bluuebunny/crossref_metadata_2025 huggingface dataset:
Degradability, in vitro fermentation parameters, and kinetic degradation of diets with increasing levels of forage and chitosan
Authors: Jacaúna Amanna Gonzaga , de Goes Rafael Henrique de Tonissi e Buschinelli , Seno Leonardo de Oliveira , Ítavo Luis Carlos Vinhas , Gandra Jefferson Rodrigues , da Silva Nayara Gonçalves , Anschau Douglas Gabriel , de Oliveira Raquel Tenório , Bezerra Leilson Rocha , Oliveira Ronaldo Lopes
Published: May 2021

Chitosan is the second most important natural biopolymer in the world, extracted from crustaceans, shrimps, and crabs and can modulate rumen fermentation. Our hypothesis is that the addition of chitosan alters the fermentation patterns of different diets for ruminants. This study aimed to evaluate the effects of different levels of chitosan and forage on in vitro dry degradation kinetics and fermentation in a gas production system. The chitosan levels (0, 1625, 3,500, or 7,500 mg/kg of dry matter [DM]) were arranged in a completely randomized block design, and for in vitro ruminal fermentation assay, we used a split splot arrangement. Into the incubator, all chitosan levels were distributed in the four jars, and the forage levels varying on 100, 65, 50, 35, and 20 on DM basis. There was an interaction effect for chitosan and forage levels (P ≤ 0.05) on IVDMD; IVOMD. IVDCP and IVDNDF. Chitosan negatively affected IVDMD in all roughage levels evaluated. The pH and ammonia concentration present effect only for roughage levels and incubation hours. The chitosan did not change (P = 0.3631) the total short-chain fatty acid concentration (overall mean = 21.19 mmol/L) and the C2:C3 ratio (overall mean = 5.85). The IVDCP showed the same decreasing quadratic behavior (P < 0.0001). The increasing chitosan addition increases (P < 0.0001) the gas production and decreases (P < 0.0001) the lag time (parameter C) of diets with greater concentrate participation, characterizing greater efficiency in the degradability of the diet, confirming its potential use in diets for ruminants. Chitosan changes in vitro dry degradation kinetics and fermentation at the minimum dose of 1,722 mg/kg DM for all diets. The roughage level influenced the in vitro nutrients degradability and cumulative gas production.
Genome Sequence Resource of Phytophthora colocasiae from China Using Nanopore Sequencing Technology
Authors: Wang Zhixin , Bao Jiandong , Lv Lin , Lin Lianyu , Li Zhiting , Shi Mingyue , Huang Yuting , Wang Rongbo , Li Benjin , Liu Peiqing , Chen Qinghe
Published: May 2021

Phytophthora colocasiae is a destructive oomycete pathogen of taro (Colocasia esculenta), which causes taro leaf blight. To date, only one highly fragmented Illumina short-read-based genome assembly is available for this species. To address this problem, we sequenced strain Lyd2019 from China using Oxford Nanopore Technologies long-read sequencing and Illumina short-read sequencing. We generated a 92.51-Mb genome assembly consisting of 105 contigs with an N50 of 1.70 Mb and a maximum length of 4.17 Mb. In the genome assembly, we identified 52.78% repeats and 18,322 protein-coding genes, of which 12,782 genes were annotated. We also identified 191 candidate RXLR effectors and 1 candidate crinkling and necrosis effector. The updated near-chromosome genome assembly and annotation resources will provide a better understanding of the infection mechanisms of P. colocasiae.
Triple Challenge: How Medical Students May Solve 3 Long-Standing Problems Bedeviling Health Systems and Medical Education
Authors: Elliott Victoria Stagg , Jackson Jasmyne , Santen Sally A. , Richardson Judee , Heckman Kevin , Hammoud Maya M.
Published: May 2021

Medical education and the health system must address challenges that, despite significant effort, seem unsolvable. Health systems science (HSS)—the fundamental understanding of how care is delivered, how health professionals work together to deliver that care, and how the health system can improve patient care and health care delivery—is increasingly being recognized as a potential source of solutions to these challenges.

In this article, the authors review the 43 abstracts submitted to the American Medical Association Accelerating Change in Medical Education 2018 Health Systems Science Student Impact Competition that aligned with the goals of HSS. Their qualitative review identified 3 long-standing problems in medicine and medical education that were frequently addressed by the submissions: improving care for those with mental illness (5 submissions), improving diversity in medicine (4 submissions), and improving teamwork and interprofessional education (4 submissions). The authors extracted lessons learned from these abstracts.

Many of the projects detailed in this article continue to make an impact at multiple levels. While not all projects were scientifically rigorous enough to be published on their own and the quality of the data presented in the abstracts varied widely, many provide innovative ideas for potentially solving long-standing problems that may have been overlooked or not considered sufficiently.

