bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics of the MACS/WIHS Combined Cohort Study: Opportunities for Research on Aging With HIV in the Longest US Observational Study of HIV
Authors: D’Souza Gypsyamber , Bhondoekhan Fiona , Benning Lorie , Margolick Joseph B , Adedimeji Adebola A , Adimora Adaora A , Alcaide Maria L , Cohen Mardge H , Detels Roger , Friedman M Reuel , Holman Susan , Konkle-Parker Deborah J , Merenstein Daniel , Ofotokun Igho , Palella Frank , Altekruse Sean , Brown Todd T , Tien Phyllis C
Published: February 2021

In 2019, the National Institutes of Health combined the Multicenter AIDS Cohort Study (MACS) and the Women’s Interagency HIV Study (WIHS) into the MACS/WIHS Combined Cohort Study (MWCCS). In this paper, participants who made a study visit during October 2018–September 2019 (targeted for MWCCS enrollment) are described by human immunodeficiency virus (HIV) serostatus and compared with people living with HIV (PLWH) in the United States. Participants include 2,115 women and 1,901 men with a median age of 56 years (interquartile range, 48–63); 62% are PLWH. Study sites encompass the South (18%), the Mid-Atlantic/Northeast (45%), the West Coast (22%), and the Midwest (15%). Participant race/ethnicity approximates that of PLWH throughout the United States. Longitudinal data and specimens collected for 35 years (men) and 25 years (women) were combined. Differences in data collection and coding were reviewed, and key risk factor and comorbidity data were harmonized. For example, recent use of alcohol (62%) and tobacco (28%) are common, as are dyslipidemia (64%), hypertension (56%), obesity (42%), mildly or severely impaired daily activities (31%), depressive symptoms (28%), and diabetes (22%). The MWCCS repository includes serum, plasma, peripheral blood mononuclear cells, cell pellets, urine, cervicovaginal lavage samples, oral samples, B-cell lines, stool, and semen specimens. Demographic differences between the MACS and WIHS can confound analyses by sex. The merged MWCCS is both an ongoing observational cohort study and a valuable resource for harmonized longitudinal data and specimens for HIV-related research.
The use of a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide–based colorimetric assay in the viability analysis of the filamentous cyanobacterium Arthrospira platensis
Authors: Shiraishi Hideaki , Toyoda Akiko
Published: February 2021

The applicability of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to an industrially valuable filamentous cyanobacterium Arthrospira platensis was examined. When it was applied to A. platensis NIES-39, as few as 10 viable trichomes were quantitatively detected. However, depending on the experimental conditions, it also generated artifactual viability signals. The results should help clarify the scope and limits of the MTT assay in viability analysis.
Psychrophile-based simple biocatalysts for effective coproduction of 3-hydroxypropionic acid and 1,3-propanediol
Authors: Mojarrad Mohammad , Tajima Takahisa , Hida Akiko , Kato Junichi
Published: February 2021

3-Hydroxypropionic acid (3-HP) and 1,3-propanediol (1,3-PDO) have tremendous potential markets in many industries. This study evaluated the simultaneous biosynthesis of the 2 compounds using the new psychrophile-based simple biocatalyst (PSCat) reaction system. The PSCat method is based on the expression of glycerol dehydratase, 1,3-propanediol dehydrogenase, and aldehyde dehydrogenase from Klebsiella pneumoniae in Shewanella livingstonensis Ac10 and Shewanella frigidimarina DSM 12253, individually. Heat treatment at 45 °C for 15 min deactivated the intracellular metabolic flux, and the production process was started after adding substrate, cofactor, and coenzyme. In the solo production process after 1 h, the maximum production of 3-HP was 62.0 m m. For 1,3-PDO, the maximum production was 25.0 m m. In the simultaneous production process, productivity was boosted, and the production of 3-HP and 1,3-PDO increased by 13.5 and 4.9 m m, respectively. Hence, the feasibility of the individual production and the simultaneous biosynthesis system were verified in the new PSCat approach.
HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis
Authors: Ren Mingyang , Zhang Sanguo , Zhang Qingzhao , Ma Shuangge
Published: February 2021

Heterogeneity is a hallmark of many complex human diseases, and unsupervised heterogeneity analysis has been extensively conducted using high-throughput molecular measurements and histopathological imaging features. ‘Classic’ heterogeneity analysis has been based on simple statistics such as mean, variance and correlation. Network-based analysis takes interconnections as well as individual variable properties into consideration and can be more informative. Several Gaussian graphical model (GGM)-based heterogeneity analysis techniques have been developed, but friendly and portable software is still lacking. To facilitate more extensive usage, we develop the R package HeteroGGM, which conducts GGM-based heterogeneity analysis using the advanced penaliztaion techniques, can provide informative summary and graphical presentation, and is efficient and friendly.

Availabilityand implementation

The package is available at https://CRAN.R-project.org/package=HeteroGGM.

Supplementary information

Supplementary data are available at Bioinformatics online.
Validation of the Skåne University Hospital nomogram for the preoperative prediction of a disease-free axilla in patients with breast cancer
Authors: Majid S , Bendahl P-O , Huss L , Manjer J , Rydén L , Dihge L
Published: February 2021

Background

Axillary staging via sentinel lymph node biopsy (SLNB) is performed for clinically node-negative (N0) breast cancer patients. The Skåne University Hospital (SUS) nomogram was developed to assess the possibility of omitting SLNB for patients with a low risk of nodal metastasis. Area under the receiver operating characteristic curve (AUC) was 0.74. The aim was to validate the SUS nomogram using only routinely collected data from the Swedish National Quality Registry for Breast Cancer at two breast cancer centres during different time periods.

