bluuebunny/crossref_metadata_2025 huggingface dataset:
STI policies in the Dominican Republic: the influence of economic rationales from a context-development perspective
Authors: Gómez-Valenzuela Víctor
Published: March 2020

This article examines the influence of different economic rationales in the Dominican Republic’s science, technology, and innovation (STI) policies from a context-development perspective. For this purpose, four STI policy frameworks are reviewed: the National Competitiveness Plan; the Strategic Plan of Science, Technology, and Innovation; the Ten-year Plan of Higher Education; and the National Development Strategy 2030. Three cycles of STI policies are covered: the industrialization and import substitution cycle; the structural adjustment cycle; and the post-structural adjustment cycle. Five economic rationales are considered: neoclassical, Schumpeterian growth, neo-Marshallian, systemic–institutional, and evolutionary thought. Based on the results, three rationales prevail a systemic–institutional approach; a neo-Marshallian perspective; and a Schumpeterian growth approach. These rationales may refer to the country’s challenges to spur its potential for economic growth and development.
Staffing Trends in Magnet and Non-Magnet Hospitals After State Legislation
Authors: de Cordova Pamela B. , Jones Terry , Riman Kathryn A. , Rogowski Jeannette , McHugh Matthew D.
Published: March 2020

Background:

Evidence suggests that Magnet and non-Magnet hospitals differ with respect to quality of care.

Purpose:

Our study examined registered nurse (RN) staffing over time in Magnet and non-Magnet hospitals using unit-level, publicly available data in New Jersey.

Methods:

A secondary analysis of longitudinal RN staffing data was conducted using mandated, publicly reported data of 64 hospitals representing 12 nursing specialties across 8 years (2008-2015). Staffing ratios were trended over time to compare RN staffing changes in Magnet and non-Magnet hospitals.

Results:

Staffing was comparable in Magnet and non-Magnet hospitals for 9 of 12 specialties. On average, from 2008 until 2015, RN staffing slightly increased, with a greater percent increase in Magnet hospitals (6.9%) than in non-Magnet hospitals (4.7%).

Conclusions:

Over 8 years in New Jersey, RN staffing improved in Magnet and non-Magnet hospitals. Although there was a slight increase for Magnet hospitals, there was no meaningful difference in staffing for all 12 specialties.
Using Palliative Care Nurses in a Supportive Care Program to Reduce Hospital Utilization for Patients With Multiple Chronic Conditions
Authors: Allen Alicia , Frederick Logan , Hovey Susan L.
Published: March 2020

Background:

Health care organizations are designing comprehensive care programs to reduce hospital utilization by high-risk patients with multiple chronic illnesses.

Local Problem:

A community hospital recognized patients with multiple chronic conditions had higher rates of inpatient stays and emergency department (ED) visits.

Methods:

Patients (n = 36) with multiple chronic conditions enrolled in a supportive care program. Researchers analyzed hospital utilization, inpatient stays, and ED visits preintervention and postgraduation for the participants enrolled. Palliative care nurses were assigned to patients enrolled in the supportive care program.

Results:

There was a statistically significant decrease in hospital utilization (Z = −2.540, P = .011) and inpatient stays (Z = −4.037, P < .001) following the implementation of the supportive care program.

Conclusions:

The study met its aim of reducing hospital utilization and inpatient stays by creating a comprehensive approach to support high-risk patients in self-management of their chronic illnesses.
Daily Practice of Mechanical Ventilation and Weaning in Turkish PICUs: A Multicenter Prospective Survey
Authors: Tekgüç Hakan , Can Fulya Kamit , Şik Güntülü , Demirkol Demet , Özel Deniz , Yaman Ayhan , Işgüder Rana , Yildiztaş Dinçer , Yener Nazik A , Öztürk Nilufer Y. , Karaarslan Utku , Erdoğan Seher , Yazci Pinar , Dinleyici Ener C. , Dalkiran Tahir , Şevketoğlu Esra , Anil Ayse Berna , Çitak Agop , Aygün Fatih , Kendirli Tanil , Ağin Hasan , Horoz Ozden O. , Paksu Şükrü , İnceköy Feyza G. , Davutoğlu Mehmet , Köroğlu Tolga , Boşnak Mehmet , Karapinar Bülent , Dursun Oğuz
Published: March 2020

Objectives:

To investigate conventional mechanical ventilation weaning characteristics of patients requiring conventional mechanical ventilation support for greater than 48 hours within the PICU.

Design:

The prospective observational multicenter cohort study was conducted at 15 hospitals. Data were being collected from November 2013 to June 2014, with two designated researchers from each center responsible for follow-up and data entry.

Setting:

Fifteen tertiary PICUs in Turkey.

Patients:

Patients between 1 month and 18 years old requiring conventional mechanical ventilation for greater than 48 hours were included. A single-center was not permitted to surpass 20% of the total sample size. Patients with no plans for conventional mechanical ventilation weaning were excluded.