These projects and their subsequent analysis demonstrate that not only do medical students make significant impacts on the health system, patients, and other health professionals when equipped with HSS skills, working in health care teams, and advised by mentors, but they also may be able to address some of medicine’s and medical education’s long-standing challenges. The fresh perspective and high energy of medical students are valuable and should be nurtured and encouraged.
Virtual Reality Tailored to the Needs of Post-ICU Patients: A Safety and Immersiveness Study in Healthy Volunteers
Authors: Vlake Johan H. , Wils Evert-Jan , van Bommel Jasper , Korevaar Tim I. M. , Gommers Diederik , van Genderen Michel E.
Published: May 2021

Objectives:

ICU treatments frequently result in long-term psychologic impairments, negatively affecting quality of life. An effective treatment strategy is still lacking. The aim of this study was to describe and evaluate the safety and immersiveness of a newly designed ICU-specific virtual reality module.

Design:

A randomized controlled healthy volunteer trial.

Setting:

ICU of the Franciscus Gasthuis & Vlietland Hospital (Rotterdam, the Netherlands), a large teaching hospital.

Participants:

Forty-five virtual reality–naive healthy volunteers.

Interventions:

Volunteers were randomized to three arms: the head-mounted display virtual reality group (n = 15), the 2D group (n = 15), and the crossover group (n = 15). Safety was assessed by changes in vital signs and the occurrence of simulator sickness (Simulator Sickness Questionnaire). Immersiveness was assessed using the Igroup Presence Questionnaire.

Measurements and Main Results:

Volunteers in the head-mounted display virtual reality group experienced more mild symptoms of simulator sickness, expressed as symptoms of dizziness (p = 0.04) and stomach awareness (p = 0.04), than the 2D group. Nevertheless, none of the individual Simulator Sickness Questionnaire items were scored as being severe, no changes in vital signs were observed, and no sessions were prematurely stopped. Volunteers in the crossover group experienced a higher total presence (p < 0.001) when using head-mounted display virtual reality, expressed as a higher sense of presence (p < 0.001), more involvement (p < 0.01), and more experienced realism (p < 0.001).

Conclusions:

ICU-specific virtual reality appears safe and more immersive than 2D, implicating that ICU-specific virtual reality is feasible for clinical use. One should however be aware of simulator sickness-related symptoms. Future research is needed to confirm these findings in survivors of critical illness.
Leukocyte Activation Profile Assessed by Raman Spectroscopy Helps Diagnosing Infection and Sepsis
Authors: Ramoji Anuradha , Thomas-Rüddel Daniel , Ryabchykov Oleg , Bauer Michael , Arend Natalie , Giamarellos-Bourboulis Evangelos J. , Eugen-Olsen Jesper , Kiehntopf Michael , Bocklitz Thomas , Popp Jürgen , Bloos Frank , Neugebauer Ute
Published: May 2021

Objectives:

Leukocytes are first responders to infection. Their activation state can reveal information about specific host immune response and identify dysregulation in sepsis. This study aims to use the Raman spectroscopic fingerprints of blood-derived leukocytes to differentiate inflammation, infection, and sepsis in hospitalized patients. Diagnostic sensitivity and specificity shall demonstrate the added value of the direct characterization of leukocyte’s phenotype.

Design:

Prospective nonrandomized, single-center, observational phase-II study (DRKS00006265).

Setting:

Jena University Hospital, Germany.

Patients:

Sixty-one hospitalized patients (19 with sterile inflammation, 23 with infection without organ dysfunction, 18 with sepsis according to Sepsis-3 definition).

Interventions:

None (blood withdrawal).

Measurements AND MAIN RESULTS:

Individual peripheral blood leukocytes were characterized by Raman spectroscopy. Reference diagnostics included established clinical scores, blood count, and biomarkers (C-reactive protein, procalcitonin and interleukin-6). Binary classification models using Raman data were able to distinguish patients with infection from patients without infection, as well as sepsis patients from patients without sepsis, with accuracies achieved with established biomarkers. Compared with biomarker information alone, an increase of 10% (to 93%) accuracy for the detection of infection and an increase of 18% (to 92%) for detection of sepsis were reached by adding the Raman information. Leukocytes from sepsis patients showed different Raman spectral features in comparison to the patients with infection that point to the special immune phenotype of sepsis patients.

Conclusions:

Raman spectroscopy can extract information on leukocyte’s activation state in a nondestructive, label-free manner to differentiate sterile inflammation, infection, and sepsis.
Optimizing Critical Illness Recovery: Perspectives and Solutions From the Caregivers of ICU Survivors
Authors: Sevin Carla M. , Boehm Leanne M. , Hibbert Elizabeth , Bastin Anthony J. , Jackson James C. , Meyer Joel , Quasim Tara , Bakhru Rita N. , Montgomery-Yates Ashley , Slack Andrew , Still Mary , Netzer Giora , Mikkelsen Mark E. , Iwashyna Theodore J. , Haines Kimberley J. , McPeake Joanne
Published: May 2021

Objectives:

To understand the unmet needs of caregivers of ICU survivors, how they accessed support post ICU, and the key components of beneficial ICU recovery support systems as identified from a caregiver perspective.

Design:

International, qualitative study.

Subjects:

We conducted 20 semistructured interviews with a diverse group of caregivers in the United States, the United Kingdom, and Australia, 11 of whom had interacted with an ICU recovery program.

Setting:

Seven hospitals in the United States, United Kingdom, and Australia.

Interventions:

None.