Method

This retrospective study included patients with primary breast cancer who were treated at centres in Lund and Malmö during 2008–2013. Clinicopathological predictors in the SUS nomogram were age, mode of detection, tumour size, multifocality, lymphovascular invasion and surrogate molecular subtype. Multiple imputation was used for missing data. Validation performance was assessed using AUC and calibration.

Results

The study included 2939 patients (1318 patients treated in Lund and 1621 treated in Malmö). Node-positive disease was detected in 1008 patients. The overall validation AUC was 0.74 (Lund cohort AUC: 0.75, Malmö cohort AUC: 0.73), and the calibration was satisfactory. Accepting a false-negative rate of 5 per cent for predicting N0, a possible SLNB reduction rate of 15 per cent was obtained in the overall cohort.

Conclusion

The SUS nomogram provided acceptable power for predicting a disease-free axilla in the validation cohort. This tool may assist surgeons in identifying and counselling patients with a low risk of nodal metastasis on the omission of SLNB staging.
Matrix-induced autologous chondrocyte implantation versus autologous matrix-induced chondrogenesis for chondral defects of the talus: a systematic review
Authors: Migliorini Filippo , Maffulli Nicola , Baroncini Alice , Knobe Matthias , Tingart Markus , Eschweiler Jörg
Published: February 2021

Introduction

Chondral defects of the talus are common and their treatment is challenging.

Source of data

Recent published literatures.

Areas of agreement

Membrane-induced Autologous Chondrocyte Implantation (mACI) and Autologous Matrix-Induced Chondrogenesis (AMIC) have been proposed as management for chondral defects of the talus.

Areas of controversy

It is debated whether AMIC provides greater outcomes compared to mACI for chondral regeneration. Several clinical studies showed controversial results, and the best treatment has not yet been clarified.

Growing points

To investigate whether AMIC provide superior outcomes than mACI at midterm follow-up.

Areas timely for developing research

AMIC exhibits similar clinical results to mACI. However, AMIC involves one single surgical procedure, no articular cartilage harvest and hence no morbidity from it, no need for chondrocyte expansion in a separate laboratory setting. For these reasons, AMIC may be preferred to mACI.
A neurogenetic analysis of female autism
Authors: Jack Allison , Sullivan Catherine A W , Aylward Elizabeth , Bookheimer Susan Y , Dapretto Mirella , Gaab Nadine , Van Horn John D , Eilbott Jeffrey , Jacokes Zachary , Torgerson Carinna M , Bernier Raphael A , Geschwind Daniel H , McPartland James C , Nelson Charles A , Webb Sara J , Pelphrey Kevin A , Gupta Abha R ,   the GENDAAR Consortium, Bernier Raphael A , McPartland James C , Ventola Pamela , Kresse Anna , Neuhaus Emily , Corrigan Sarah , Wolf Julie , McDonald Nicole , Ankenman Katy , Webb Sara J , Jeste Shafali , Nelson Charles A , Naples Adam , Libsack Erin , Pelphrey Kevin A , Aylward Elizabeth , Bookheimer Susan Y , Gaab Nadine , Dapretto Mirella , Van Horn John D , Jack Allison , Guilford Desiree , Torgerson Carinna , Welker Olivia , Geschwind Daniel H , Gupta Abha R , W Sullivan Catherine A , Lowe Jennifer K , Jacokes Zachary , MacDonnell Erin , Tsapelas Heidi , Depedro-Mercier Dianna , Keifer Cara M , Ventola Pamela
Published: February 2021

Females versus males are less frequently diagnosed with autism spectrum disorder (ASD), and while understanding sex differences is critical to delineating the systems biology of the condition, female ASD is understudied. We integrated functional MRI and genetic data in a sex-balanced sample of ASD and typically developing youth (8–17 years old) to characterize female-specific pathways of ASD risk. Our primary objectives were to: (i) characterize female ASD (n = 45) brain response to human motion, relative to matched typically developing female youth (n = 45); and (ii) evaluate whether genetic data could provide further insight into the potential relevance of these brain functional differences. For our first objective we found that ASD females showed markedly reduced response versus typically developing females, particularly in sensorimotor, striatal, and frontal regions. This difference between ASD and typically developing females does not resemble differences between ASD (n = 47) and typically developing males (n = 47), even though neural response did not significantly differ between female and male ASD. For our second objective, we found that ASD females (n = 61), versus males (n = 66), showed larger median size of rare copy number variants containing gene(s) expressed in early life (10 postconceptual weeks to 2 years) in regions implicated by the typically developing female > female functional MRI contrast. Post hoc analyses suggested this difference was primarily driven by copy number variants containing gene(s) expressed in striatum. This striatal finding was reproducible among n = 2075 probands (291 female) from an independent cohort. Together, our findings suggest that striatal impacts may contribute to pathways of risk in female ASD and advocate caution in drawing conclusions regarding female ASD based on male-predominant cohorts.
Low-Intensity Pulsed Ultrasound Stimulation Inhibits Cortical Spreading Depression
Authors: Bian Nannan , Yuan Yi , Li Yingwei , Liu Mengyang , Li Xiaoli
Published: February 2021