Interventions:

Conventional mechanical ventilation

Measurements and Main Results:

Pertinent variables included PICU and patient demographics, including clinical data, chronic diseases, comorbid conditions, and reasons for intubation. Conventional mechanical ventilation mode and weaning data were characterized by daily ventilator parameters and blood gases. Patients were monitored until hospital discharge. Of the 410 recruited patients, 320 were included for analyses. A diagnosis of sepsis requiring intubation and high initial peak inspiratory pressures correlated with a longer weaning period (mean, 3.65 vs 1.05–2.17 d; p < 0.001). Conversely, age, admission Pediatric Risk of Mortality III scores, days of conventional mechanical ventilation before weaning, ventilator mode, and chronic disease were not related to weaning duration.

Conclusions:

Pediatric patients requiring conventional mechanical ventilation with a diagnosis of sepsis and high initial peak inspiratory pressures may require longer conventional mechanical ventilation weaning prior to extubation. Causative factors and optimal weaning for this cohort needs further consideration.
Prediction of Poor Outcomes for Septic Children According to Ferritin Levels in a Middle-Income Setting*
Authors: Tonial Cristian T. , Costa Caroline A. D. , Andrades Gabriela R. H. , Crestani Francielly , Einloft Paulo R. , Bruno Francisco , Miranda Ana P. , Fiori Humberto H. , Garcia Pedro Celiny R.
Published: March 2020

Objectives:

To evaluate serum ferritin measured within 48 hours of admission as a prognostic marker and examine the association with unfavorable outcomes in a population of pediatric patients with sepsis and high prevalence of iron deficiency anemia in which this biomarker is routinely measured.

Design:

Retrospective cohort study.

Setting:

PICU of a tertiary care teaching hospital in a middle-income country in South America.

Patients:

All patients 6 months to 18 years old (n = 350) admitted with a diagnosis of sepsis, suspected or proven, were eligible for inclusion. Exclusion criteria were length of PICU stay less than 8 hours and inherited or acquired disorder of iron metabolism that could interfere with serum ferritin levels.

Interventions:

None.

Measurements and Main Results:

Three-hundred twelve patients had their ferritin levels measured within 48 hours, and only 38 did not. The prevalence of iron deficiency anemia (hemoglobin < 11 g/dL and mean corpuscular volume < 80 fl was 40.3%. The median of the highest serum ferritin level within 48 hours was 150.5 ng/mL (interquartile range, 82.25–362 ng/mL), being associated with mortality (p < 0.001; Exp(B), 5.170; 95% CI, 2.619–10.205). A 10-fold increase in ferritin level was associated with a five-fold increase in mortality. There was a monotonic increase in mortality with increasing ferritin levels (p < 0.05). Regarding the discriminatory power of ferritin for mortality, the area under the receiver operating characteristic curve was 0.787 (95% CI, 0.737–0.83; p < 0.0001).

Conclusions:

Serum ferritin at lower thresholds predicts mortality in children with sepsis admitted to the ICU in a middle-income country with high prevalence of iron deficiency anemia.
Early Left Ventricular Dysfunction and Severe Pulmonary Hypertension Predict Adverse Outcomes in “Low-Risk” Congenital Diaphragmatic Hernia
Authors: Dao Duy T. , Patel Neil , Harting Matthew T. , Lally Kevin P. , Lally Pamela A. , Buchmiller Terry L.
Published: March 2020

Objectives:

Given significant focus on improving survival for “high-risk” congenital diaphragmatic hernia, there is the potential to overlook the need to identify risk factors for suboptimal outcomes in “low-risk” congenital diaphragmatic hernia cases. We hypothesized that early cardiac dysfunction or severe pulmonary hypertension were predictors of adverse outcomes in this “low-risk” congenital diaphragmatic hernia population.

Design:

This is a retrospective cohort study using data from the Congenital Diaphragmatic Hernia Study Group registry. “Low-risk” congenital diaphragmatic hernia was defined as Congenital Diaphragmatic Hernia Study Group defect size A/B without structural cardiac and chromosomal anomalies. Examined risk factors included left ventricular dysfunction, right ventricular dysfunction, and severe pulmonary hypertension on the first postnatal echocardiogram. The primary outcome was composite adverse events, defined as either death, extracorporeal membrane oxygenation utilization, oxygen requirement on day 30 of life, or hospitalization greater than or equal to 8 weeks. Multivariable adjustment was performed with logistic regression and inverse probability weighting.

Setting:

Neonatal index hospitalization for congenital diaphragmatic hernia.

Patients:

“Low-risk” congenital diaphragmatic hernia infants born between January 2015 and December 2018.

Interventions:

First postnatal echocardiogram performed within 24 hours from birth.

Measurements and Main Results:

Seven-hundred seventy-eight patients were identified as “low-risk” congenital diaphragmatic hernia. Left ventricular dysfunction, right ventricular dysfunction, and severe pulmonary hypertension were present in 10.8%, 20.5%, and 57.5%, respectively. The primary outcome occurred in 21.3%. Death occurred in 3.0% and 9.1% used extracorporeal membrane oxygenation. On unadjusted analysis, all three risk factors were associated with the primary outcome. On all multivariable adjustment methods, left ventricular dysfunction and severe pulmonary hypertension remained significant predictors of adverse outcomes while right ventricular dysfunction no longer demonstrated any effect.