Measurements and Main Results:

Content analysis was used to explore prevalent themes related to unmet needs, as well as perceived strategies to improve ICU outcomes. Post-ICU care was perceived to be generally inadequate. Desired caregiver support fell into two main categories: practical support and emotional support. Successful care delivery initiatives included structured programs, such as post discharge telephone calls, home health programs, post-ICU clinics, and peer support groups, and standing information resources, such as written educational materials and online resources.

Conclusions:

This qualitative, multicenter, international study of caregivers of critical illness survivors identified consistently unmet needs, means by which caregivers accessed support post ICU, and several care mechanisms identified by caregivers as supporting optimal ICU recovery.
Two or Three? Approaches to Staging of the Paramedian Forehead Flap for Nasal Reconstruction
Authors: Oleck Nicholas C. , Hernandez J. Andres , Cason Roger W. , Glener Adam D. , Shammas Ronnie L. , Avashia Yash J. , Marcus Jeffrey R.
Published: May 2021

The paramedian forehead flap is a historic cornerstone of plastic surgery and a mainstay of complex nasal reconstruction. Although initially described as a 2-stage procedure, several procedural advancements and modifications have been proposed, with the most notable being the addition of a third, intermediate stage. Proponents of this 3-stage approach argue that the addition of an intermediate stage improves flap perfusion, expands lining and structural support options, and provides superior aesthetic outcomes. Although this technique has grown in popularity, studies comparing the 2- versus 3-stage approach are relatively scarce in the literature. Existing comparative studies seem to suggest that the 3-stage paramedian forehead flap may have advantages in large, complex nasal defects and patients at high risk for vascular compromise. Additionally, comparative analyses with respect to aesthetic outcome were found to be largely equivocal, suggesting that surgeon comfort and preference should guide flap selection.
Antioxidant activity of water-soluble polysaccharide extracts
produced from perilla seed cake by enzymatic hydrolysis
Authors: Hwang Yeo Jin , Kim Ja Min , Yoon Kyung Young
Published: May 2021

This study was conducted for the production of water-soluble polysaccharide (WSP)
extracts from perilla seed cake (PSC), a byproduct of food processing, by using
commercial enzymes. PSC was divided into cellulose fraction (CF) and
hemicellulose fraction (HF), and the enzymatic hydrolysis conditions of each
fraction were determined for the production of WSP extracts. Afterwards, the
antioxidant activity of these WSP extracts was measured. The hydrolysis
conditions of the CF for producing WSP extracts were pH 5.0, 50℃, and 30
units of Celluclast while those of HF were pH 4.0, 50℃, and 30 units of
Viscozyme. The yield of WSP extracts increased from 176 g/kg at 0 h of
hydrolysis to 233.1 g/kg after 72 h of hydrolysis. Futhermore, the polyphenol
content of WSP extracts from CF and HF were significantly higher after enzymatic
hydrolysis for 24 h, but decreased after 48 h of hydrolysis. In addtion, WSP
extracts obtained after 24 h of hydolysis showed the lowest IC50
values for hydroxy radical scavenging activity, reducing power activity, and
superoxide dismutase-like activity. From the result, WSP extracts with
antioxidant activity could be effectively extracted by enzymatic hydrolysis, and
the extracts are considered to be used as a functional substance in the food
industry.
Quality characteristics of tomato ‘Soksungjang’ prepared with
Rhizopus oligosporus Koji
Authors: Jeon Sung-Hee , Youn Young , Jeong Do-Youn , Kim Young-Soo
Published: May 2021

This study aimed to investigate and optimize the quality of tomato ‘Soksungjang’.
Tomato ‘Soksungjang’ was prepared using 10% tomato paste with the addition of
Rhizopus oligosporus Koji. Various quality characteristics
were determined including proximate composition, physicochemical properties,
free sugar and organic acid contents, free amino acid content, total microbial
count, enzyme activity, and the presence of volatile compounds. The results
showed that the free sugar content of tomato ‘Soksungjang’ was 14.81 mg%. The
individual sugars identified were glucose, galactose, fructose, sucrose,
maltose, and lactose. The total organic acid content was 162.79 mg% and the
identified individual organic acids were citric acid, lactic acid, acetic acid,
malic acid, formic acid, and succinic acid. The total free amino acid content
was 1,440 mg%, including major amino acids, such as glutamic acid, lysine, and
arginine. The α-amylase activity of the tomato ‘Soksungjang’ was 74.42
unit/mL, whereas lipase and neutral protease activities were 93.59 and 35.79
unit/mL, respectively. Total 30 compounds including alcohols, esters, ketones,
and aldehydes were detected in tomato ‘Soksungjang’. Ethyl alcohol,
3-methyl-1-butanol, and ethyl acetate were among the major volatile
compounds.
The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2
Authors: Kurihara Yoko , Kiyasu Yoshihiko , Akashi Yusaku , Takeuchi Yuto , Narahara Kenji , Mori Sunao , Takeshige Tomonori , Notake Shigeyuki , Ueda Atsuo , Nakamura Koji , Ishikawa Hiroichi , Suzuki Hiromichi
Published: May 2021

Introduction

Rapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser® Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests.

Methods

A prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser® Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests.