Cortical spreading depression (CSD), which is closely correlated with migraine aura, cerebral ischemia, seizure, and brain injury, is a spreading wave of neuronal and glial depolarization. The purpose of this study is to investigate whether low-intensity pulsed ultrasound stimulation (PUS) inhibits CSD by modulating neural activity and hemodynamics. Behavioral test, intrinsic signal optical imaging and western blot analysis were used for evaluating the inhibition effect of PUS on CSD in rat. We found that: 1) 30 min of PUS can significantly improve motor activity of rat with CSD. 2) Both 30 s and 30 min of PUS can significantly reduce count and propagation speed of CSD in rat and the inhibitory effect was enhanced with increase of ultrasound intensity. 3) 30 min of PUS significantly enhanced levels of brain-derived neurotrophic factor protein in brain tissue with CSD. These results suggest that PUS has the potential to treat brain disorders associated with CSD.
Improving Selection Detection with Population Branch Statistic on Admixed Populations
Authors: Yelmen Burak , Marnetto Davide , Molinaro Ludovica , Flores Rodrigo , Mondal Mayukh , Pagani Luca
Published: February 2021

Detecting natural selection signals in admixed populations can be problematic since the source of the signal typically dates back prior to the admixture event. On one hand, it is now possible to study various source populations before a particular admixture thanks to the developments in ancient DNA (aDNA) in the last decade. However, aDNA availability is limited to certain geographical regions and the sample sizes and quality of the data might not be sufficient for selection analysis in many cases. In this study, we explore possible ways to improve detection of pre-admixture signals in admixed populations using a local ancestry inference approach. We used masked haplotypes for population branch statistic (PBS) and full haplotypes constructed following our approach from Yelmen et al. (2019) for cross-population extended haplotype homozygosity (XP-EHH), utilizing forward simulations to test the power of our analysis. The PBS results on simulated data showed that using masked haplotypes obtained from ancestry deconvolution instead of the admixed population might improve detection quality. On the other hand, XP-EHH results using the admixed population were better compared with the local ancestry method. We additionally report correlation for XP-EHH scores between source and admixed populations, suggesting that haplotype-based approaches must be used cautiously for recently admixed populations. Additionally, we performed PBS on real South Asian populations masked with local ancestry deconvolution and report here the first possible selection signals on the autochthonous South Asian component of contemporary South Asian populations.
Genomic prediction of hybrid crops allows disentangling dominance and epistasis
Authors: González-Diéguez David , Legarra Andrés , Charcosset Alain , Moreau Laurence , Lehermeier Christina , Teyssèdre Simon , Vitezica Zulma G
Published: February 2021

We revisited, in a genomic context, the theory of hybrid genetic evaluation models of hybrid crosses of pure lines, as the current practice is largely based on infinitesimal model assumptions. Expressions for covariances between hybrids due to additive substitution effects and dominance and epistatic deviations were analytically derived. Using dense markers in a GBLUP analysis, it is possible to split specific combining ability into dominance and across-groups epistatic deviations, and to split general combining ability (GCA) into within-line additive effects and within-line additive by additive (and higher order) epistatic deviations. We analyzed a publicly available maize data set of Dent × Flint hybrids using our new model (called GCA-model) up to additive by additive epistasis. To model higher order interactions within GCAs, we also fitted “residual genetic” line effects. Our new GCA-model was compared with another genomic model which assumes a uniquely defined effect of genes across origins. Most variation in hybrids is accounted by GCA. Variances due to dominance and epistasis have similar magnitudes. Models based on defining effects either differently or identically across heterotic groups resulted in similar predictive abilities for hybrids. The currently used model inflates the estimated additive genetic variance. This is not important for hybrid predictions but has consequences for the breeding scheme—e.g. overestimation of the genetic gain within heterotic group. Therefore, we recommend using GCA-model, which is appropriate for genomic prediction and variance component estimation in hybrid crops using genomic data, and whose results can be practically interpreted and used for breeding purposes.
Results of a Randomized Trial Testing the Efficacy of Tele-Savvy, an Online Synchronous/Asynchronous Psychoeducation Program for Family Caregivers of Persons Living with Dementia
Authors: Hepburn Kenneth , Nocera Joe , Higgins Melinda , Epps Fayron , Brewster Glenna S , Lindauer Allison , Morhardt Darby , Shah Raj , Bonds Kalisha , Nash Rachel , Griffiths Patricia C
Published: February 2021

Background and Objectives

Family caregivers will grow in number as dementia prevalence increases, underscoring the continued importance of equipping these individuals for their new roles and ameliorating the adverse effects of caregiving.

Research Design and Methods

A three-armed, waitlist, randomized trial design tested Tele-Savvy, an online adaptation of a successful in-person psychoeducation program, the Savvy Caregiver. Tele-Savvy is delivered over 43 days to groups of 6–8 caregivers in 7 weekly synchronous sessions accompanied by 36 brief asynchronous video lessons. We enrolled 23 cohorts of 15 eligible caregivers (N = 261), randomized 2:2:1 to active, attention control, and usual care arms. We assessed caregiver psychological well-being and caregiving mastery at baseline and 3, 6, 9, and 12 months. Multilevel linear models assessed outcomes over the 3 time points examined. The trial was slightly truncated, with Data and Safety Monitoring Board approval, because of the apparent confounding psychological effects of coronavirus disease 2019 restrictions.

Results

Study findings indicate statistically and clinically significant benefits to Tele-Savvy arm caregivers (with moderate to large effect sizes) in the areas of depression, perceived stress, reaction to care recipients’ behaviors, and enhancement of caregiver mastery. Expected benefits for caregiver burden and anxiety were not found.