Conclusions:

Early left ventricular dysfunction and severe pulmonary hypertension are independent predictors of adverse outcomes among “low-risk” congenital diaphragmatic hernia infants. Early recognition may lead to interventions that can improve outcome in this at-risk cohort.
Classification of sinonasal pathology associated with dental pathology or dental treatment
Authors: Pardal-Peláez Beatriz , Pardal-Refoyo José Luis , Montero-Martín Javier , González-Serrano José , López-Quiles-Martínez Juan
Published: March 2020

Background

As is known, the pathologies of the posterior teeth in the first and second quadrant and their treatments can be associated with pathology of the maxillary sinus. Both implant and pre-implant surgery have increased their incidence. It is necessary, therefore, to address sinonasal pathology (SN) related to dental pathology (DP) or dental treatments (DT) from an interdisciplinary point of view by establishing collaborative working groups between Dentistry (DEN) and Otolaryngology (ENT), as well as by developing registries and establishing coordinated diagnosis and treatment protocols of sinonasal pathology. The aim of this study is to design a useful classification of SN pathology associated with DP or DT to record information of DEN and ENT.

Material and methods

Bibliographic review and design of a classification system of SN, DP and DT pathology.

Results

Six categories are described in our system: 0- absence of SN pathology and DP; 1 and 4- patients with DP associated or associated with SN pathology, respectively; 2 and 5- patients with DT not associated or associated with SN pathology, respectively and 3- patients with SN pathology without DP. The classification has applications in diagnosis (association and possible causal relationship between the SN pathology and DP) and in the treatment of NS and DP simultaneously or sequentially.

Conclusions

The classification proposed integrates the presence or absence of DP or DT, and its causal association or the lack of it with SN pathology. Moreover, it facilitates the communication between DEN and ENT and eases the registration of information and the planning of dental, implant and pre-implant treatments.
Clinical Efficacy and Target Engagement of Glutamatergic Drugs: Placebo-Controlled RCTs of Pomaglumetad and TS-134 for Reversal of Ketamine-Induced Psychotic Symptoms and PharmacoBOLD in Healthy Volunteers
Authors: Kantrowitz Joshua T. , Grinband Jack , Goff Donald C. , Lahti Adrienne C. , Marder Stephen R. , Kegeles Lawrence S. , Girgis Ragy R. , Sobeih Tarek , Wall Melanie M. , Choo Tse-Hwei , Green Michael F. , Yang Yvonne S. , Lee Junghee , Horga Guillermo , Krystal John H. , Potter William Z. , Javitt Daniel C. , Lieberman Jeffrey A.
Published: March 2020

We tested two metabotropic glutamate receptor 2/3 (mGluR2/3) agonist prodrugs – pomaglumetad (POMA) and TS-134 – including a high-dose of POMA that was four times the dose tested in the failed phase schizophrenia III trials – in two proof of mechanism, Phase Ib studies using identical pharmacoBOLD target-engagement methodology.

The POMA study was a double-blind, NIMH-sponsored, 10-day study of 80 or 320 mg/d POMA or placebo (1:1:1 ratio), designed to detect d>0.8 sd between-group effect-size differences. The TS-134 study was a single-blind, industry-sponsored, 6-day study of 20 or 60 mg/d TS-134 or placebo (5:5:2 ratio), designed to permit effect-size estimation for future studies. Primary outcomes were ketamine-induced changes in pharmacoBOLD in the dorsal anterior cingulate cortex (dACC) and Brief Psychiatric Rating Scale (BPRS).

95 healthy controls were randomized to POMA and 63 to TS-134. High-dose POMA had significant within and between-group reduction in ketamine-induced BPRS total symptoms (p<0.01, d=-0.41; p=0.04, d=-0.44, respectively) but neither POMA dose significantly suppressed ketamine-induced dACC pharmacoBOLD. In contrast, low-dose TS-134 had significant/trend level, moderate to large within and between group effects on BPRS positive symptoms (p=0.02, d=-0.36; p=0.008, d=-0.82, respectively) and dACC pharmacoBOLD (p=0.004, d=-0.56; p=0.079, d=-0.50, respectively) using pooled across-study placebo data.

High-dose POMA exerted significant effects on clinical symptoms, but not on target engagement, suggesting a higher dose may yet be needed. TS-134 20 mg showed evidence of symptom reduction and target engagement, indicating a curvilinear dose-response curve. These results warrant further investigation of mGluR2/3 and other glutamate-targeted treatments for schizophrenia.
Inhibition of SARS-CoV-2 infection (previously 2019-nCoV) by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion
Authors: Xia Shuai , Liu Meiqin , Wang Chao , Xu Wei , Lan Qiaoshuai , Feng Siliang , Qi Feifei , Bao Linlin , Du Lanying , Liu Shuwen , Qin Chuan , Sun Fei , Shi Zhengli , Zhu Yun , Jiang Shibo , Lu Lu
Published: March 2020

The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be confirmed. Therefore, we herein used a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed plasma membrane fusion capacity superior to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. We then generated a series of lipopeptides and found that the EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than that of EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, potently inhibiting replication of 4 live human coronaviruses, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by currently circulating SARS-CoV-2 and emerging SARSr-CoVs.
Complete genome sequence and analysis of nine Egyptian females with clinical information from different geographic regions in Egypt
Authors: ElHefnawi Mahmoud , Hegazy Elsayed , ElFiky Asmaa , Jeon Yeonsu , Jeon Sungwon , Bhak Jong , Metwally Fateheya Mohamed , Sugano Sumio , Horiuchi Terumi , Kazumi Abe , Blazyte Asta
Published: March 2020