Results

A total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0–83.6%), 99.8% (95% CI: 99.5–100%), 96.9% (95% CI: 89.2–99.6%), and 98.4% (95% CI: 97.6–99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser® Auto SARS-CoV-2 detected 34–120 copies/test, which indicated greater sensitivity than the other rapid antigen tests.

Conclusions

QuickChaser® Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.
What is known from the existing literature about the available treatments for pelvic floor dysfunction among female athletes? A scoping review protocol
Authors: Giagio Silvia , Salvioli Stefano , Pillastrini Paolo , Fiorucci Marika , Innocenti Tiziano
Published: May 2021

Background

Pelvic floor dysfunction (PFD) is a term used to describe a variety of symptoms, signs and conditions involving different impairments on the pelvic floor muscles.

The existing literature suggests that some sports may lead to a higher risk of developing PFD, in particular among female athletes. Despite a recent scoping review highlighted a great number of studies dealing with epidemiologic data on this topic, no study has been conducted to map the available treatments.

In this framework, the aim of the present scoping review will be to map and summarize the literature to identify the available evidence concerning the treatments for PFD among female athletes.

Inclusion criteria

Studies considering female athletes practicing sports at any performance level with any type of PFD will be eligible for inclusion. Any treatment options (i.e. preventive, conservative, surgery) reported by each study and any context will be considered.

Methods

This scoping review will be performed in accordance with the Joanna Briggs Institute methodology. MEDLINE, Cochrane Central, Scopus, CINAHLComplete, Embase, PEDro and SPORTDiscus database will be searched from inception to May 2021. Additional records will be identified through searching in grey literature and the reference lists of all relevant studies. No study design, publication type, data and language restrictions will be applied.

Two reviewers will independently screen all abstracts and full-text studies for inclusion. A data collection form will be developed by the research team to extract the characteristics of the studies included. A tabular and accompanying narrative summary of the information will be provided.

Conclusions

This will be the first scoping review to provide a comprehensive overview of the topic. The results will add meaningful information for clinicians in the management of PFD among female athletes. Furthermore, any knowledge gaps of the topic will be identified. The results of this research will be published in a peer-reviewed journal and will be presented at relevant (inter)national scientific events.
Methodological proposal to explore and design future health innovation policies and opportunities for Responsible Research and Innovation (RRI)
Authors: Argüello Arturo , Ortega-Rodriguez Alicia , Álvarez Pablo
Published: May 2021

Responsible Research and Innovation (RRI) seeks to align the research results with the needs of society to respond to current and future problems, also encompassing financial instruments, innovative public policies, and the distribution of resources. These policies should prioritize research in those areas with the greatest impact on society, and particularly in health research, this impact should be focused on responding to clinical problems of the population rather than economic impact. A methodology is proposed that uses information from open sources to identify discrepancies between the results of the most translational research of a region and its health needs, in order to provide useful information for the formulation of innovation policies.
Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B
Authors: Liu Jun , Budylowski Patrick , Samson Reuben , Griffin Bryan D. , Babuadze Giorgi , Rathod Bhavisha , Colwill Karen , Abioye Jumai A. , Schwartz Jordan A , Law Ryan , Yip Lily , Ahn Sang Kyun , Chau Serena , Naghibosadat Maedeh , Arita Yuko , Hu Queenie , Yue Feng Yun , Banerjee Arinjay , Mossman Karen , Mubareka Samira , Kozak Robert A. , Pollanen Michael S. , Orozco Natalia Martin , Gingras Anne-Claude , Marcusson Eric G. , Ostrowski Mario A.
Published: May 2021

Safe and effective vaccines are needed to end the COVID-19 pandemic caused by SARS-CoV-2. Here we report the preclinical development of a lipid nanoparticle (LNP) formulated SARS-CoV-2 mRNA vaccine, PTX-COVID19-B. PTX-COVID19-B was chosen among three candidates after the initial mouse vaccination results showed that it elicited the strongest neutralizing antibody response against SARS-CoV-2. Further tests in mice and hamsters indicated that PTX-COVID19-B induced robust humoral and cellular immune responses and completely protected the vaccinated animals from SARS-CoV-2 infection in the lung. Studies in hamsters also showed that PTX-COVID19-B protected the upper respiratory tract from SARS-CoV-2 infection. Mouse immune sera elicited by PTX-COVID19-B vaccination were able to neutralize SARS-CoV-2 variants of concern (VOCs), including the B.1.1.7, B.1.351 and P.1 lineages. No adverse effects were induced by PTX-COVID19-B in both mice and hamsters. These preclinical results indicate that PTX-COVID19-B is safe and effective. Based on these results, PTX-COVID19-B was authorized by Health Canada to enter clinical trials in December 2020 with a phase 1 clinical trial ongoing (ClinicalTrials.govnumber:NCT04765436).

