bluuebunny/crossref_metadata_2025 huggingface dataset:
Trump’s and Biden’s styles during the 2020 US presidential election
Authors: Savoy Jacques , Wehren Marylène
Published: April 2021

This study analyzes the stylistic and rhetorical characteristics of Donald Trump and Joe Biden during the 2020 US presidential election. As communication channels, the oral (TV debates and radio interviews), written speeches, and tweets sent during the last 2 months have been examined. As stylometric markers, the most frequent functional words indicate that Trump employs more diverse personal pronouns more frequently than Biden. For the Democratic nominee, the first-person pronouns (I and we) are mainly used with, compared to Trump, a higher rate of prepositions, signaling the use of a larger number of nouns. When comparing the three media of communication, this study shows that the oral form is closer to the written one and that tweet-based communication presents a distinct type compared with the other two. Usually, written texts tend to contain more functional words than either the oral form or tweets. When comparing the two nominees, the frequency of familiar words (e.g. the, to, of, a) tends to be higher in Biden’s addresses, whereas Trump opts more often for grandiose terms (e.g. great, just, strong). As rhetorical features, the Republican president uses more emotional words, both positive and negative. The Democratic candidate does not propound negative messages and opts for symbolic (e.g. nation, country) and achievement terms (e.g. plan, win, work) with numerous references to people and family (e.g. folks, Americans, son).
Infrared variable stars in the compact elliptical galaxy M32
Authors: Jones O C , Nally C , Sharp M J , McDonald I , Boyer M L , Meixner M , Kemper F , Ferguson A M N , Goldman S R , Rich R M
Published: April 2021

Variable stars in the compact elliptical galaxy M32 are identified, using three epochs of photometry from the Spitzer Space Telescope at 3.6 and 4.5 μm, separated by 32 to 381 d. We present a high-fidelity catalogue of sources detected in multiple epochs at both 3.6 and 4.5 μm, which we analysed for stellar variability using a joint probability error-weighted flux difference. Of these, 83 stars are identified as candidate large-amplitude, long-period variables, with 28 considered high-confidence variables. The majority of the variable stars are classified as asymptotic giant branch star candidates using colour-magnitude diagrams. We find no evidence supporting a younger, infrared-bright stellar population in our M32 field.
MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution
Authors: Gallardo Christian M , Wang Shiyi , Montiel-Garcia Daniel J , Little Susan J , Smith Davey M , Routh Andrew L , Torbett Bruce E
Published: April 2021

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolved genetic interactions given the read-length limitations of next-generation sequencing platforms. This has hampered the direct observation of these genetic interactions that code for protein-protein interfaces with relevance in both drug and vaccine development. Here we overcome these technical limitations by developing a nanopore-based long-range viral sequencing pipeline that yields accurate single molecule sequences of circulating virions from clinical samples. We demonstrate its utility in observing the evolution of individual HIV Gag-Pol genomes in response to antiviral pressure. Our pipeline, called Multi-read Hairpin Mediated Error-correction Reaction (MrHAMER), yields >1000s of viral genomes per sample at 99.9% accuracy, maintains the original proportion of sequenced virions present in a complex mixture, and allows the detection of rare viral genomes with their associated mutations present at <1% frequency. This method facilitates scalable investigation of genetic correlates of resistance to both antiviral therapy and immune pressure and enables the identification of novel host-viral and viral-viral interfaces that can be modulated for therapeutic benefit.
MutationTaster2021
Authors: Steinhaus Robin , Proft Sebastian , Schuelke Markus , Cooper David N , Schwarz Jana Marie , Seelow Dominik
Published: April 2021

Here we present an update to MutationTaster, our DNA variant effect prediction tool. The new version uses a different prediction model and attains higher accuracy than its predecessor, especially for rare benign variants. In addition, we have integrated many sources of data that only became available after the last release (such as gnomAD and ExAC pLI scores) and changed the splice site prediction model. To more easily assess the relevance of detected known disease mutations to the clinical phenotype of the patient, MutationTaster now provides information on the diseases they cause. Further changes represent a major overhaul of the interfaces to increase user-friendliness whilst many changes under the hood have been designed to accelerate the processing of uploaded VCF files. We also offer an API for the rapid automated query of smaller numbers of variants from within other software. MutationTaster2021 integrates our disease mutation search engine, MutationDistiller, to prioritise variants from VCF files using the patient's clinical phenotype. The novel version is available at https://www.genecascade.org/MutationTaster2021/. This website is free and open to all users and there is no login requirement.
Light-induced degradation of SPA2 via its N-terminal kinase domain is required for photomorphogenesis
Authors: Schenk Tobias , Trimborn Laura , Chen Song , Schenkel Christian , Hoecker Ute
Published: April 2021