Egyptians are at a crossroad between Africa and Eurasia, providing useful genomic resources for analyzing both genetic and environmental factors for future personalized medicine. Two personal Egyptian whole genomes have been published previously and here nine female whole genome sequences with clinical information have been added to expand the genomic resource of Egyptian personal genomes. Here we report the analysis of whole genomes of nine Egyptian females from different regions using Illumina short-read sequencers. At 30x sequencing coverage, we identified 12 SNPs that were shared in most of the subjects associated with obesity which are concordant with their clinical diagnosis. Also, we found mtDNA mutation A4282G is common in all the samples and this is associated with chronic progressive external ophthalmoplegia (CPEO). Haplogroup and Admixture analyses revealed that most Egyptian samples are close to the other north Mediterranean, Middle Eastern, and European, respectively, possibly reflecting the into-Africa influx of human migration. In conclusion, we present whole-genome sequences of nine Egyptian females with personal clinical information that cover the diverse regions of Egypt. Although limited in sample size, the whole genomes data provides possible geno-phenotype candidate markers that are relevant to the region’s diseases.
Filamentous Bacteriophage Delay Healing of Pseudomonas-Infected Wounds
Authors: Bach Michelle S. , de Vries Christiaan R. , Khosravi Arya , Sweere Johanna M. , Popescu Medeea , Van Belleghem Jonas D. , Kaber Gernot , Burgener Elizabeth B. , Liu Dan , Tran Quynh-Lam , Dharmaraj Tejas , Birukova Maria , Sunkari Vivekananda , Balaji Swathi , Ghosh Nandini , Mathew-Steiner Shomita S. , Keswani Sundeep G. , Banaei Niaz , Nedelec Laurence , Sen Chandan K. , Chandra Venita , Secor Patrick R. , Suh Gina A. , Bollyky Paul L.
Published: March 2020

We have identified a novel role for filamentous bacteriophage in the delayed healing associated with chronicPseudomonas aeruginosa (Pa)wound infections. Pf phage delays wound re-epithelialization in the absence of livePa,indicative that Pf effects on wound healing are independent ofPapathogenesis. Pf phage directly inhibits autocrine signaling of CXCL1 (KC) to impede keratinocyte migration and wound re-epithelization. In agreement with these studies, a prospective cohort study of 36 human patients with chronicPawound infections revealed that wounds infected with Pf positive strains ofPatook longer to heal and were more likely to increase in size compared to wounds infected with Pf negative strains. Together, these data implicate Pf phage in the delayed wound healing associated withPainfection through direct manipulation of mammalian target cells. We propose that Pf phage may have potential as a biomarker and therapeutic target in delayed wound healing.
Aging increases the systemic molecular degree of inflammatory perturbation in patients with tuberculosis
Authors: Oliveira-de-Souza Deivide , Vinhaes Caian L. , Arriaga María B. , Kumar Nathella Pavan , Queiroz Artur T. L. , Fukutani Kiyoshi F. , Babu Subash , Andrade Bruno B.
Published: March 2020

Tuberculosis (TB) in a chronic infection that can affect individuals of all ages. The description of determinants of immunopathogenesis in TB is a field of tremendous interest due to the perspective of finding a reliable host-directed therapy to reduce disease burden. The association between specific biomarker profiles related to inflammation and the diverse clinical disease presentations in TB has been extensively studied in adults. However, relatively scarce data on profiling the inflammatory responses in pediatric TB are available. Here, we employed the molecular degree of perturbation (MDP) score adapted to plasma biomarkers in two distinct databanks from studies that examined either adults or children presenting with pulmonary or extrapulmonary disease. We used multidimensional statistical analyses to characterize the impact of age on the overall changes in the systemic inflammation profiles in subpopulation of TB patients. Our findings indicated that TB results in significant increases in MDP values, with the highest values being detected in adult patients. Furthermore, there were unique differences in the biomarker perturbation patterns and the overall degree of inflammation according to disease site and age. Importantly, the molecular degree of perturbation was not influenced by sex. Our results revealed that aging is an important determinant of the differences in quality and magnitude of systemic inflammatory perturbation in distinct clinical forms of TB.
Comparison of read mapping and variant calling tools for the analysis of plant NGS data
Authors: Schilbert Hanna Marie , Rempel Andreas , Pucker Boas
Published: March 2020

High-throughput sequencing technologies have rapidly developed during the past years and became an essential tool in plant sciences. However, the analysis of genomic data remains challenging and relies mostly on the performance of automatic pipelines. Frequently applied pipelines involve the alignment of sequence reads against a reference sequence and the identification of sequence variants. Since most benchmarking studies of bioinformatics tools for this purpose have been conducted on human datasets, there is a lack of benchmarking studies in plant sciences. In this study, we evaluated the performance of 50 different variant calling pipelines, including five read mappers and ten variant callers, on six real plant datasets of the model organismArabidopsis thaliana. Sets of variants were evaluated based on various parameters including sensitivity and specificity. We found that all investigated tools are suitable for analysis of NGS data in plant research. When looking at different performance metrices, BWA-MEM and Novoalign were the best mappers and GATK returned the best results in the variant calling step.
Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing to Define Immune Cell Chimerism in the Rejecting Kidney Transplant
Authors: Malone Andrew F. , Wu Haojia , Fronick Catrina , Fulton Robert , Gaut Joseph P. , Humphreys Benjamin D.
Published: March 2020