One Sentence Summary

PTX-COVID19-B is a SARS-CoV-2 mRNA vaccine that is highly immunogenic, safe, and effective in preventing SARS-CoV-2 infection in mice and hamsters and is currently being evaluated in human clinical trials.
Early cross-coronavirus reactive signatures of protective humoral immunity against COVID-19
Authors: Kaplonek Paulina , Wang Chuangqi , Bartsch Yannic , Fischinger Stephanie , Gorman Matthew J. , Bowman Kathryn , Kang Jaewon , Dayal Diana , Martin Patrick , Nowak Radoslaw , Hsieh Ching-Lin , Feldman Jared , Julg Boris , Nilles Eric J. , Musk Elon R. , Menon Anil S. , Fischer Eric S. , McLellan Jason S. , Schmidt Aaron , Goldberg Marcia B. , Filbin Michael , Hacohen Nir , Lauffenburger Douglas A , Alter Galit
Published: May 2021

The introduction of vaccines has inspired new hope in the battle against SARS-CoV-2. However, the emergence of viral variants, in the absence of potent antivirals, has left the world struggling with the uncertain nature of this disease. Antibodies currently represent the strongest correlate of immunity against COVID-19, thus we profiled the earliest humoral signatures in a large cohort of severe and asymptomatic COVID-19 individuals. While a SARS-CoV-2-specific immune response evolved rapidly in survivors of COVID-19, non-survivors exhibited blunted and delayed humoral immune evolution, particularly with respect to S2-specific antibody evolution. Given the conservation of S2 across β-coronaviruses, we found the early development of SARS-CoV-2-specific immunity occurred in tandem with pre-existing common β-coronavirus OC43 humoral immunity in survivors, which was selectively also expanded in individuals that develop paucisymptomatic infection. These data point to the importance of cross-coronavirus immunity as a correlate of protection against COVID-19.
The recent evolutionary rescue of a staple crop depended on over half a century of global germplasm exchange
Authors: Muleta Kebede T. , Felderhoff Terry , Winans Noah , Walstead Rachel , Charles Jean Rigaud , Armstrong J. Scott , Mamidi Sujan , Plott Chris , Vogel John P. , Lemaux Peggy G. , Mockler Todd C. , Grimwood Jane , Schmutz Jeremy , Pressoir Gael , Morris Geoffrey P.
Published: May 2021

Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA;Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively intercrossed, and subjected to intense selection under SCA infestation. We conducted evolutionary population genomics analyses of 296 post-selection Haitian lines compared to 767 global accessions at 159,683 single nucleotide polymorphisms. Despite intense selection, the Haitian population retains high nucleotide diversity through much of the genome due to diverse founders and an intercrossing strategy. A genome-wide fixation (FST) scan and geographic analyses suggests that adaptation to SCA in Haiti is conferred by a globally-rare East African allele ofRMES1, which has also spread to other breeding programs in Africa, Asia, and the Americas.De novogenome sequencing data for SCA resistant and susceptible lines revealed putative causative variants atRMES1. Convenient low-cost markers were developed from theRMES1selective sweep and successfully predicted resistance in independent U.S. × African breeding lines and eight U.S. commercial and public breeding programs, demonstrating the global relevance of the findings. Together, the findings highlight the potential of evolutionary genomics to develop adaptive trait breeding technology and the value of global germplasm exchange to facilitate evolutionary rescue.
Comparison of Approaches to Transcriptomic Analysis in Multi-Sampled Tumors
Authors: Ku Anson T. , Wilkinson Scott , Sowalsky Adam G.
Published: May 2021

Intratumoral heterogeneity is a well-documented feature of human cancers associated with outcome and treatment resistance. However, a heterogeneous tumor transcriptome contributes an unknown level of variability to analyses of differentially expressed genes that may contribute to phenotypes of interest, including treatment response. Although current clinical practice and the vast majority of research studies use a single sample from each patient, decreasing costs in sequencing technologies and computing costs have made repeated-measures analyses increasingly economical. Repeatedly sampling the same tumor increases the statistical power of differentially expressed gene analysis that is indispensable towards downstream analysis and also increases ones understanding of within-tumor variance that may affect conclusions. Here, we compared five different methods for analyzing gene expression profiles derived from repeated sampling of human prostate tumors in two separate cohorts of patients. We also benchmarked the sensitivity of generalized linear models to linear mixed models for identifying differentially expressed genes contributing to relevant prostate cancer pathways based on a ground truth model.
Absolute proteome quantification in the gas-fermenting acetogen Clostridium autoethanogenum
Authors: Valgepea Kaspar , Talbo Gert , Takemori Nobuaki , Takemori Ayako , Ludwig Christina , Mueller Alexander P. , Tappel Ryan , Köpke Michael , Simpson Séan Dennis , Nielsen Lars Keld , Marcellin Esteban
Published: May 2021

Microbes that can recycle one-carbon (C1) greenhouse gases into fuels and chemicals are vital for the biosustainability of future industries. Acetogens are the most efficient known microbes for fixing carbon oxides CO2 and CO. Understanding proteome allocation is important for metabolic engineering as it dictates metabolic fitness. Here, we use absolute proteomics to quantify intracellular concentrations for >1,000 proteins in the model-acetogen Clostridium autoethanogenum grown on three gas mixtures. We detect prioritisation of proteome allocation for C1 fixation and significant expression of proteins involved in the production of acetate and ethanol as well as proteins with unclear functions. The data also revealed which isoenzymes are important. Integration of proteomic and metabolic flux data demonstrated that enzymes catalyse high fluxes with high concentrations and high in vivo catalytic rates. We show that flux adjustments were dominantly accompanied with changing enzyme catalytic rates rather than concentrations. Our work serves as a reference dataset and advances systems-level understanding and engineering of acetogens.
Dissecting and Tuning Primer Editing by Proofreading Polymerases
Authors: Gohl Daryl M. , Auch Benjamin , Certano Amanda , LeFrançois Brice , Bouevitch Anne , Doukhanine Evgueni , Fragel Christina , Macklaim Jean , Hollister Emily , Garbe John , Beckman Kenneth B.
Published: May 2021