Arabidopsis (Arabidopsis thaliana) CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and members of the SUPPRESSOR OF PHYTOCHROMEA-105 (SPA) protein family form an E3 ubiquitin ligase that suppresses light signaling in darkness by polyubiquitinating positive regulators of the light response. COP1/SPA is inactivated by light to allow photomorphogenesis to proceed. Mechanisms of inactivation include light-induced degradation of SPA1 and, in particular, SPA2, corresponding to a particularly efficient inactivation of COP1/SPA2 by light. Here, we show that SPA3 and SPA4 proteins are stable in the light, indicating that light-induced destabilization is specific to SPA1 and SPA2, possibly related to the predominant function of SPA1 and SPA2 in dark-grown etiolating seedlings. SPA2 degradation involves cullin and the COP10-DEETIOLATED-DAMAGED-DNA BINDING PROTEIN (DDB1) CDD complex, besides COP1. Consistent with this finding, light-induced SPA2 degradation required the DDB1-interacting Trp-Asp (WD)-repeat domain of SPA2. Deletion of the N-terminus of SPA2 containing the kinase domain led to strong stabilization of SPA2 in darkness and fully abolished light-induced degradation of SPA2. This prevented seedling de-etiolation even in very strong far-red and blue light and reduced de-etiolation in red light, indicating destabilization of SPA2 through its N-terminal domain is essential for light response. SPA2 is exclusively destabilized by phytochrome A in far-red and blue light. However, deletion of the N-terminal domain of SPA2 did not abolish SPA2-phytochrome A interaction in yeast nor in vivo. Our domain mapping suggests there are two SPA2-phytochrome A interacting domains, the N-terminal domain and the WD-repeat domain. Conferring a light-induced SPA2-phyA interaction only via the WD-repeat domain may thus not lead to COP1/SPA2 inactivation.
Habitual Path Dependence of Interorganizational Relationships?—A Commentary on Sedgwick and Jensen
Authors: Sydow Jörg
Published: April 2021

This is a commentary to a former paper by Sedwick and Jensen published in this very journal. On the one hand, the commentary praises the paper’s urgently needed focus on interorganizational relationships and empirical richness. On the other, the commentary questions habitual path dependence as a theoretically useful concept.
Death, Creation, and Future Bias
Authors: Rabenberg Michael
Published: April 2021

A much discussed question in the philosophy of death is whether both of the following claims are true: (1) it is at least typically appropriate to prefer dying further in the future to dying less far in the future; and (2) it is at least typically appropriate not to prefer having been created further in the past to having been created less far in the past. Some philosophers have tried to defend (1) and (2) by appeal to the alleged appropriateness of future bias—roughly, greater concern for certain goods and bads in one's future than for certain goods and bads in one's past. I argue that such approaches to defending (1) and (2) probably cannot succeed, by arguing that even if a very strong version of future bias is appropriate, it does not follow that (1) and (2) are both true. Philosophers attracted to the conjunction of (1) and (2) ought to try to defend it by appeal to something other than future bias.
Personality and insomnia symptoms in older adults: the Baltimore Longitudinal Study of Aging
Authors: Rojo-Wissar Darlynn M , Wanigatunga Amal A , Simonsick Eleanor M , Terracciano Antonio , Wu Mark N , Zipunnikov Vadim , Schrack Jennifer A , Hossain Sharmin , Ferrucci Luigi , Costa Paul T , Spira Adam P
Published: April 2021

Study Objective

To examine associations of personality dimensions and facets with insomnia symptoms in a community sample of older adults.

Methods

We studied 1049 participants aged 60–97 years in the Baltimore Longitudinal Study of Aging. Personality was assessed by the Revised NEO Personality Inventory (NEO-PI-R), and insomnia symptom severity was measured by the Women’s Health Initiative Insomnia Rating Scale (WHIIRS).

Results

Adjusting for demographic characteristics, higher neuroticism, lower conscientiousness, and lower extraversion were associated with greater insomnia symptom severity. These associations remained significant for neuroticism and conscientiousness when further adjusting for depressive symptoms and comorbidities. Higher scores on neuroticism facets Anxiety, Angry Hostility, and Depression, and lower scores on conscientiousness facets Competence, Order, and Achievement Striving and on agreeableness facet Altruism were associated with greater insomnia symptom severity in fully adjusted models. Results were similar among cognitively normal older adults (N = 966), except higher scores on extraversion facets Warmth and Assertiveness associated with lower insomnia symptom severity, and agreeableness facet Altruism was unassociated.

Conclusion

Among older adults, insomnia symptoms appear partially related to personality, with persons higher in neuroticism experiencing greater insomnia symptom severity, and those higher in conscientiousness experiencing lower insomnia symptom severity. Exploring facets of the Big-Five dimensions may provide additional insight regarding the etiology and resolution of sleep disturbance, and some of these associations may differ based on cognitive status. Future studies should investigate the hypothesis that sleep impairment mediates part of the association between specific personality traits and health-related outcomes.
The interplay between anxiety, fear, protective behaviors, compassion, and resilience among older adults during a COVID-19 lockdown: a structural equation modeling study
Authors: Lim Xin Ying , Yap Ai Che , Mahendran Rathi , Yu Junhong
Published: April 2021