In solid organ transplantation, donor derived immune cells are assumed to decline with time after surgery. Whether donor leukocytes persist within kidney transplants or play any role in rejection is unknown, however, in part because of limited techniques for distinguishing recipient and donor cells. To address this question, we performed paired whole exome sequencing of donor and recipient DNA and single cell RNA sequencing (scRNA-seq) of 5 human kidney transplant biopsy cores. Exome sequences were used to define single nucleotide variations (SNV) across all samples. By analyzing expressed SNVs in the scRNA-seq dataset we could define recipient vs. donor cell origin for all 81,139 cells. The leukocyte donor to recipient ratio varied with rejection status for macrophages and with time post-transplant for lymphocytes. Recipient macrophages were characterized by inflammatory activation and donor macrophages by antigen presentation and complement signaling. Recipient origin T cells expressed cytotoxic and pro-inflammatory genes consistent with an effector cell phenotype whereas donor origin T cells are likely quiescent expressing oxidative phosphorylation genes relative to recipient T cells. Finally, both donor and recipient T cell clones were present within the rejecting kidney, suggesting lymphoid aggregation. Our results indicate that donor origin macrophages and T cells have distinct transcriptional profiles compared to their recipient counterparts and donor macrophages can persist for years post transplantation. This study demonstrates the power of this approach to accurately define leukocyte chimerism in a complex tissue such as the kidney transplant coupled with the ability to examine transcriptional profiles at single cell resolution.
Larger viral genome size facilitates emergence of zoonotic diseases
Authors: Grewelle Richard E.
Published: March 2020

Emergence of new viral diseases is linked to mutation or recombination events. The likelihood of cross-species transmission is related to phenotypic plasticity of a virus and its capacity to produce genetically variable progeny. Herein a model is described connecting the production of genetic variability with increasing genome size. Comparing all known zoonotic viral genome sizes to known non-zoonotic viral genome sizes demonstrates that zoonotic viruses have significantly larger genomes. These results support the notion that large viral genomes are important in producing new zoonotic disease, and suggest that genome size may be a useful surrogate in screening for potential zoonotic viruses.
Age-related trajectories of DNA methylation network markers: a parenclitic network approach to a family-based cohort of patients with Down Syndrome
Authors: Krivonosov M. , Nazarenko T. , Bacalini M.G. , Vedunova M.V. , Franceschi C. , Zaikin A. , Ivanchenko M.
Published: March 2020

Despite the fact that the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and the phenotype of accelerated aging remain largely unknown. DNA methylation profiles are largely altered in DS, but it remains unclear how different methylation regions and probes are structured into a network of interactions. We develop and generalize the Parenclitic Networks approach that enables finding correlations between distant CpG probes (which are not pronounced as stand-alone biomarkers) and quantifies hidden network changes in DNA methylation. DS and a familybased cohort (including healthy siblings and mothers of persons with DS) are used as a case study. Following this approach, we constructed parenclitic networks and obtained different signatures that indicate (i) differences between individuals with DS and healthy individuals; (ii) differences between young and old healthy individuals; (iii) differences between DS individuals and their age-matched siblings, and (iv) difference between DS and the adult population (their mothers). The Gene Ontology analysis showed that the CpG network approach is more powerful than the single CpG approach in identifying biological processes related to DS phenotype. This includes the processes occurring in the central nervous system, skeletal muscles, disorders in carbohydrate metabolism, cardiopathology, and oncogenes. Our open-source software implementation is accessible to all researchers. The software includes a complete workflow, which can be used to construct Parenclitic Networks with any machine learning algorithm as a kernel to build edges. We anticipate a broad applicability of the approach to other diseases.
The 16S microbiota of Budu, the Malaysian fermented anchovy sauce
Authors: Md Zoqratt Muhammad Zarul Hanifah , Gan Han Ming
Published: March 2020

Budu is a Malaysian fermented anchovy sauce produced by immersing small fishes into a brine solution for 6 to 18 months. Fermentation of the anchovy sauce is contributed partly by microbial enzymes, but little is known about the microbial community in Budu. Therefore, a better understanding of the Budu microbiome is necessary to better control the quality, consistency and safety of the product. In this study, we collected 60 samples from twenty bottles of Budu produced by seven different manufacturers. We analyzed their microbiota based on V3-V4 16S rRNA amplicon sequencing at the time of opening the bottle as well as 3- and 7-months post-opening.Tetragenococcuswas the dominant genus in many samples, reaching a maximum proportion of 98.62%, but was found in low abundance, or absent, in other samples. When Budu samples were not dominated by a dominant taxa, we observed a wider genera diversity such asStaphylococcus, Acinetobacter, HalanaerobiumandBacillus. While the taxonomic composition was relatively stable across sampling periods, samples from two brands showed a sudden increase in relative abundance of the genusChromobacteriumin the 7thmonth. Based on prediction of metagenome functions, non-Tetragenococcus-dominated samples were predicted to have enriched functional pathways related to amino acid metabolism and purine metabolism compared toTetragenococcus-dominated microbiome; these two pathways are fundamental fermented quality and health attributes of fish sauce. Within the non-Tetragenococcus-dominated group, contributions towards amino acid metabolism and purine metabolism were biased towards the dominant taxa when species evenness is low, while in samples with higher species evenness, the contributions towards the two pathways were predicted to be evenly distributed between taxa.
Pathogenic LRRK2 R1441C mutation is associated with striatal alterations
Authors: Xenias Harry S. , Chen Chuyu , Kang Shuo , Cherian Suraj , Situ Xiaolei , Shanmugasundaram Bharanidharan , Scesa Giuseppe , Chan C. Savio , Parisiadou Loukia
Published: March 2020

