciliary arteries) and venous pressures at four exit sites (vortex veins). In the model, the heart rate was varied from 60 bpm to 120 bpm (increment: 20 bpm). We assessed the ocular pulse amplitude (OPA), pulse volume, ONH deformations and the dynamic modulus of the LC at different heart rates.

Results

With an increasing heart rate, the OPA decreased by 0.04 mmHg for every 10 bpm increase in heart rate. The ocular pulse volume decreased linearly by 0.13 µL for every 10 bpm increase in heart rate. The storage modulus and the loss modulus of the LC increased by 0.014 MPa and 0.04 MPa, respectively, for every 10 bpm increase in heart rate.

conclusions

In our model, the OPA, pulse volume, and ONH deformations decreased with an increasing heart rate, while the LC became stiffer. The effects of blood pressure / heart rate changes on ONH stiffening may be of interest for glaucoma pathology.

Support

Singapore Ministry of Education, Academic Research Fund, Tier 2 (R-397-000-280-112).

Commercial relationship

None
The social dynamics of collective problem-solving
Authors: Yahosseini Kyanoush Seyed , Moussaïd Mehdi
Published: September 2019

When searching for solutions to a problem, people often rely on the observation of their peers. How does this process of social learning impact the individual and the group’s performance? On the one hand, research has shown that individuals benefit from social learning in numerous situations and across many domains. Through social learning, individuals can access good solutions found by others, improve them, and share them in turn. On the other hand, this individual benefit may come at a cost: An excessive tendency to copy others often decreases the overall exploration volume of the group, thus reducing the diversity of discovered solutions, and eventually impairing the collective performance.

Here we investigate the conditions under which social learning can be beneficial or detrimental to individuals and to the group. For that, we model problem-solving as a search task and simulate various amounts of social learning. We avoid model specific considerations by relying on a simple framework whereby individuals gradually explore the search environment – a two-dimensional landscape of solutions – while being attracted to the best solution of the group.

Our results highlight a collective search dilemma: When group members learn from one another, they tend to improve their own individual performance at the expense of the collective performance. How is this dilemma affected by the structure of the search environment? By varying two structural aspects of the search environment, our results reveal that the negative effect of the dilemma is mitigated in more difficult environments.

Finally, we show that single individuals can profit from a high propensity of social learning, which in turn is damaging for the other group members. As a consequence, if individuals continually adapt their behavior to maximize their own payoff, groups converge to a sub-optimal level of social learning. Unraveling these intricate social dynamics helps to understand the complex picture of collective problem-solving.
Controlling septum thickness by a large protein ring
Authors: Wenzel Michaela , Celik Gulsoy Ilkay N. , Gao Yongqiang , Willemse Joost , van Rosmalen Mariska G. M. , Wuite Gijs J. L. , Roos Wouter H. , Hamoen Leendert W.
Published: September 2019

Gram-positive bacteria divide by forming a thick cross wall. How the thickness of this septal wall is controlled is unknown. In this type of bacteria, the key cell division protein FtsZ is anchored to the cell membrane by two proteins, FtsA and SepF. We have isolated SepF homologues from different bacterial species and found that they all polymerize into large protein rings with diameters varying from 19 to 41 nm. Importantly, these values correlated well with the thickness of their septa. To test whether ring diameter determines septal thickness, we tried to construct different SepF chimeras with the purpose to manipulate the diameter of the SepF protein ring. This was indeed possible and confirmed that the conserved core domain of SepF determines ring diameter. Importantly, when SepF chimeras with a smaller diameter were expressed in the bacterial host Bacillus subtilis, the thickness of its septa also became smaller. These results strongly support a model in which septal thickness is controlled by curved molecular clamps formed by SepF polymers attached to the leading edge of nascent septa. This also implies that the intrinsic shape of a protein polymer can function as a mould to shape the cell wall.

Significance Statement

Many bacteria form a thick cell wall and divide by forming a cross wall. How they control the thickness of their cell wall and cross wall is unknown. In this study we show that in these bacteria the cell division protein SepF forms very large protein rings with diameters that correspond to the diameter of their cross walls. Importantly, when we reduced the diameter of SepF rings in the bacterial host Bacillus subtilis the cross wall also became thinner. These results provide strong evidence that a large protein ring can function as a mould to control the thickness of the cell wall that divides these bacterial cells.