Proofreading polymerases have 3’ to 5’ exonuclease activity that allows the excision and correction of mis-incorporated bases during DNA replication. In a previous study, we demonstrated that in addition to correcting substitution errors and lowering the error rate of DNA amplification, proofreading polymerases can also edit PCR primers to match template sequences. Primer editing is a feature that can be advantageous in certain experimental contexts, such as amplicon-based microbiome profiling. Here we develop a set of synthetic DNA standards to report on primer editing activity and use these standards to dissect this phenomenon. The primer editing standards allow next-generation sequencing-based enzymological measurements, reveal the extent of editing, and allow the comparison of different polymerases and cycling conditions. We demonstrate that proofreading polymerases edit PCR primers in a concentration-dependent manner, and we examine whether primer editing exhibits any sequence specificity. In addition, we use these standards to show that primer editing is tunable through the incorporation of phosphorothioate linkages. Finally, we demonstrate the ability of primer editing to robustly rescue the drop-out of taxa with 16S rRNA gene-targeting primer mismatches using mock communities and human skin microbiome samples.
Inferring population structure in biobank-scale genomic data
Authors: Chiu Alec M. , Molloy Erin K. , Tan Zilong , Talwalkar Ameet , Sankararaman Sriram
Published: May 2021

Inferring the structure of human populations from genetic variation data is a key task in population and medical genomic studies. While a number of methods for population structure inference have been proposed, current methods are impractical to run on biobank-scale genomic datasets containing millions of individuals and genetic variants. We introduce SCOPE, a method for population structure inference that is orders of magnitude faster than existing methods while achieving comparable accuracy. SCOPE infers population structure in about a day on a dataset containing one million individuals and variants as well as on the UK Biobank dataset containing 488,363 individuals and 569,346 variants. Furthermore, SCOPE can leverage allele frequencies from previous studies to improve the interpretability of population structure estimates.
Validity and Reliability of a Behavior Assessment Questionnaire for Children with Obesity
Authors: Paek So Yeon , Roy Lonnie C. , DeHaven Mark J. , Carson Elyse , Barlow Sarah E. , Kridelbaugh LeAnn
Published: May 2021

The 10-item Behavior Assessment Questionnaire (BAQ) was developed to assess parent-report of child screen time, physical activity, and food consumption during the past 3 months in children with obesity. Response options were on a 5-point scale, converted to 0-100, with higher scores indicating healthier behavior. To evaluate, two convenience samples of parents of children 5-18 years completed the questionnaire: a cohort presenting to an obesity program (n=83) and a cohort of community events attenders and hospital employee parents (n=147). Scores had a normal distribution without floor or ceiling effects. Cronbach’s alpha for the 10-item scale was .71. Factor analysis yielded three component factors with Cronbach’s alpha of .66, .75, and .59 for the Screen Time, Physical Activity, and Food Consumption dimensions respectively. Scores of the obesity group (49.02 [SD 14.52]) were lower than scores of the community group (55.44 [SD 13.55]), p=.001. The BAQ demonstrated reliability and validity for use as an index of lifestyle behaviors.

Key Messages

A short, easily administered questionnaire, completed by parents, about obesity-associated lifestyle behaviors of children demonstrates reliability and validity

This questionnaire could help pediatric providers assess behaviors in order to provide more targeted lifestyle counseling for children to reduce obesity risk.
The Impact of Universal Transport Media and Viral Transport Media Liquid Samples on a SARS-CoV-2 Rapid Antigen Test
Authors: Mayfield J , Hesse P , Ledden D
Published: May 2021

The impact of universal transport media (UTM) and viral transport media (VTM) liquid samples on the performance of the Healgen Scientific Rapid COVID-19 Antigen Test was investigated. Twelve different UTM/VTM liquid samples were added at different dilutions to the extraction buffer, and 2 of 12 generated false-positive results. To understand the cause of these false-positive results, the effect of extraction buffer dilution on sample pH, surfactant concentration, and ionic strength were investigated. The most important factor in UTM/VTM liquid sample dilution of the extraction buffer was ionic strength as measured by conductivity. Dilutions with conductivity below ∼17 mS/cm can induce a false-positive result. It was also noted that the ionic strength of UTM/VTMs can vary, and those with low ionic strength can be problematic. To rule out the effect of other common components found in UTMs/VTMs, several materials were mixed with extraction buffer and tested at high concentrations. None was shown to produce false-positive results.
Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions
Authors: Hessler Tomas , Harrison Susan T.L. , Banfield Jillian F. , Huddy Robert J.
Published: May 2021