LRRK2 mutations are associated with both familial and sporadic forms of Parkinson’s disease (PD). Convergent evidence suggests that LRRK2 plays critical roles in regulating striatal function. Here, by using knock-in mouse lines that express the two most common LRRK2 pathogenic mutations—G2019S and R1441C—we investigated how pathogenic LRRK2 mutations altered striatal physiology. We found that R1441C mice displayed a reduced nigrostriatal dopamine release and hypoexcitability in indirect-pathway striatal projection neurons. These alterations were associated with an impaired striatal-dependent motor learning. This deficit in motor learning was rescued following the subchronic administration of the LRRK2 kinase inhibitor Mli-2. In contrast, though a decreased release of dopamine was observed in the G2019S knock-in mice no concomitant cellular and behavioral alterations were found. In summary, our data argue that the impact of LRRK2 mutations cannot be simply generalized. Our findings offer mechanistic insights for devising treatment strategies for PD patients.
Glucose-dependent activation, activity, and deactivation of beta cell networks in acute mouse pancreas tissue slices
Authors: Stožer Andraž , Klemen Maša Skelin , Gosak Marko , Bombek Lidija Križančić , Pohorec Viljem , Rupnik Marjan Slak , Dolenšek Jurij
Published: March 2020

Many details of glucose-stimulated intracellular calcium changes in beta cells during activation, activity and deactivation, as well as their concentration-dependence, remain to be described. Classical physiological experiments indicated that in islets functional differences between individual cells are largely attenuated, but recent findings suggest considerable intercellular heterogeneity, with some cells possibly coordinating the collective responses. To address the above with an emphasis on heterogeneity and describing the relations between classical physiological and functional network properties, we performed functional multicellular calcium imaging in mouse pancreas tissue slices over a wide range of glucose concentrations. During activation, delays to activation of cells and first responder-any cell delays shortened, and the sizes of simultaneously responding clusters increased with increasing glucose. Exactly the opposite characterized deactivation. The frequency of fast calcium oscillations during activity increased with increasing glucose up to 12 mM glucose, beyond which oscillation duration became longer, resulting in a homogenous increase in active time. In terms of functional connectivity, islets progressed from a very segregated network to a single large functional unit with increasing glucose. A comparison between classical physiological and network parameters revealed that the first-responders during activation had longer active times during plateau and the most active cells during the plateau tended to deactivate later. Cells with the most functional connections tended to activate sooner, have longer active times, and deactivate later. Our findings provide a common ground for recent differing views on beta cell heterogeneity and an important baseline for future studies of stimulus-secretion and intercellular coupling.
Binding dynamics of alpha-actinin-4 in dependence of actin cortex tension
Authors: Hosseini K. , Sbosny Leon , Poser Ina , Fischer-Friedrich E.
Published: March 2020

Mechano-sensation of cells is an important prerequisite for cellular function, e.g. in the context of cell migration, tissue organisation and morphogenesis. An important mechano-chemical-transducer is the actin cytoskeleton. In fact, previous studies have shown that actin cross-linkers, such asα-actinin-4, exhibit mechanosensitive properties in its binding dynamics to actin polymers. However, to date, a quantitative analysis of tension-dependent binding dynamics in live cells is lacking. Here, we present a new technique that allows to quantitatively characterize the dependence of cross-linking lifetime of actin cross-linkers on mechanical tension in the actin cortex of live cells. We use an approach that combines parallel plate confinement of round cells, fluorescence recovery after photo-bleaching, and a mathematical mean-field model of cross-linker binding. We apply our approach to the actin cross-linkerα-actinin-4 and show that the cross-linking time ofα-actinin-4 homodimers increases approximately twofold within the cellular range of cortical mechanical tension renderingα-actinin-4 a catch bond in physiological tension ranges.
Inhibition of KDM1A activity restores adult neurogenesis and improves hippocampal memory in a mouse model of Kabuki syndrome
Authors: Zhang Li , Pilarowski Genay , Pich Emilio Merlo , Nakatani Atsushi , Dunlop John , Baba Rina , Matsuda Satoru , Daini Masaki , Hattori Yasushi , Matsumoto Shigemitsu , Ito Mitsuhiro , Kimura Haruhide , Bjornsson Hans Tomas
Published: March 2020