The implementation of lockdown measures to curb the transmission of Coronavirus disease-2019 (COVID-19) has brought about significant psychological impacts and older adults have been identified as one of the vulnerable groups. In the current COVID-19 context among older adults in the community, the fear of COVID-19, anxiety symptoms, compassion, resilience, and the practice of protective behaviors are possibly related to each other in several ways. How these factors relate to each other would have important implications in managing the spread of the disease and its mental health consequences. To this end, we modeled their interrelationships using a structural equation model. Older adults (N = 421), aged 60 and above completed various questionnaires—COVID-19 Fear Inventory, Short form of the Geriatric Anxiety Inventory, COVID-19 Risky and Protective Behaviours, Resilience Appraisals Scale, and Compassion Scale during a COVID-19 lockdown. The relationships between these variables were assessed within a structural equation model. The findings showed that older adults who are more compassionate engage in protective behaviors more frequently. Additionally, frequent practice of protective behaviors and greater resilience predicted lower anxiety among older adults. Greater fear predicted higher anxiety levels but did not significantly influence an individual’s engagement in protective behaviors. Mental health services are crucial in fostering resilience and supporting older adults psychologically. Social services are also necessary in maintaining and enhancing social support for older adults. Importantly, these findings suggest that public health communications could promote compassion and avoid using a fear-based approach to increase engagement in protective behaviors.
Insight into Canary Island pine physiology provided by stable isotope patterns of water and plant tissues along an altitudinal gradient
Authors: Miranda José Carlos , Lehmann Marco M , Saurer Matthias , Altman Jan , Treydte Kerstin
Published: April 2021

The Canary Islands, an archipelago east of Morocco’s Atlantic coast, present steep altitudinal gradients covering various climatic zones from hot deserts to subalpine Mediterranean, passing through fog-influenced cloud forests. Unlike the majority of the Canarian flora, Pinus canariensis C. Sm. ex DC. in Buch grow along most of these gradients, allowing the study of plant functioning in contrasting ecosystems. Here we assess the water sources (precipitation, fog) of P. canariensis and its physiological behavior in its different natural environments. We analyzed carbon and oxygen isotope ratios of water and organics from atmosphere, soil and different plant organs and tissues (including 10-year annual time series of tree-ring cellulose) of six sites from 480 to 1990 m above sea level on the Canary Island La Palma. We found a decreasing δ18O trend in source water that was overridden by an increasing δ18O trend in needle water, leaf assimilates and tree-ring cellulose with increasing altitude, suggesting site-specific tree physiological responses to relative humidity. Fog-influenced and fog-free sites showed similar δ13C values, suggesting photosynthetic activity to be limited by stomatal closure and irradiance at certain periods. In addition, we observed an 18O-depletion (fog-free and timberline sites) and 13C-depletion (fog-influenced and fog-free sites) in latewood compared with earlywood caused by seasonal differences in: (i) water uptake (i.e., deeper ground water during summer drought, fog water frequency and interception) and (ii) meteorological conditions (stem radial growth and latewood δ18O correlated with winter precipitation). In addition, we found evidence for foliar water uptake and strong isotopic gradients along the pine needle axis in water and assimilates. These gradients are likely the reason for an unexpected underestimation of pine needle water δ18O when applying standard leaf water δ18O models. Our results indicate that soil water availability and air humidity conditions are the main drivers of the physiological behavior of pine along the Canary Island’s altitudinal gradients.
Urosepsis and the urologist!
Authors: Ryan James , O’Neill Eoghan , McLornan Liza
Published: April 2021

Introduction:

Sepsis is a life-threatening organ dysfunction that is caused by a dysregulated host response to the infection. Urosepsis contributes up to 25% of all sepsis cases. An important part of the management of urosepsis is to rule out possible surgical causes such as urolithiasis, obstructive uropathy, or abscess formation along the urogenital tract.

Objective:

The aim of this study is to look at whether urological conditions and recent urological surgery contribute significantly to all patients admitted with urosepsis.

Methods:

A total of 2679 urine cultures and 654 blood cultures performed in Connolly Hospital Emergency Department were reviewed between 2016 and 2018. Patients were included if they had a matching urine culture and blood culture performed within 24 hours of admission. A retrospective chart review was performed for all patients included in the study.

Results:

Our study included 85 patients admitted with urosepsis between 2016 and 2018. The average age was 70.3 years (21–100 years), in which 61% (n = 52) of patients were female, 18% (n = 16) had a long-term indwelling catheter, 11.8% (n = 10) were admitted as urosepsis with a urological condition. The most common urological condition predisposing patients to urosepsis in this study was bladder outlet obstruction secondary to benign prostatic hyperplasia. A total of 4.7% (n = 4) of patients died during their admission. The complications as a result of urosepsis included a prostatic abscess, a psoas abscess, an ileus, an infected cyst, and 1 case of emphysematous pyelonephritis.

Conclusion:

In this study, the majority of patients admitted with urosepsis did not have an underlying urological condition or recent urological instrumentation. Clinicians should be aware of potential complications as a result of a urosepsis.
Exploring Stakeholder Service Navigation Needs for Children with Developmental and Mental Health Diagnoses
Authors: Yaseen Wid , Steckle Valerie , Sgro Michael , Barozzino Tony , Suleman Shazeen
Published: April 2021

Objective:

Service navigation programs are necessary for children with neurodevelopmental and/or mental health diagnoses to facilitate access to specialized therapies, social services, and community programs, especially those who are socially and economically marginalized. Few studies have included diverse stakeholders in the development and implementation of such programs in resource-limited settings. In this qualitative formative study, we aimed to explore stakeholder experiences after the implementation of a pilot service navigation program in resource-limited settings and identify the perceived elements of an effective service navigator, to develop a revised service navigation program for this patient population.