Discussion and Implications

Findings attest to program efficacy and the viability of employing distance means to improve family caregivers’ emotional well-being and sense of mastery in the caregiving role over a 6-month period. Next steps entail finding alternate ways to deliver the program to those with connectivity and/or time constraint problems.
Operationalizing positive masculinity: a theoretical synthesis and school-based framework to engage boys and young men
Authors: Wilson Michael , Gwyther Kate , Swann Ray , Casey Kate , Featherston Ross , Oliffe John L , Englar-Carlson Matt , Rice Simon M
Published: February 2021

Scholars have consistently documented the relationship between conformity to traditional masculine norms and maladaptive psychosocial outcomes among boys and young men. Given current social commentary, including debate around ‘toxic masculinity’, intervention is needed to encourage boys to embody healthy expressions and identities of masculinity. Whilst new approaches grounded in positive masculinity show promise, the construct requires further definition and phenomenological clarity. Here we review divergent perspectives on positive masculinity, and forward a refined definition, specific to psychosocial health promotion among boys and young men. We then outline the theoretical basis of a positive masculinity framework to guide the content of future interventions, aiming to achieve positive identity development among boys and young men for the good of all. This framework represents a necessary unification of scholarship around male adolescent development, education and health. Future health promotion interventions may benefit from applying the framework to support a positive psychosocial trajectory among boys and young men, with a focus on connection, motivation and authenticity.
Individual variability in sub-Arctic krill material properties, lipid composition, and other scattering model inputs affect acoustic estimates of their population
Authors: Lucca Brandyn M , Ressler Patrick H , Harvey H Rodger , Warren Joseph D
Published: February 2021

Target strength model inputs including morphometry, material properties, lipid composition, and in situ orientations were measured for sub-Arctic krill (Euphausia pacifica, Thysanoessa spinifera, T. inermis, and T. raschii) in the eastern Bering Sea (EBS, 2016) and Gulf of Alaska (GOA, 2017). Inter-species and -regional animal lengths were significantly different (F1,680 = 114.10, p < 0.01), while animal shape was consistent for all species measured. The polar lipid phosphatidycholine was the dominant lipid, comprising 86 ± 16% (mean ± SD) and 56 ± 22% of total lipid mass in GOA and EBS krill, respectively. Krill density contrasts varied by species and region rather than with morphometry, lipid composition, or local chla fluorescence. Mean in situ krill orientation was 1 ± 31°, with 25% of observed krill within ±5° of broadside incidence. Modelled target strength sensitivity was frequency independent for variations in material properties but was primarily sensitive to morphometry and orientation at lower (38 kHz) and higher (200 kHz) frequencies, respectively. Measured variability in material properties corresponded to an order of magnitude difference in acoustic estimates of biomass at 120 kHz. These results provide important inputs and constraints for acoustic scattering models of ecologically important sub-Arctic krill species.
Myasthenia gravis affects overall survival in patients with thymoma: an analysis of multicentre database using propensity score matching
Authors: Tian Wenxin , Li Xiao , Sun Yaoguang , Wang Jun , Jiang Guanchao , Tong Hongfeng
Published: February 2021

OBJECTIVES

About one-third of patients with thymoma have myasthenia gravis (MG). It remains controversial whether MG affects the prognosis of patients with thymoma. The aim of this study was to evaluate the effect of MG on the prognosis of patients with thymoma in a multicentre database.

METHODS

Patients with thymoma who underwent thymectomy were identified from 2 prospectively collected databases in 2 medical centres from 2010 to 2018. Kaplan–Meier curves and the log-rank test were used to assess overall survival and recurrence-free survival, and a Cox proportional hazards model was used to determine significant contributors to survival. Propensity score matching was performed to eliminate selection bias.

RESULTS

A total of 514 patients with thymoma were included in this study, of whom 320 patients were MG-free and 194 had MG. Patients with MG were younger (median age 50 vs 54 years, P = 0.001) and had smaller tumours (4.4 ± 2.0 vs 4.9 ± 2.3 cm, P = 0.020). Pathological analysis showed that type B tumours especially B2−B3 (B2 + B3 + mix B tumours, 55.2%) are more common in patients with MG, while type AB (37.2%) was the most common in patients without MG. A larger proportion of Masaoka III–IV stage tumour (25.7% vs 11.0%, P < 0.001) was seen in patients with thymoma and MG. Multivariable Cox regression analysis demonstrated that MG (hazard ratio [HR] = 3.729, 95% confidence interval [CI]: 1.398–9.947, P = 0.009), incomplete resection (HR = 5.441, 95% CI: 1.500–19.731, P = 0.010) and Masaoka stage III + IV (HR = 3.390, 95% CI: 1.196–9.612, P = 0.022) were negative prognostic factors of overall survival. Meanwhile, MG (HR =3.489, 95% CI: 1.403–8.680, P = 0.007) and Masaoka stage III + IV (HR = 6.582, 95% CI: 2.575–16.828, P < 0.001) were negative prognostic factors of recurrence-free survival. Propensity-matched analysis compared 148 patient pairs. K-M survival analysis demonstrated that MG was associated with worse overall survival and recurrence-free survival in propensity score-matched patients (log-rank, P = 0.034 and 0.017, respectively).