Kabuki syndrome (KS) is a rare cause of intellectual disability primarily caused by loss of function mutations in lysine-specific methyltransferase 2D (KMT2D), which normally adds methyl marks to lysine 4 on histone 3. Previous studies have shown that a mouse model of KS (Kmt2d+/βGeo) demonstrates disruption of adult neurogenesis and hippocampal memory. Proof-of-principle studies have shown postnatal rescue of neurological dysfunction following treatments that promote chromatin opening, however, these strategies are non-specific and do not directly address the primary defect of histone methylation. Since lysine-specific demethylase 1A (LSD1/KDM1A) normally removes the H3K4 methyl marks added by KMT2D, we hypothesize that inhibition of KDM1A demethylase activity may ameliorate molecular and phenotypic defects stemming from KMT2D loss. To test this hypothesis, we evaluated a recently developed KDM1A inhibitor (TAK-418) inKmt2d+/βGeomice. We find that orally administered TAK-418 increases the numbers of newly born Doublecortin (DCX)+cells and processes in hippocampus in a dose dependent manner. We also observe TAK-418-dependent rescue of histone modification defects in hippocampus both by Western blot and ChIP-Seq. Treatment rescues gene expression abnormalities including those of immediate early genes such as FBJ osteosarcoma oncogene (Fos)and FBJ osteosarcoma oncogene homolog B (Fosb). After 2 weeks of TAK-418,Kmt2d+/βGeomice demonstrate normalization of hippocampal memory defects. In summary, our data suggest that KDM1A inhibition is a plausible treatment strategy for KS and support the hypothesis that the epigenetic dysregulation secondary to KMT2D dysfunction plays a major role in the postnatal neurological disease phenotype in KS.
Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aureliaspp.)
Authors: Lacaux Céline , Desolneux Agnès , Gadreaud Justine , Martin-Garin Bertrand , Thiéry Alain
Published: March 2020

Abstract

Variations of the animal body plan morphology and morphometry can be used as prognostic tools of their habitat quality. The potential of the moon jellyfish (Aureliaspp.) as a new model organism has been poorly tested. However, as a tetramerous symmetry organism, it exhibits some variations in radial symmetry number. A pertinent list of morphological – number of gonads – and morphometric characteristics – e.g. ratio of the gonads area on the umbrella area – has been established to describe the morphology of 19 specimens through an image analysis. The method uses for the first time the Hough transform to approximate the gonads and the umbrella by ellipses and automatically extracts the morphometric data. A statistical comparison has been done to compare the morphometric characteristics of tetramerous jellyfish and of jellyfish with 5 gonads: it is only provided as a first step for testing biological hypotheses, since the small size of the data set leads to relativize its conclusions. It suggests that two parameters are discriminant: distance between the center of the gonads and the center of the umbrella, and the individual variability of the gonad eccentricity, both higher in jellyfish with 5 gonads. Additionally, the relative size of the gonads does not seem to be different between tetramerous and non-tetramerous. Combined to ecotoxicological bioassays to better understand the causes of this developmental alteration, this optimizable method can become a powerful tool in the symmetry description of anin situpopulation.
An Assay for Apoptosis detection based on Quantification of Multi nuclei feature and Nucleus to Cytoplasm ratio inS. cerevisiaecells treated with Acetic Acid and Hydrogen peroxide
Authors: Bairwa Narendra K , Shoket Heena , Pandita Monika , Sharma Meenu
Published: March 2020

The programmed cell death, apoptosis is a complex universal biological process in all types of eukaryotes ranging from single cell to multi-cellular organisms. The markers for apoptosis have been studied by assays based on both biochemical as well as microscopy however most assays are not affordable for many smaller labs. Acetic acid and hydrogen peroxide both induce apoptosis at higher concentrations inS. cerevisiae.Here we describe an assay system for the detection of apoptosis features based on DAPI staining followed by fluorescence microscopy in the cells treated with apoptosis inducing concentration of acetic acid and hydrogen peroxide. In this assay both untreated and cells treated with acetic acid and hydrogen peroxide were stained with DAPI and observed for the late stage apoptosis feature, Nuclear DNA fragmentation based multi nuclei centers and increase in the nuclear region enlargement. Further the multi nuclei feature and enlarged nuclei region as nucleus to cytoplasm ratio was quantified using Image J software. We report thatS. cerevisiaestrain BY4741 cells when treated with apoptosis inducing doses of acetic acid (140mM) and hydrogen peroxide (10mM) for 200 minutes, showed apoptosis marker feature such as nuclear region enlargement with multi-nuclei feature due to nuclear DNA fragmentation and increased nucleus to cytoplasm ratio when compared with untreated cells. We propose that this assay can be utilized for scoring the quantitative apoptotic feature as increase in multi-nuclei centers due to DNA fragmentation and nucleus to cytoplasm ratio as an indicator of apoptosis inS. cerevisiaeupon treatment with apoptosis inducing agents. The assay system described here is easy to perform and affordable for the smaller lab to analyze the apoptotic features inS. cerevisiaecells which can be applied to other system as well.
Endogenous retroviruses drive species-specific germline transcriptomes in mammals
Authors: Sakashita Akihiko , Maezawa So , Alavattam Kris G. , Yukawa Masashi , Barski Artem , Pavlicev Mihaela , Namekawa Satoshi H.
Published: March 2020