Methods:

A novel navigation pilot program was implemented in an urban inner-city setting. Using phenomenology as a methodology, we conducted qualitative in-depth interviews with patient caregivers, pediatricians, allied health staff, clinic administrators, and the patient navigator. Data were analyzed within and across stakeholder groups using thematic analysis and supported by group discussion.

Results:

Twenty-five stakeholders participated. All stakeholders reported challenges with accessing services before the implementation of the navigation program. Caregivers expressed frustration navigating a fragmented health care system, while providers felt limited by time and knowledge. The navigator's role was described as multifaceted: finding and completing applications for funding and programs, offering emotional support, liaising between physicians and patients, and advocating with schools and agencies. Based on stakeholder input, a revised service navigation model of care is proposed.

Conclusion:

Caregivers and providers face immense barriers trying to help children with mental health and developmental diagnoses access necessary services and funding. Service navigation programs can be effectively embedded within pediatric clinical teams to improve access to required services for this patient population.
A Longitudinal Study of Assisted Infant Toilet Training During the First Year of Life
Authors: Bender Jeffrey M. , Lee Yelim , Ryoo Ji Hoon , Boucke Laurie , Sun Min , Ball Thomas S. , Rugolotto Simone , She Rosemary C.
Published: April 2021

Objective:

Previous retrospective studies have examined elimination signals, stool toileting refusal, and completion age in Assisted Infant Toilet Training (AITT). The aim of this longitudinal cohort study was to describe the practice of AITT and caregiver satisfaction in a primarily Western setting during the first year of life.

Methods:

Families who started AITT before 4 months of age were recruited. Standardized interviews of caregivers were conducted at 1- to 2-month intervals. To identify trends over time, data were fitted to a linear mixed-effect model. Data were analyzed according to five 2-month blocks, starting at 3 to 4 months.

Results:

Of 85 participating families, 87 children started AITT at a mean age of 2.5 months. At all age intervals, 88% to 94% of caregivers could identify elimination signals. Toileting attempts decreased from 10/day at 3 to 4 months to 7/day at 11 to 12 months (p < 0.001). Many families (45%–53%) practiced AITT on a part-time basis. Daytime dryness was noted in 12% to 14% of infants throughout the first year. Although more than 63% of families used cloth or disposable diapers throughout this study, use of trainers and underwear increased significantly by 2- to 3-fold (p < 0.01 for both). Caregiver satisfaction was high overall. Although negatively associated with potty refusal, it was positively associated with daytime and nighttime dryness, perceived elimination signals, and a better understanding of their infant's needs (p < 0.001 for all).

Conclusion:

This study demonstrates that AITT is a worthy viable alternative to the use of diapers even in Western settings. Better understanding of AITT provides a new perspective to properly meet infants' basic needs.
Peer Relationship Trajectories in Very Preterm and Term Individuals from Childhood to Early Adulthood
Authors: Reyes Lucia M. , Jaekel Julia , Bartmann Peter , Wolke Dieter
Published: April 2021

Objective:

To identify trajectories of peer relationships in very preterm and term-born individuals from 6 to 26 years of age and test early-life predictors of these trajectories.

Method:

As part of the Bavarian Longitudinal Study, 218 very preterm/very low birth weight (VP/VLBW; <32 weeks' gestation/<1500 grams) and 220 healthy term-born (37–42 weeks' gestation) individuals were followed prospectively from birth to adulthood. Parent and self-reports at 6, 8, 13, and 26 years were combined into comprehensive developmentally appropriate scores across 3 domains: peer acceptance, friendships, and peer problems. Latent profile analyses were used to identify trajectories across these 3 domains. Binary and multinomial logistic regressions were used to test the following potential predictors of trajectories: VP/VLBW status, sex, socioeconomic status, neonatal medical risk, parent-infant relationship at 5 months, child inhibitory control at 20 months, and child cognitive abilities at 20 months.

Results:

Three trajectories were identified for peer acceptance and friendships, and 2 trajectories were identified for peer problems. Higher cognitive abilities predicted more optimal trajectories in peer acceptance (odds ratio: 1.03 [95% confidence interval = 1.01–1.05]), friendships (1.03 [1.00–1.05]), and peer problems (1.06 [1.04–1.09]). In addition, good parent-infant relationships predicted lower peer problem trajectories (1.61 [1.03–2.50]).

Conclusion:

Early cognitive deficits may underlie persistent peer relationship difficulties in VP/VLBW samples. Positive parent-infant relationships may help reduce preterm children's risk for long-term peer problems.
Clinical Nurse Specialists in the United States Registered With a National Provider Identifier
Authors: Reed Sean M. , Arbet Jaron , Staubli Linda
Published: April 2021

Purpose/Aims

This study illuminates the workforce of the clinical nurse specialist (CNS), using data from the National Provider Identifier (NPI) registry.

Design

This is a descriptive exploratory study using CNSs' self-reported data within the NPI registry through December 2019.

Methods

Tabulations for frequencies of available demographics, population foci/specialty, and tests for differences in urban/rural locations were conducted. Clinical nurse specialists practicing as nurse practitioners were also counted and identified. Run charts were used to assess quarterly trends for CNSs obtaining new NPIs.

