bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating both genetic and tobacco smoking data to identify high-risk smokers for lung cancer screening
Authors: Jia Guochong , Wen Wanqing , Massion Pierre P , Shu Xiao-Ou , Zheng Wei
Published: February 2021

The US Preventive Services Task Force (USPSTF) recently proposed to widen the current lung cancer screening guideline to include less-heavy smokers. We sought to incorporate both genetic and tobacco smoking data to evaluate the proposed new guideline in white smokers. We constructed a polygenic risk score (PRS) using lung cancer risk variants. Using data from 308 490 participants of European descent in the UK Biobank, a population-based cohort study, we estimated hazard ratios of lung cancer associated with both tobacco smoking and PRS to identify individuals at a similar or higher risk than the group of heavy smokers who are recommended for screening under the USPSTF-2014 guideline (≥30 pack-years, either current or former smokers who quit within 15 years). During a median follow-up of 5.8 years, 1449 incident cases of lung cancer were identified. We found a similar lung cancer risk for current smokers with 20–29 pack-years [hazard ratio = 20.7, 95% confidence interval: 16.3–26.4] and the ‘heavy smoker group’ defined above (hazard ratio = 19.9, 95% confidence interval: 16.8–23.6) compared with never smokers. Current smokers with 20–29 pack-years did not reach a 6-year absolute risk of 0.0151, a suggested risk threshold for using low-dose computed tomography screening, until the age of 55 years. However, these smokers at high genetic risk (PRS ≥ 80%) reached this risk level at the age of 50. Our findings support the USPSTF proposal to lower the smoking pack-year eligibility to 20 pack-years for current smokers and suggest that PRS for lung cancer could be considered to identify high-risk smokers for screening.
Natural variation in social conditions affects male mate choosiness in the amphipodGammarus roeselii
Authors: Lipkowski Konrad , Steigerwald Sophie , Schulte Lisa M , Sommer-Trembo Carolin , Jourdan Jonas
Published: February 2021

The extent of male mate choosiness is driven by a trade-off between various environmental factors associated with the costs of mate acquisition, quality assessment and opportunity costs. Our knowledge about natural variation in male mate choosiness across different populations of the same species, however, remains limited. In this study, we compared male mate choosiness across 10 natural populations of the freshwater amphipod Gammarus roeselii (Gervais 1835), a species with overall high male mating investments, and evaluated the relative influence of population density and sex ratio (both affecting mate availability) on male mate choosiness. We investigated amplexus establishment after separating mating pairs and presenting focal males with a novel, size-matched female from the same population. Our analysis revealed considerable effects of sex ratio and (to a lesser extent) population density on time until amplexus establishment (choosiness). Male amphipods are able to perceive variable social conditions (e.g., sex ratio) and modify their mating strategy accordingly: We found choosiness to be reduced in increasingly male-biased populations, whereas selectivity increases when sex ratio becomes female biased. With this, our study expands our limited knowledge on natural variations in male mate choosiness and illustrates the importance of sex ratio (i.e., level of competition) for male mating decisions in natural environments. Accounting for variation in sex ratios, therefore, allows envisioning a distinctive variation of choosiness in natural populations and highlights the importance of considering social background information in future behavioral studies.
Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’
Authors: Shirasawa Kenta , Itai Akihiro , Isobe Sachiko
Published: February 2021

We analyzed the genome sequence of a Japanese pear (Pyrus pyrifolia) to facilitate its genetics and genomics as well as breeding programs, in which a variety 'Nijisseiki' with superior flesh texture has been used as a parent for most Japanese pear cultivars. De novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 high-confidence protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of genome-wide duplication was observed, consistent with related species. This is the first chromosome-scale genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.
Still taboo? Using machine translation for low-level EFL writers
Authors: Lee Yoo-Jean
Published: February 2021

This study investigates the application of machine translation (MT) in an EFL writing class and its impact on lower proficiency level writers. Theoretically grounded in the social nature of learning, the MT-based writing class is applied to students in four steps: planning, drafting with MT, revising MT output, and individual writing with MT. The peer-editing process and the teacher’s guidance have been found to be critical factors in terms of enhancing students’ metalinguistic awareness at both the micro-level and macro-level revisions of MT output. Additionally, by gaining confidence and motivation, the students become more autonomous and self-directed. The results of this study provide insights into how an MT-based EFL writing class can be conducted successfully by including peer and teacher feedback and thus result in MT being viewed as an effective tool, rather than being considered taboo for helping lower level EFL learners in writing.
Genomic Evidence for Convergent Molecular Adaptation in Electric Fishes
Authors: Wang Ying , Yang Liandong
Published: February 2021