Gene regulation in the germline ensures the production of high-quality gametes, long-term maintenance of the species, and speciation. Germline transcriptomes undergo dynamic changes after the mitosis-to-meiosis transition in males and have been subject to evolutionary divergence among mammals. However, the mechanism that underlies germline regulatory divergence remains undetermined. Here, we show that endogenous retroviruses influence species-specific germline transcriptomes in mammals. We show that the expression of endogenous retroviruses, particularly the evolutionarily young K family (ERVK), is associated with gene activation after the mitosis-to-meiosis transition in male mice. We demonstrate that accessible chromatin and H3K27ac, a marker of active enhancers, are tightly associated with ERVK loci as well as with the activation of neighboring evolutionarily young germline genes. Thus, ERVKs serve as evolutionarily novel enhancers in mouse spermatogenesis. These ERVK loci bear binding motifs for critical regulators of spermatogenesis such as A-MYB. The genome-wide transposition of ERVKs might have rewired germline gene expression in a species-specific manner. Notably, these features are present in human spermatogenesis, but independently evolved ERVs are associated with expression of germline genes, demonstrating the prevalence of ERV-driven mechanisms in mammals. Together, we propose a model whereby species-specific transcriptomes are fine-tuned by endogenous retroviruses in the mammalian germline.
Membrane-proximal external region is a superior target for mediating effector activity of HIV-1 specific chimeric antigen receptor modified T cells
Authors: Kranz Emiko , Chan Joshua , Hashimoto Maya , Kanazawa Toshio , Wang Hanlu , Kamata Masakazu
Published: March 2020

The use of chimeric antigen receptor modified-T (CAR-T) cells in adoptive immunotherapy has been popularized through recent success in the field of cancer treatment research. CD4ζ CAR, which targets HIV-1-infected cells, has been developed and evaluated in patients. Though well-tolerated for over a decade, efficacy was disappointingly limited. This result encourages us to develop a novel CAR more effective than CD4ζ CAR. To quantitatively compare anti-HIV-1 activity of different CAR constructs in a highly sensitive and reproducible manner, we developed a multicolor flow cytometry method for assessing anti-HIV-1 effector T-cell activity. “Target” Jurkat cells inducibly expressing an HIV-1HXBC2envelope protein and “Non-target” control cells were genetically labeled with red and blue fluorescent protein, respectively, and co-incubated with human primary T cells transduced with anti-HIV-1 “Effector” CARs at various Effector vs Target cell ratios. Absolute cell numbers of each population were collected by MACSQuant Analyzer and used for calculation of relative cytotoxicity. We successfully ranked the cytotoxicity of three previously reported single chain-antibody CARs and six newly developed single-domain antibody CARs in comparison to CD4ζ CAR. Interestingly, three CARs—10E8, 2E7, and 2H10—which demonstrate high cytotoxic activity were all known to target the membrane-proximal external region. Use of this novel assay will simplify assessment of new CAR constructs and in turn accelerate the development of new effective CARs against HIV-1.

Author Summary

Adoptive immunotherapies that utilize autologous T cells expressing a desired antigen-specific CAR aim to elicit directed immune responses. In recent years, CAR immunotherapies have been promoted extensively in B cell malignancy treatments. The HIV-1-targeting CAR, known as CD4ζ, was developed over 20 years ago and has been widely and longitudinally tested in patients. However, its effectiveness was hindered by poor survival and functionality of the transduced cells. To conduct quantitative evaluation of newly designed anti-HIV-1 CARs, we developed a novel multicolor flow-based assay for HIV-1-specific cytotoxicity, enabling sensitive and quantitative assessment in a high-throughput fashion. This assay would be also useful in screening HIV-1-targeting immune receptors—including CARs and T cell receptors—and other immunotherapeutic drugs such as anti-HIV-1 antibodies.
An approach to stress assessment during hunting: Cortisol levels of wild boar (Sus scrofa) during drive hunts
Authors: Güldenpfennig Justine , Schmicke Marion , Hoedemaker Martina , Siebert Ursula , Keuling Oliver
Published: March 2020

Only little is known about the effect of stress (both short-term and long-term) on wildlife species. To get an idea of stress in wildlife, we investigated the cortisol level of wild boar during drive hunts in Lower Saxony, Germany. Cortisol as one of the main stress hormone in mammals is considered to have negative impacts on the animal’s well-being if expressed excessively (repeatedly over a longer period). We analysed serum cortisol levels of 115 samples using a radioimmunoassay and compared sampling month, hunting grounds, age classes and sexes, as well as possible correlations between cortisol level and weight and pregnancy status of female wild boar. We found that cortisol levels during these drive hunts exhibit wide variation. The mean cortisol level was 411.16 nmol/L with levels ranging from 30.60 nmol/L (minimum) to 1,457.92 nmol/L (maximum). Comparing age groups and sexes, we found significant differences between the sexes, with females having a higher cortisol levels than males. After grouping age groups and sexes together, we also found significant differences based on the age-sex group. We found no correlation between cortisol levels and weight, but significantly higher cortisol levels in pregnant females compared to non-pregnant females. No differences were found between sampling months and locations, respectively. These results show the impact of drive hunts on stress in wild boar; nevertheless, this impact of drive hunts as performed in most parts of Central Europe seems to be not as high as imagined. Still, we need more information about cortisol levels and stress in (hunted) wildlife species.