Results

Ten thousand CNSs were registered with an NPI, and 9470 reported 1 population foci/specialty. Furthermore, 1932 CNSs (19.3%) also report working as a nurse practitioner. Only 2 CNS specialties differed by more than 4% between urban and rural areas (respectively): family health (7.7% and 15.5%) and CNSs without a specialty (17.1% and 12.6%). Run charts identified 5 specialties with changing trends in new NPI enumerations (family health, adult-gero, postacute care, pediatrics, and women's health).

Conclusions

Of the estimated 89 122 CNSs in the United States, only 11.2% of the CNS workforce was described and accounted for within the NPI registry. Clinical nurse specialists are encouraged to register for an NPI. Further research is necessary to describe the location and type of work CNSs are performing within the US healthcare system.
Clinical Nurse Specialist Impact on COVID-19 Preparation at a Military Treatment Facility
Authors: Lucciola Megan E. , Nelson Nicole M. , Rea Jessica M. , Boudreaux Allan J. , Fedderson Daniel J. , Hodge Nancy S.
Published: April 2021

Purpose

The COVID-19 pandemic has significantly challenged healthcare organizations across the globe, forcing innovation, resourcefulness, and flexibility. The purpose of this article is to describe the impact of clinical nurse specialist practice on COVID-19 preparation at a military hospital.

Environment of Care Changes

The pandemic required facilities to develop expansion plans to facilitate a potential surge of COVID-19 patients. Clinical nurse specialists collaborated to develop a plan to expand care capacity and streamline testing while designating specific critical care and medical-surgical areas for COVID-19 patients.

Staffing Considerations

To capitalize on the expanded bed capacity, clinical nurse specialists identified and trained outpatient nursing staff to serve as nurse extenders.

Discussion

Early in the pandemic, a lack of strong evidence-based interventions to mitigate transmission and treatment necessitated the development of innovative solutions. The clinical nurse specialist team established designated transport routes for COVID-19 patients, leveraged technology to improve methods of care, and cultivated a culture of innovation by providing on-the-spot meaningful recognition to staff.

Conclusion

As leaders in healthcare, clinical nurse specialists are change agents that work to maintain high-quality, safe patient care even during a global pandemic.
The Wash-Out of Contrast-Enhanced Ultrasound for Evaluation of Hypoxic Ischemic Injury in Neonates and Infants
Authors: Sridharan Anush , Riggs Becky , Darge Kassa , Huisman Thierry A. G. M. , Hwang Misun
Published: April 2021

We evaluated the use of quantitative contrast-enhanced ultrasound (CEUS) to study wash-out behavior of ultrasound contrast agents in the pediatric brain in cases of hypoxic ischemic injury (HII). Six neonates and young infants were imaged using CEUS for suspected HII in the Neonatal Intensive Care Unit/Pediatric Intensive Care Unit. After receiving a bolus of ultrasound contrast agent Lumason (Bracco Diagnostics Inc.), analysis was performed in the whole brain, cortex, cortical/subcortical gray and white matter and central gray nuclei to quantify wash-out metrics and ratios. On magnetic resonance imaging clinical imaging findings, 3 children were classified as unaffected and 3 with classical imaging findings consistent with HII. A lower wash-out rate was found in the case of HII compared with the unaffected cases. Here, we present initial work exploring the wash-out behavior for differentiation between unaffected and HII in the brain. These preliminary findings are indicative of altered hemodynamics in HII and are promising for the potential use of CEUS to quantitatively differentiate between the unaffected and HII brain. Little is known about the CEUS wash-out dynamics, especially in the setting of the pediatric brain injury. Our preliminary findings are encouraging and warrant further investigation into the mechanisms behind delayed clearance of the ultrasound contrast agent in the setting of HII.
Approach of visual stimuli facilitates the prediction of tactile events and suppresses beta band oscillations around the primary somatosensory area
Authors: Kimura Tsukasa
Published: April 2021

The purpose of the present study was to investigate whether the approach of visual stimuli influences prediction of subsequent tactile events. For this purpose, we examined electroencephalograms (EEGs) during the prediction of tactile events when visual stimuli did or did not approach. Tactile stimuli were presented with a high probability (80%) of being applied to the left (or right) index finger and a low probability (20%) of being applied to the opposite index finger. In the approach condition, visual stimuli were presented towards the hand to which the high-probability tactile stimuli were presented; in the neutral condition, visual stimuli did not approach. The result of time-frequency analysis for the EEGs showed that beta band event-related spectral perturbation at the electrodes around the primary somatosensory area (C3 and C4) was suppressed about 300 ms before the presentation of a tactile stimulus and that event-related desynchronization (ERD) occurred in all conditions. Moreover, the beta band ERD of the approach condition was larger than that of the neutral condition. These results provide evidence that the approach of visual stimuli facilitates prediction itself for subsequent tactile events.
Detection of cross-reactive IgA against SARS-CoV-2 spike 1 subunit in saliva
Authors: Tsukinoki Keiichi , Yamamoto Tatsuo , Handa Keisuke , Iwamiya Mariko , Saruta Juri , Ino Satoshi , Sakurai Takashi
Published: April 2021