CONCLUSIONS

Thymoma patients with MG have smaller tumours and a higher percentage of late-stage tumours, which are mainly of WHO B types, especially B2−B3 types. In addition, MG is significantly associated with worse overall survival and recurrence-free survival in thymoma.
Mid-term outcomes of Contegra implantation for the reconstruction of the right ventricular outflow tract to proximal branch pulmonary arteries: Japan multicentre study
Authors: Hoashi Takaya , Ichikawa Hajime , Hirose Keiichi , Horio Naohiro , Sakurai Takahisa , Matsuhisa Hironori , Ohsima Yoshihiro , Sakurai Hajime , Kasahara Shingo , Sakamoto Kisaburo
Published: February 2021

OBJECTIVES

To reveal the mid-term outcomes of Contegra implantation for the reconstruction of the right ventricular outflow tract to proximal branch pulmonary arteries in a multicentre study.

METHODS

Between April 2013 and December 2019, 178 Contegra conduits were implanted at 5 Japanese institutes. The median age and body weight at operation were 16 months (25th–75th percentile: 8–32) and 8.3 kg (6.4–10.6). Sixteen patients were neonates (9.0%). Selected conduit sizes were 12 mm in 28 patients (15.7%), 14 mm in 67 patients (37.6%), 16 mm in 66 patients (37.1%), 18 mm in 5 patients (2.8%) and <12 mm in 12 patients (6.7%). Fifty-six grafts (31.4%) were ring supported. Proximal branch pulmonary arteries were concomitantly augmented in 85 patients (47.5%). Follow-up was completed in all patients and the median follow-up period was 3.1 years (1.3–5.1).

RESULTS

The overall, conduit explantation-free and conduit infection-free survival rates at 5 years were 91.3%, 71.0% and 83.7%, respectively. Infection (P = 0.009) and common arterial trunk (P = 0.024) were risk factors for explantation. Conduit durability was shorter in smaller one (P < 0.001). Catheter interventions (for conduit to proximal branch pulmonary artery)-free survival rates at 5 years was 52.9%; however, need for catheter interventions was not a risk factor for conduit explantation.

CONCLUSIONS

Mid-term outcomes of reconstruction of the right ventricular outflow tract to the proximal branch pulmonary arteries with Contegra were acceptable. The need for explantation over time was higher in smaller conduits. Conduit infection was a strong risk factor for conduit explantation. Frequently and repeated catheter interventions effectively extended the conduit durability.
Energy and exergy analyses of single flash geothermal power plant at optimum separator temperature
Authors: Assad Mamdouh El Haj , Aryanfar Yashar , Radman Salar , Yousef Bashria , Pakatchian Mohammadreza
Published: February 2021

In this work, a thermodynamic analysis consisting of energy and exergy analyses is carried out to determine the performance of a single flash geothermal power plant. A new derivation for determination of the optimum separator temperature, which results in maximum turbine power output, is achieved. The energy and exergy analyses are carried out at that optimum separator temperature. The thermodynamic derivation showed that the separator would result in maximum performance of the power plant when it operates at the average value of the production well and condenser temperatures. Moreover, the derivation was numerically validated by calculating three different values for the geothermal well temperatures. The results show that the highest exergy destruction rate is in the expansion valve followed by the steam turbine, the mixing process and the pump. The separator has exactly zero exergy destruction rate while the condenser has almost zero exergy destruction rate. The results also show that the exergy destruction rate for all components of the power plant decreases with reduction in the geofluid temperature of the production well except for the condenser. The maximum energy efficiency of the power plant is about 12.5, 11 and 9.5% when the geofluid of the geothermal well temperature is 300, 275 and 250°C, respectively.
ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1
Authors: Morota Gota , Cheng Hao , Cook Dianne , Tanaka Emi
Published: February 2021

Statistical graphics, and data visualization, play an essential but under-utilized, role for data analysis in animal science, and also to visually illustrate the concepts, ideas, or outputs of research and in curricula. The recent rise in web technologies and ubiquitous availability of web browsers enables easier sharing of interactive and dynamic graphics. Interactivity and dynamic feedback enhance human–computer interaction and data exploration. Web applications such as decision support systems coupled with multimedia tools synergize with interactive and dynamic graphics. However, the importance of graphics for effectively communicating data, understanding data uncertainty, and the state of the field of interactive and dynamic graphics is underappreciated in animal science. To address this gap, we describe the current state of graphical methodology and technology that might be more broadly adopted. This includes an explanation of a conceptual framework for effective graphics construction. The ideas and technology are illustrated using publicly available animal datasets. We foresee that many new types of big and complex data being generated in precision livestock farming create exciting opportunities for applying interactive and dynamic graphics to improve data analysis and make data-supported decisions.
Formulating diets based on digestible calcium instead of total calcium does not affect growth performance or carcass characteristics, but microbial phytase ameliorates bone resorption caused by low calcium in diets fed to pigs from 11 to 130 kg
Authors: Lagos L Vanessa , Lee Su A , Bedford Mike R , Stein Hans H
Published: February 2021