Biological sulfate reduction (BSR) represents a promising bioremediation strategy, yet the impact of metabolic interactions on performance has been largely unexplored. Here, genome-resolved metagenomics was used to characterise 17 microbial communities associated with reactors operated with defined sulfate-contaminated solutions. Pairs of reactors were supplemented with lactate or with acetate plus a small amount of fermentable substrate. At least thirty draft quality genomes, representing all the abundant bacteria, were recovered from each metagenome. All of the 22 SRB genomes encode genes for H2 consumption. And of the total 163 genomes recovered, 130 encode 321 NiFe and FeFe hydrogenases. The lactate-supplemented packed-bed bioreactor was particularly interesting as it resulted in stratified microbial communities that were distinct in their predominant metabolisms. Pathways for fermentation of lactate and hydrogen production were enriched towards the inlet whereas increased autotrophy and acetate-oxidizing SRB were evident towards the end of the flow path. We hypothesized that high sulfate removal towards the end of the flow path, despite acetate being an electron donor that typically sustains low SRB growth rates, was stimulated by H2 consumption. This hypothesis was supported by sustained performance of the predominantly acetate-supplemented stirred-tank reactor, which was dominated by diverse fermentative, hydrogen-evolving bacteria and low-abundance SRB capable of acetate and hydrogen consumption. We conclude that the performance of BSR reactors supplemented with inexpensive acetate can be improved by the addition of a low concentration of fermentable material due to stimulation of syntrophic relationships among hydrogen-producing non-SRB and dual hydrogen- and acetate-utilising SRB.
microRNA-138 controls hippocampal interneuron function and short-term memory
Authors: Daswani R. , Gilardi C. , Soutschek M. , Nanda P. , Weiss K. , Bicker S. , Fiore R. , Dieterich C. , Germain P.L. , Winterer J , Schratt G
Published: May 2021

The proper development and function of neuronal circuits relies on a tightly regulated balance between excitatory and inhibitory (E/I) synaptic transmission, and disrupting this balance can cause neurodevelopmental disorders, e.g. schizophrenia. microRNA-dependent gene regulation in pyramidal neurons is important for excitatory synaptic function and cognition, but its role in inhibitory interneurons is poorly understood. Here, we identify miR-138-5p as a regulator of short-term memory and inhibitory synaptic transmission in the hippocampus. Sponge-mediated miR-138-5p inactivation specifically in parvalbumin (PV)-expressing interneurons impairs spatial recognition memory and enhances GABAergic synaptic input onto pyramidal neurons. Cellular and behavioural phenotypes associated with miR-138-5p inactivation are paralleled by an upregulation of the schizophrenia-associated Erbb4, which we validated as a direct miR-138-5p target gene. Our findings suggest that miR-138-5p is a critical regulator of PV interneuron function, with implications for cognition and schizophrenia. More generally, they provide evidence that microRNAs orchestrate neural circuit development by fine-tuning both excitatory and inhibitory synaptic transmission.
Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole cell mechanics
Authors: Vahabikashi Amir , Sivagurunathan Suganya , Nicdao Fiona Ann Sadsad , Han Yu Long , Park Chan Young , Wong Xianrong , Tran Joseph R. , Gundersen Gregg G. , Reddy Karen L. , Luxton G.W. Gant , Guo Ming , Fredberg Jeffrey J. , Zheng Yixian , Adam Stephen A. , Goldman Robert D.
Published: May 2021

The ability of a cell to regulate its mechanical properties is central to its function. Emerging evidence suggests that interactions between the cell nucleus and cytoskeleton influence cell mechanics through poorly understood mechanisms. Here we show that A- and B-type nuclear lamin isoforms distinctively modulate both nuclear and cellular volume and selectively stabilize the linker of nucleoskeleton and cytoskeleton (LINC) complexes that couple the nucleus to cytoskeletal actin and vimentin. We reveal, further, that loss of each of the four-known lamin isoforms in the mouse embryonic fibroblasts differentially affects cortical and cytoplasmic stiffness as well as cellular contractility, and then propose a LINC complex mediated model that explains these impaired mechanical phenotypes. Finally, we demonstrate that loss of each lamin isoform softens the nucleus in a manner that correlates with loss of heterochromatin. Together, these findings uncover distinctive roles for each lamin isoform in maintaining cellular and nuclear mechanics.
Visuo-proprioceptive integration and recalibration with multiple visual stimuli
Authors: Debats Nienke B , Heuer Herbert , Kayser Christoph
Published: May 2021

To organize the plethora of sensory signals from our environment into a coherent percept, our brain relies on the processes of multisensory integration and sensory recalibration. We here asked how visuo-proprioceptive integration and recalibration are shaped by the presence of more than one potentially relevant visual stimulus, hence paving the way to studying multisensory perception under more naturalistic settings with multiple signals per sensory modality. By manipulating the spatio-temporal correspondence between the hand position and two visual stimuli during a cursor-control task, we contrasted two alternative accounts: that only the temporally more proximal signal enters integration and recalibration similar to a winner-takes-all process, or that the influences of both visual signals superpose. Our results show that integration - and likely also recalibration - are shaped by the superposed contributions of multiple stimuli rather than by only individual ones.
Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin
Authors: Aman Andrew J. , Saunders Lauren M. , Carr August A. , Srivatsan Sanjay R. , Eberhard Colten D. , Carrington Blake , Watkins-Chow Dawn , Pavan William J. , Trapnell Cole , Parichy David M.
Published: May 2021