Abundant secretory IgA (sIgA) in mucus, breast milk, and saliva provides immunity that prevents infection of mucosal surfaces. sIgA in pre-pandemic breast milk samples have been reported to cross-react with SARS-CoV-2, but whether it also occurs in saliva and, if so, whether it cross-reacts with SARS-CoV-2, has remained unknown. We aimed to clarify whether sIgA in saliva cross-reacts with SARS-CoV-2 spike 1 subunit in individuals who have not been infected with this virus. The study included 137 (male, n = 101; female, n = 36; mean age, 38.7 [24–65] years) of dentists and doctors in the Kanagawa Dental University Hospital. Saliva and blood samples were analyzed by PCR and immunochromatography for IgG and IgM, respectively. We then identified patients with saliva samples that were confirmed as PCR- and IgM-negative for COVID-19. Proportions of SARS-CoV-2 cross-reactive IgA-positive individuals were determined by enzyme-linked immunosorbent assay using a biotin-labeled spike S1-mFc recombinant protein covering the receptor-binding domain of SARS-CoV-2. The proportion of SARS-CoV-2 cross-reactive IgA-positive individuals was 46.7%, and this correlated negatively with age (r = −0.218, p = 0.01). The proportion of IgA-positive individuals ≥ 50 y was significantly lower than that of patients aged ≤ 49 y (p = 0.008). sIgA was purified from the saliva of all patients, and the salivary sIgA was found to suppress the binding of SARS-CoV-2 spike protein to the ACE-2 receptor. We found SARS-CoV-2 cross-reactive sIgA in the saliva of some participants who had never been infected with the virus, suggesting that sIgA helps prevent SARS-CoV-2 infection.
Gene name errors: lessons not learned
Authors: Abeysooriya Mandhri , Soria Megan , Kasu Mary Sravya , Ziemann Mark
Published: April 2021

Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. To assess this, we performed a scan of supplementary files published in PubMed Central from 2014 to 2020. Overall, gene name errors continued to accumulate unabated in the period after 2016. An improved scanning software we developed identified gene name errors in 30.9% of articles with supplementary Excel gene lists; a figure significantly higher than previously estimated. This is due to gene names being converted not just to dates and floating-point numbers, but also to internal date format (five-digit numbers). These findings further reinforce that spreadsheets are ill-suited to use with large genomic data.
Deletion of hypoxia-inducible factor prolyl 4-hydroxylase 2 inFoxD1-lineage mesenchymal cells leads to congenital truncal alopecia
Authors: Rosendahl Ann-Helen , Monnius Mia , Laitala Anu , Railo Antti , Miinalainen Ilkka , Heljasvaara Ritva , Mäki Joni M. , Myllyharju Johanna
Published: April 2021

Hypoxia-inducible factors (HIFs) induce hundreds of genes regulating oxygen homeostasis in tissues. Oxygen sensors of the cells, the HIF prolyl 4-hydroxylases (HIF-P4Hs), regulate the stability and activity of HIFs in an oxygen-dependent manner. In this study, we show that lack ofHif-p4h-2inFoxD1-lineage mesodermal cells interferes the normal development of hair follicles (HF) in mice. TheFoxD1-lineage cells were found to be mainly mesenchymal cells located in the dermis of truncal skin, including the cells composing the dermal papilla of the HF. UponHif-p4h-2inactivation, HF development was disturbed during the first catagen leading to formation of large epithelial lined HF cysts filled by unorganized keratins, which eventually manifested as truncal alopecia. The depletion ofHif-p4h-2led to HIF stabilization and dysregulation of multiple genes involved in keratin formation, HF differentiation, and HIF, TGFβ and Notch signaling. The failure of the controlled process of HF cycling is likely to be mechanistically caused by disruption of the precise and timely interplay of the HIF, TGFβ and Notch pathways. In summary, we show here for the first time that HIF-P4H-2 function inFoxD1-lineage cells is essential for the normal development and homeostasis of HFs.
Mobius Assembly for Plant Systems highlights promoter-terminator interaction in gene regulation
Authors: Andreou Andreas I. , Nirkko Jessica , Ochoa-Villarreal Marisol , Nakayama Naomi
Published: April 2021

Plant synthetic biology is a fast-evolving field that employs engineering principles to empower research and bioproduction in plant systems. Nevertheless, in the whole synthetic biology landscape, plant systems lag compared to microbial and mammalian systems. When it comes to multigene delivery to plants, the predictability of the outcome is decreased since it depends on three different chassis:E. coli,Agrobacterium, and the plant species. Here we aimed to develop standardised and streamlined tools for genetic engineering in plant synthetic biology. We have devised Mobius Assembly for Plant Systems (MAPS), a user-friendly Golden Gate Assembly system for fast and easy generation of complex DNA constructs. MAPS is based on a new group of small plant binary vectors (pMAPs) that contains an origin of replication from a cryptic plasmid ofParacoccus pantotrophus. The functionality of the pMAP vectors was confirmed by transforming the MM1 cell culture, demonstrating for the first time that plant transformation is dependent on theAgrobacteriumstrains and plasmids; plasmid stability was highly dependent on the plasmid and bacterial strain. We made a library of new short promoters and terminators and characterised them using a high-throughput protoplast expression assay. Our results underscored the strong influence of terminators in gene expression, and they altered the strength of promoters in some combinations and indicated the presence of synergistic interactions between promoters and terminators. Overall this work will further facilitate plant synthetic biology and contribute to improving its predictability, which is challenged by combinatorial interactions among the genetic parts, vectors, and chassis.
Candida albicansenhances the progression of oral squamous cell cancrinomain vitroandin vivo
Authors: Vadovics M , Igaz N , Alföldi R , Rakk D , Veres É , Szücs B , Horváth M , Tóth R , Szücs A , Horváth P , Tiszlavicz L , Vágvölgyi C , Nosanchuk JD , Szekeres A , Kiricsi M , Puskás LG , Gácser A
Published: April 2021