An experiment was conducted to test the hypothesis that the requirement for Ca expressed as a ratio between standardized total tract digestible (STTD) Ca and STTD P obtained in short-term experiments may be applied to pigs fed diets without or with microbial phytase from 11 to 130 kg. In a 5-phase program, 160 pigs (body weight: 11.2 ± 1.8 kg) were randomly allotted to 32 pens and 4 corn–soybean meal-based diets in a 2 × 2 factorial design with 2 diet formulation principles (total Ca or STTD Ca), and 2 phytase inclusion levels (0 or 500 units/kg of feed) assuming phytase released 0.11% STTD P and 0.16% total Ca. The STTD Ca:STTD P ratios were 1.40:1, 1.35:1, 1.25:1, 1.18:1, and 1.10:1 for phases 1 to 5, and STTD P was at the requirement. Weights of pigs and feed left in feeders were recorded at the end of each phase. At the conclusion of phase 1 (day 24), 1 pig per pen was euthanized and a blood sample and the right femur were collected. At the end of phases 2 to 5, a blood sample was collected from the same pig in each pen. At the conclusion of the experiment (day 126), the right femur of 1 pig per pen was collected and carcass characteristics from this pig were measured. No interactions were observed between diet formulation principle and phytase inclusion for growth performance in any phase and no differences among treatments were observed for overall growth performance. Plasma Ca and P and bone ash at the end of phase 1 were also not influenced by dietary treatments. However, on day 126, pigs fed nonphytase diets formulated based on total Ca had greater bone ash than pigs fed STTD Ca-based diets, but if phytase was used, no differences were observed between the 2 formulation principles (interaction P < 0.05). At the end of phases 2 and 3, pigs fed diets without phytase had greater (P < 0.05) plasma P than pigs fed diets with phytase, but no differences were observed at the end of phases 4 and 5. A negative quadratic effect (P < 0.05) of phase (2 to 5) on the concentration of plasma Ca was observed, whereas plasma P increased (quadratic; P < 0.05) from phases 2 to 5. However, there was no interaction or effect of diet formulation principle or phytase inclusion on any carcass characteristics measured. In conclusion, STTD Ca to STTD P ratios can be used in diet formulation for growing-finishing pigs without affecting growth performance or carcass characteristics and phytase inclusion ameliorates bone resorption caused by low dietary Ca and P.
Docking domain-mediated subunit interactions in natural product megasynth(et)ases
Authors: Smith Helen G , Beech Matthew J , Lewandowski Józef R , Challis Gregory L , Jenner Matthew
Published: February 2021

Polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) multienzymes produce numerous high value metabolites. The protein subunits which constitute these megasynth(et)ases must undergo ordered self-assembly to ensure correct organisation of catalytic domains for the biosynthesis of a given natural product. Short amino acid regions at the N- and C-termini of each subunit, termed docking domains (DDs), often occur in complementary pairs, which interact to facilitate substrate transfer and maintain pathway fidelity. This review details all structurally characterised examples of NRPS and PKS DDs to date and summarises efforts to utilise DDs for the engineering of biosynthetic pathways.
Anti-cryptococcal activity of preussolides A and B, phosphoethanolamine-substituted 24-membered macrolides, and leptosin C from coprophilous isolates of Preussia typharum
Authors: Perlatti Bruno , Lan Nan , Xiang Meichun , Earp Cody E , Spraker Joseph E , Harvey Colin J B , Nichols Connie B , Alspaugh J Andrew , Gloer James B , Bills Gerald F
Published: February 2021

Cryptococcus neoformans is a serious human pathogen with limited options for treatment. We have interrogated extracts from fungal fermentations to find Cryptococcus-inhibiting natural products using assays for growth inhibition and differential thermosensitivity. Extracts from fermentations of four fungal strains from wild and domestic animal dung from Arkansas and West Virginia, USA were identified as Preussia typharum. The extracts exhibited two antifungal regions. Purification of one region yielded new 24-carbon macrolides incorporating both a phosphoethanolamine unit and a bridging tetrahydrofuran ring. The structures of these metabolites were established mainly by analysis of high-resolution mass spectrometry and 2D NMR data. Relative configurations were assigned using NOESY data, and the structure assignments were supported by NMR comparison with similar compounds. These new metabolites are designated preussolides A and B. The second active region was caused by the cytotoxin, leptosin C. Genome sequencing of the four strains revealed biosynthetic gene clusters consistent with those known to encode phosphoethanolamine-bearing polyketide macrolides and the biosynthesis of dimeric epipolythiodioxopiperazines. All three compounds showed moderate to potent and selective antifungal activity toward the pathogenic yeast C. neoformans.
MHD convection flow of Ag–water nanofluid in inclined enclosure with center heater
Authors: Thangavelu Mahalakshmi , Nagarajan Nithyadevi , Oztop Hakan F , Yang Ruey-Jen
Published: February 2021

Simulations are performed to examine magnetohydrodynamic convection of an Ag–water nanofluid within an inclined enclosure containing a center heater oriented in different directions. In performing the analysis, the left and right vertical walls are assumed to be isothermally cooled, while the bottom wall is isothermally heated and the top wall is adiabatic. The governing equations are solved numerically using the finite-volume method. The simulations focus on the effects of the Rayleigh number (Ra = 104, 105 and 106), Hartmann number (Ha = 0, 25 and 50), inclination angle (γ = 0°, 45°, 90° and 135°), orientation of heater (horizontal or vertical) and internal heat generation (S = 0, 10 and 20) on the convective heat transfer performance within the enclosure. The results show that the heat transfer performance is dominated by the inclination angle of the enclosure and the Hartmann number. In particular, the heat transfer rate reduces as inclination angle and Hartmann number increase. The maximum heat transfer performance is obtained with a vertical center heater, an inclination angle of γ = 45° and a Rayleigh number of Ra = 106. It is additionally shown that the heat transfer performance improves with an increasing volume fraction of nanoparticles.
AI-assisted reliability life prediction model for wafer-level packaging using the random forest method
Authors: Hsiao H Y , Chiang K N
Published: February 2021