Pigment patterns and skin appendages are prominent features of vertebrate skin. In zebrafish, regularly patterned pigment stripes and an array of calcified scales form simultaneously in the skin during post-embryonic development. Understanding mechanisms that regulate stripe patterning and scale morphogenesis may lead to discovery of fundamental mechanisms that govern development of animal form. To learn about cell types and signaling interactions that govern skin patterning and morphogenesis we generated and analyzed single cell transcriptomes of skin from wild-type fish as well as fish having genetic or transgenically induced defects in squamation or pigmentation. These data reveal a previously undescribed population of epidermal cells that express transcripts encoding enamel matrix proteins, suggest hormonal control of epithelial-mesenchymal signaling, clarify the signaling network that governs scale papillae development, and identify a critical role for the hypodermis in supporting pigment cell development. Additionally, these comprehensive single-cell transcriptomic data representing skin phenotypes of biomedical relevance should provide a useful resource for accelerating discovery of mechanisms that govern skin development and homeostasis.
ABA homeostasis and long-distance translocation is redundantly regulated by ABCG ABA importers
Authors: Zhang Yuqin , Vasuki Himabindu , Liu Jie , Bar Hamutal , Lazary Shani , Egbaria Aiman , Ripper Dagmar , Charrier Laurence , Aharoni Asaph , Ragni Laura , Strader Lucia , Sade Nir , Weinstain Roy , Geisler Markus , Shani Eilon
Published: May 2021

The effects of abscisic acid (ABA) on plant growth, development and response to the environment depend on local ABA concentrations. Here, we exploited a genome-scale amiRNA screen, targeting theArabidopsistransportome, to show that ABA homeostasis is regulated by two previously unknown ABA transporters. ABCG17 and ABCG18 are localized to the plasma membranes of leaf mesophyll and stem cortex cells to redundantly promote ABA import, leading to conjugated inactive ABA sinks, thus restricting stomatal closure.ABCG17andABCG18double knockdown revealed that the transporters encoded by these genes not only limit stomatal aperture size, conductance and transpiration while increasing water-use efficiency but also control ABA translocation from the shoot to the root to regulate lateral root emergence. The proposed ABCG17- and ABCG18-dependent ABA glucosyl ester shoot sink mechanism is restrained under abiotic stress conditions to further activate the ABA responses.
Total Biosynthesis of Triacsin Featuring an N-hydroxytriazene Pharmacophore
Authors: Del Rio Flores Antonio , Twigg Frederick F. , Du Yongle , Cai Wenlong , Aguirre Daniel Q. , Sato Michio , Dror Moriel J. , Narayanamoorthy Maanasa , Geng Jiaxin , Zill Nicholas A. , Zhang Wenjun
Published: May 2021

Triacsins are an intriguing class of specialized metabolites possessing a conserved N-hydroxytriazene moiety not found in any other known natural products. Triacsins are notable as potent acyl-CoA synthetase inhibitors in lipid metabolism, yet their biosynthesis has remained elusive. Through extensive mutagenesis and biochemical studies, we here report all enzymes required to construct and install the N-hydroxytriazene pharmacophore of triacsins. Two distinct ATP-dependent enzymes were revealed to catalyze the two consecutive N-N bond formation reactions, including a glycine-utilizing hydrazine-forming enzyme, Tri28, and a nitrous acid-utilizing N-nitrosating enzyme, Tri17. This study paves the way for future mechanistic interrogation and biocatalytic application of enzymes for N-N bond formation.
ThruTracker: Open-Source Software for 2-D and 3-D Animal Video Tracking
Authors: Corcoran Aaron J. , Schirmacher Michael R. , Black Eric , Hedrick Tyson L.
Published: May 2021

Tracking animal movement patterns using videography is an important tool in many biological disciplines ranging from biomechanics to conservation. Reduced costs of technology such as thermal videography and unmanned aerial vehicles has made video-based animal tracking more accessible, however existing software for processing acquired video limits the application of these methods.

Here, we present a novel software program for high-throughput 2-D and 3-D animal tracking. ThruTracker provides tools to allow video tracking under a variety of conditions with minimal technical expertise or coding background and without the need for paid licenses. Notable capabilities include calibrating the intrinsic properties of thermal cameras; tracking and counting hundreds of animals at a time; and the ability to make 3-D calibrations without dedicated calibration objects. Automated 2-D and 3-D workflows are integrated to allow for analysis of largescale datasets.

We tested ThruTracker with two case studies. The 2-D workflow is demonstrated by counting bats emerging from bridges and caves using thermal Videography. Tests show that ThruTracker has a similar accuracy compared to humans under a variety of conditions. The 3-D workflow is shown for making accurate calibrations for tracking bats and birds at wind turbines using only the wind turbine itself as a calibration object.

ThruTracker is a robust software program for tracking moving animals in 2-D and 3-D. Major applications include counting animals such as bats, birds, and fish that form large aggregations, and documenting movement trajectories over medium spatial scales (∼100,000 m3). When combined with emerging technologies, we expect videographic techniques to continue to see widespread adoption for an increasing range of biological applications.