Oral squamous cell carcinoma (OSCC) is a serious health issue worldwide. OSCC is highly associated with oral candidiasis, although it is unclear whether the fungus promotes the genesis and progression of OSCC or cancer facilitates the growth of the fungus. Therefore, we investigated whetherCandidacould directly influence OSCC development and progression. Ourin vitroresults suggest that the presence of liveC. albicans, but notC. parapsilosis, enhances the progression of OSCC by stimulating the production of matrix metalloproteinases, oncometabolites, pro-tumor signaling routes, and overexpression of prognostic marker genes associated with metastatic events. We also found that oral candidiasis triggered byC. albicansenhanced the progression of OSCCin vivothrough the induction of inflammation and overexpression of metastatic genes and markers of epithelial-mesenchymal transition. Taken together, these results suggest thatC. albicansactively participates in the complex process of OSCC progression.
Are some commercial diets inadequate in essential nutrients?
Authors: Preston Alan M. , Rodriguez Cindy A. , Preston Marianna M.
Published: April 2021

Background

Commercial manufacturers have formulated diets to promote not only weight reduction but also to reduce risks of chronic diseases. The objective of this study is to determine if these formulations satisfy requirements for essential nutrients.

Methods

We have selected two established commercial diets, one low fat, high carbohydrate (diet 1) and the other, high fat, low carbohydrate (diet 2) and determined “representative meals” through use of recipes suggested in the manufacturer’s manuals. Nutrition Data System for Research (NDSR) software has been used to perform the most extensive nutrient analysis to date of these diets. Tables report macronutrients (energy), vitamins, minerals, essential amino acids, essential lipids and nutrient-related components for a total of 62entries.

Results

Diet 1 satisfied requirements for 50 of these (81%) with only vitamin B12, vitamin D, and essential fatty acids not reaching recommended levels, while fiber and glycemic load exceeded suggested values. Diet 2 satisfied requirements for 46 of the components (71%) but had excess percentage of fat, especially saturated fat, sodium and cholesterol as well as decreased percentage of carbohydrate resulting in suboptimal intake of B-complex vitamins (B1, niacin and total folate) as well as fiber.

Conclusions

Neither diet satisfied adequacy for all reported nutrients. However, based on nutrient content alone diet 1, if supplemented or modified, could be sustained over the long term whereas diet 2 should not be encouraged for long term adaptation
Enhancers, gene regulation, and genome organization
Authors: Dean Ann , Larson Daniel R. , Sartorelli Vittorio
Published: April 2021

How transcriptional enhancers function to activate distant genes has been the subject of lively investigation for decades. “Enhancers, gene regulation, and genome organization” was the subject of a virtual meeting held November 16–17, 2020, under sponsorship of the National Cancer Institute (NCI), the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health (NIH). The goal of the meeting was to advance an understanding of how transcriptional enhancers function within the framework of the folded genome as we understand it, emphasizing how levels of organization may influence each other and may contribute to the spatiotemporal specification of transcription. Here we focus on broad questions about enhancer function that remain unsettled and that we anticipate will be central to work in this field going forward. Perforce, we cover contributions of only some speakers and apologize to other contributors in vital areas that we could not include because of space constraints.
Crystal structure of hemoglobin from mouse (Mus musculus) compared with those from other small animals and humans
Authors: Sundaresan Selvarajan Sigamani , Ramesh Pandian , Shobana Nagaraj , Vinuchakkaravarthy Thangaraj , Yasien Sayed , Ponnuswamy Mondikalipudur Nanjappa Gounder
Published: April 2021

Mice (Mus musculus) are nocturnal small animals belonging to the rodent family that live in burrows, an environment in which significantly high CO2 levels prevail. It is expected that mouse hemoglobin (Hb) plays an important role in their adaptation to living in such a high-CO2 environment, while many other species cannot. In the present study, mouse Hb was purified and crystallized at a physiological pH of 7 in the orthorhombic space group P212121; the crystals diffracted to 2.8 Å resolution. The primary amino-acid sequence and crystal structure of mouse Hb were compared with those of mammalian Hbs in order to investigate the structure–function relationship of mouse Hb. Differences were observed from guinea pig Hb in terms of amino-acid sequence and from cat Hb in overall structure (in terms of r.m.s.d.). The difference in r.m.s.d. from cat Hb may be due to the existence of the molecule in a conformation other than the R-state. Analysis of tertiary- and quaternary-structural features, the α1β2 interface region and the heme environment without any ligands in all four heme groups showed that mouse methemoglobin is in an intermediate state between the R-state and the T-state that is much closer to the R-state conformation.
How hydrological connectivity regulates the plant recovery process in salt marshes
Authors: Wang Qing , Xie Tian , Luo Meng , Bai Junhong , Chen Cong , Ning Zhonghua , Cui Baoshan
Published: April 2021

Designing effective restoration strategies is a priority in recovering salt marsh plants. Hydrological connectivity is a main driver underpinning the success of the plant recovery process and can regulate life‐history process‐based restoration strategies. However, the relationship between these is unclear.