We applied an artificial intelligence (AI) algorithm, the random forest (RF) model, using finite element simulations to predict the reliability life of wafer-level packaging (WLP). Due to rapid growth and an increasingly fast cycle pace of integrated circuits, it is imperative to shorten the development time of electronic packaging. This study focuses on packaging reliability analysis and prediction. In recent years, package reliability analysis has been performed using finite element method simulations, which reduce the required number of accelerated thermal cyclic tests. Compared with conventional ball grid array-type packaging, WLP has become the mainstream packaging type due to its small form factor, batch-type manufacturing process and low cost. We applied the RF model, a machine learning algorithm, to predict the reliability life of WLP. The finite element procedure, theory and mesh size were validated by a set of experiments, and a large dataset was generated for AI training purposes through the finite element simulations. The RF method was built using Python®. A fast and robust reliability assessment AI model of WLP can be achieved once the AI training accuracy is located within the target range; the designer only needs to input the geometry of each WLP component to obtain the reliability life cycle. WLP structural optimization can thus be easily achieved. The AI model also significantly shortens the design cycle to meet current design demands.
Numerical simulation of wind loads on an offshore PV panel: the effect of wave angle
Authors: Su Kao-Chun , Chung Ping-Han , Yang Ray-Yeng
Published: February 2021

This numerical simulation determines the wind loads on a stand-alone solar panel in a marine environment. The initial angle of tilt is 20° and 40° and the wind is incident at an angle of 0–180° (in increments of 45°). The wave angle affects the motion of a pontoon. For a wave angle of 0–180° (in increments of 45°), the variation in the surface pressure pattern and the lift coefficient with the angle of incidence of wind and waves in a single period is determined. The lift force is determined by competing the tilt angle for the upper surface with respect to wind and variation in roll angle for a specific wave angle. The data are pertinent to structural design for photovoltaic systems in a marine environment.
Lyme borreliosis presenting as severe back pain after Shinrin-Yoku (forest bathing) in southern Germany
Authors: Weitzel Thomas , Perez Inia , Porte Lorena
Published: February 2021

Since Lyme borreliosis is endemic in the Northern Hemisphere, it is usually not in the spotlight of travel medicine. However, borreliosis is a relevant problem and diagnostic challenge in travelers from the Southern Hemisphere returning from trips to Europe and North America.
A reliable model for estimating the turbulence intensity and integrated astroclimatic parameters from sounding data
Authors: Wu Su , Yang Qike , Xu Jiangyue , Luo Tao , Qing Chun , Su Changdong , Huang Chan , Wu Xiaoqing , Li Xuebin
Published: February 2021

The vertical distributions of atmospheric turbulence ($C_n^2$) are key factors in determining the performance of ground-based telescopes and interferometers. As site-testing campaigns are extremely expensive, atmospheric modelling may represent the estimated results of astronomical sites. We propose a new outer-scale model to estimate refractive index structure constant ($C_n^2$) profiles containing potential temperature and wind shear. The integrated astroclimatic parameters (Fried parameter r0, seeing ε, isoplanatic angle θ0, and coherence time τ0) can also be calculated using this outer-scale model. Radiosonde measurements from a filed campaign at Tibet (Lhasa) and Rongcheng (Shandong) are utilized to quantify the performance of this model. Compared with the Dewan model, HMNSP99 model and Thorpe model, the new model gives better results as a profile and an astroclimatic parameter estimator. Compared with the measured median profile, the correlation coefficient reaches 0.88 in Lhasa and 0.87 in Rongcheng.
Integral field spectroscopy of luminous infrared main-sequence galaxies at cosmic noon
Authors: Hogan L , Rigopoulou D , Magdis G E , Pereira-Santaella M , García-Bernete I , Thatte N , Grisdale K , Huang J-S
Published: February 2021

We present the results of an integral field spectroscopy survey of a sample of dusty (ultra) luminous infrared galaxies (U/LIRGs) at 2 < z < 2.5 using KMOS on the Very Large Telescope. The sample has been drawn from Herschel deep field surveys and benefits from ancillary multiwavelength data. Our goal is to investigate the physical characteristics, kinematics, and the drivers of star formation in the galaxies whose contribution dominates the peak of the cosmic star formation density. Two-thirds of the sample are main-sequence galaxies in contrast to the starburst nature of local U/LIRGs. Our kinematic study, unique in its focus on z ∼ 2 dusty star-forming galaxies, uses the H α emission line to find that ∼40 per cent appear to be isolated discs based on the ratio of rotational velocity to the velocity dispersion, suggesting steady-state mechanisms are sufficient to power the large star formation rates (SFRs). The ratio of obscured to unobscured star formation indicates the sample of galaxies experiences less dust obscuration compared to intermediate and local counterparts, while also hosting cooler dust than local U/LIRGs. In addition to H α we detect [N ii] 6583 Å in our targets and show the gas-phase metallicities do not exhibit the metal deficiency of local U/LIRGs. These results indicate that, despite their extreme IR luminosity, the underlying mechanisms driving the massive SFRs found at cosmic noon are due to scaled up disc galaxies as opposed to mergers.
TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins
Authors: Garcia-Recio Adrián , Gómez-Tamayo José Carlos , Reina Iker , Campillo Mercedes , Cordomí Arnau , Olivella Mireia
Published: February 2021

The massive amount of data generated from genome sequencing brings tons of newly identified mutations, whose pathogenic/non-pathogenic effects need to be evaluated. This has given rise to several mutation predictor tools that, in general, do not consider the specificities of the various protein groups. We aimed to develop a predictor tool dedicated to membrane proteins, under the premise that their specific structural features and environment would give different responses to mutations compared to globular proteins. For this purpose, we created TMSNP, a database that currently contains information from 2624 pathogenic and 196 705 non-pathogenic reported mutations located in the transmembrane region of membrane proteins. By computing various conservation parameters on these mutations in combination with annotations, we trained a machine-learning model able to classify mutations as pathogenic or not. TMSNP (freely available at http://lmc.uab.es/tmsnp/) improves considerably the prediction power of commonly used mutation predictors trained with globular proteins.
CRISPR-SE: a brute force search engine for CRISPR design
Authors: Li Bin , Chen Poshen B , Diao Yarui
Published: February 2021

CRISPR is a revolutionary genome-editing tool that has been broadly used and integrated within novel biotechnologies. A major component of existing CRISPR design tools is the search engines that find the off-targets up to a predefined number of mismatches. Many CRISPR design tools adapted sequence alignment tools as the search engines to speed up the process. These commonly used alignment tools include BLAST, BLAT, Bowtie, Bowtie2 and BWA. Alignment tools use heuristic algorithm to align large amount of sequences with high performance. However, due to the seed-and-extend algorithms implemented in the sequence alignment tools, these methods are likely to provide incomplete off-targets information for ultra-short sequences, such as 20-bp guide RNAs (gRNA). An incomplete list of off-targets sites may lead to erroneous CRISPR design. To address this problem, we derived four sets of gRNAs to evaluate the accuracy of existing search engines; further, we introduce a search engine, namely CRISPR-SE. CRISPR-SE is an accurate and fast search engine using a brute force approach. In CRISPR-SE, all gRNAs are virtually compared with query gRNA, therefore, the accuracies are guaranteed. We performed the accuracy benchmark with multiple search engines. The results show that as expected, alignment tools reported an incomplete and varied list of off-target sites. CRISPR-SE performs well in both accuracy and speed. CRISPR-SE will improve the quality of CRISPR design as an accurate high-performance search engine.
Paraneoplastic neurological syndrome: an evolving story
Authors: Jitprapaikulsan Jiraporn , Paul Pritikanta , Thakolwiboon Smathorn , Mittal Shivam Om , Pittock Sean J , Dubey Divyanshu
Published: February 2021

Paraneoplastic neurological syndrome (PNS) comprises a group of neurological disorders that result from a misguided immune response to the nervous system triggered by a distant tumor. These disorders frequently manifest before the diagnosis of the underlying neoplasm. Since the first reported case in 1888 by Oppenheim, the knowledge in this area has evolved rapidly. Several classic PNS have been described, such as limbic encephalitis, paraneoplastic cerebellar degeneration, encephalomyelitis, opsoclonus-myoclonus, sensory neuronopathy, Lambert-Eaton Myasthenic syndrome, and chronic gastrointestinal dysmotility. It is now recognized that PNS can have varied nonclassical manifestations that extend beyond the traditional syndromic descriptions. Multiple onconeural antibodies with high specificity for certain tumor types and neurological phenotypes have been discovered over the past 3 decades. Increasing use of immune checkpoint inhibitors (ICIs) has led to increased recognition of neurologic ICI-related adverse events. Some of these resemble PNS. In this article, we review the clinical, oncologic, and immunopathogenic associations of PNS.
Associations of dietary vitamin B1, vitamin B2, vitamin B6, and vitamin B12 with the risk of depression: a systematic review and meta-analysis
Authors: Wu Yanjun , Zhang Liming , Li Suyun , Zhang Dongfeng
Published: February 2021

Context

The results from epidemiologic studies on the intake of dietary vitamin B1, B2, B6, and B12 and association with risk of developing depression have been inconsistent.

Objective

The purpose of this systematic review and meta-analysis was to summarize the existing evidence and synthesize the results.

Data Sources

The databases of Web of Science and PubMed were searched for relevant articles published in English until September 2020.

Study Selection

Observational studies that evaluated the associations between depression and dietary vitamin B1, B2, B6, and B12 were included in this study.

Data Extraction

The job of data extraction was undertaken by 2 authors, and the pooled relative risks (RRs) and 95% confidence intervals (CIs) were calculated using a fixed-effects model.

Results

Thirteen articles related to 18 studies were eligible for inclusion in this systematic review and meta-analysis. The pooled RR (95% CI) of depression for the highest vs the lowest category of dietary vitamin B1, B2, B6, and B12 was 0.69 (0.55–0.87), 0.77 (0.67–0.89), 0.81 (0.71–0.93), and 0.86 (0.75–0.99), respectively. The pooled RR (95% CI) of depression for the highest vs the lowest category of dietary vitamin B2 was 0.80 (0.64–0.99) in females and 0.83 (0.67–1.02) in males, for dietary vitamin B6 was 0.71 (0.59–0.86) in females and 0.92 (0.76–1.12) in males, and for dietary vitamin B12 was 0.79 (0.65–0.97) in females and 0.94 (0.77–1.15) in males.

Conclusion

This study suggested that the intake of dietary vitamin B1, B2, B6, and B12 may be inversely associated with the risk of depression; the inverse associations observed between depression and intake of dietary vitamin B2, B6, and B12 were significant in females, but not in males. Further studies are needed to confirm these results.