Plant recovery needs to go through a whole life‐history process, from seed to adult. Common restoration strategies are seed addition (SA) or seedling transplantation (ST), which start from seed germination and seedling growth stage. Besides these two strategies, another strategy starting from seed retention stage, microtopographic adjustment (MA), was designed to study the relationship with hydrological connectivity. A framework was also constructed to assess a gradient of hydrological connectivity between marsh plain and sea. We conducted several field experiments to test their relationships.

The composite measurement of hydrological connectivity with five geomorphic variables can well represent the variation of environmental factors. Soil moisture, inundation frequency and sediment deposition were positively correlated, while soil salinity and hardness were negatively correlated with hydrological connectivity.

The success of different restoration strategies varied with hydrological connectivity. MA showed a monotone decreasing trend, while SA and ST showed a unimodal trend as hydrological connectivity increased. Importantly, each strategy occupies a non‐overlapping optimum range along the hydrological connectivity gradient. There is low hydrological connectivity for MA (0–0.28), middle hydrological connectivity for SA (0.28–0.55) and high hydrological connectivity for ST (0.55–1).

Synthesis and applications. Our findings expand the quantification of the hydrological environment beyond elevation, distance or other single index to include a range of elements of hydrological connectivity, thus illustrating the underlying mechanisms of hydrological connectivity which regulate restoration strategies based on different life stages. The results provide a reliable framework to assess hydrological connectivity and offer guidance to select the optimum restoration strategy under different hydrological connectivities or to regulate the hydrological connectivity variables (topography on marsh plain and morphology of tidal creeks) to relief stresses. These findings will be beneficial to ecological restoration and coastal management.
Signalling pathway of U46619‐induced vascular smooth muscle contraction in mouse coronary artery
Authors: Jiang Run‐Sheng , Zhang Li , Yang Hui , Zhou Meng‐Yuan , Deng Chun‐Yu , Wu Wei
Published: April 2021

Background

Thromboxane A2 (TXA2) participates in many pathophysiological processes of coronary artery disease. However, its mechanism of TXA2‐induced contraction in the coronary artery remains to be clarified. A multi myograph system was used to measure the isometric tension of the mouse coronary arteries and identify the effect and pathway of TXA2 analogues U46619. Confocal laser scanning microscopy was used to measure the intracellular calcium concentration ([Ca2+]i) in mouse coronary artery smooth muscle cells. Results from the experiment had shown that contraction in coronary artery was generated by U46619 in a concentration‐dependent manner, which was completely abolished by a specific TXA2 receptor blocker, GR32191. PI‐PLC inhibitors U73122 and D609 and Rho‐Kinase inhibitor Y‐27632 can block the U46619 elicited coronary artery contraction in a dose‐dependent manner. Then, the vasoconstriction response to U46619 was obviously inhibited by two pan‐PKC inhibitors chelerythrine or Gӧ6983, and a selective PKCδ inhibitor rottlerin, but was not blocked by a selective PKCζ inhibitor PKC‐PS or a selective PKCβ inhibitor hispidin. Meanwhile, the PKC activator PDBu‐induced vasoconstriction was significantly inhibited by 1 μmol/L nifedipine, then mostly inhibited by 100 μmol/L 2‐APB and 10 μmol/L Y27632. We further found that the response to U46619 was inhibited, respectively, by three calcium channel blockers nifedipine, SKF96356 or 2‐APB in a concentration‐dependent manner. Although Store‐operated Ca2+ (SOC) channels generated the increase of [Ca2+]i in mouse coronary artery smooth muscle cells, SOC channels did not contribute to the vasoconstriction in mouse coronary arteries. Caffeine‐induced sarcoplasmic reticulum (SR) Ca2+ release could obviously induce coronal vasoconstriction. In addition, NPPB, a cell membrane Ca2+ activated C1− channel blocker, could obviously inhibit the U46619‐induced vasoconstriction. The U46619‐induced mouse coronary artery contraction was involved in the increase in [Ca2+]i mediated by Cav1.2, TRPC channels and SR release through the activation of G‐protein‐coupled TP receptors and the kinases signalling pathway in TP downstream proteins, while SOC channels did not participate in the vasoconstriction.
‘We have so many challenges’: Small‐scale mining, Covid‐19 and constant interruptions in West Africa
Authors: PIJPERS ROBERT JAN , LUNING SABINE
Published: April 2021

Currently, the impacts of Covid‐19 are receiving significant global attention. This also applies to the extractive industries, where this global crisis is directing the gaze of policymakers, donors and academics alike. Covid‐19 is seen as having far‐reaching and disruptive consequences, especially in the case of artisanal and small‐scale mining. While the authors consider this attention important, their work on artisanal and small‐scale mining in Ghana – and West Africa more broadly – reveals that for many miners, Covid‐19 is ‘just’ another interruption to their lives and lifeworlds which are chronically affected by interruptions of different scales, magnitudes and temporalities. As anthropologists have shown, foregrounding this structural condition – which is emblematic for the lives of many people, especially in the Global South – is key to questioning, understanding and contextualizing the current moment of ‘global’ crisis and must be an element of any policy and research emerging from it.