Fishes have independently evolved electric organs (EOs) at least six times, and the electric fields are used for communication, defense, and predation. However, the genetic basis of convergent evolution of EOs remains unclear. In this study, we conducted comparative genomic analyses to detect genes showing signatures of positive selection and convergent substitutions in electric fishes from three independent lineages (Mormyroidea, Siluriformes, and Gymnotiformes). Analysis of 4,657 orthologs between electric fishes and their corresponding control groups identified consistent evidence for accelerated evolution in electric fish lineages. A total of 702 positively selected genes (PSGs) were identified in electric fishes, and many of these genes corresponded to cell membrane structure, ion channels, and transmembrane transporter activity. Comparative genomic analyses revealed that widespread convergent amino acid substitutions occurred along the electric fish lineages. The overlap of convergent genes and PSGs was identified as adaptive convergence, and a subset of genes was putatively associated with electrical and muscular activities, especially scn4aa (a voltage-gated sodium channel gene). Our results provide hints to the genetic basis for the independent evolution of EOs during millions of years of evolution.
Short-, Medium-, and Long-term Weight Changes and All-Cause Mortality in Old Age: Findings From the National Survey of the Japanese Elderly
Authors: Murayama Hiroshi , Liang Jersey , Shaw Benjamin A , Botoseneanu Anda , Kobayashi Erika , Fukaya Taro , Shinkai Shoji
Published: February 2021

Background

Recent studies, predominantly in Western populations, suggest that both weight loss and weight gain are associated with an increased mortality risk in old age. However, evidence of this association in older Asian populations remains sparse. This study aimed to examine the association between weight change and all-cause mortality in a nationally representative sample of community-dwelling older Japanese people.

Methods

Data were obtained from the National Survey of the Japanese Elderly, which included 4869 adults aged ≥60 years. Participants were followed for up to 30 years. We considered 3 indicators of weight change according to the follow-up interval: short-term (3 years), medium-term (6–7 years), and long-term (12–13 years). Weight change was classified as loss ≥ 5%, loss 2.5%–4.9%, stable (±2.4%), gain 2.5%–4.9%, and gain ≥ 5%. Cox proportional hazards models were used to calculate the relative mortality risk of each weight change category.

Results

Weight loss ≥ 5% for all intervals was associated with higher mortality than stable weight and the effects were largely similar across all 3 intervals (hazard ratio [95% confidence interval]: 1.36 [1.22–1.51] for short-term, 1.36 [1.22–1.51] for medium-term, and 1.31 [1.11–1.54] for long-term). A similar pattern of results was observed among the young–old and old–old, and among men and women. The effect of weight loss on higher mortality was greater among those with a lower body mass index at baseline.

Conclusions

These findings could inform clinical and public health approaches to body-weight management aimed at improving the health and survival of older adults, particularly in Asian populations.
Cultural Differences in the Intended Use of Long-Term Care Services in the United States: The Role of Family Ties
Authors: Diederich Freya , König Hans-Helmut , Brettschneider Christian
Published: February 2021

Objectives

In the light of an increasingly diverse older population in the United States, there is an ongoing discussion on how cultural factors contribute to individual long-term care (LTC) needs and service use. This study empirically assesses whether the level of acculturation and cultural differences in the importance of the family shape foreign-born immigrants’ intention to use certain LTC services.

Methods

We correlated immigrants’ intention to use certain LTC services to the cultural strength of family ties that prevails in their region of origin. We used data from the National Health Interview Survey and the World Values Survey/European Values Study for analysis. Multinomial logit models were estimated and predisposing, enabling, and need factors were controlled for. Estimations were weighted to account for the sampling structure, and sensitivity analyses were conducted.

Results

Immigrants from cultures with stronger family ties are significantly more likely to intend the use of LTC options that include the family. Furthermore, immigrants are less likely to intend the use of exclusively family care when having lived in the United States for a longer time.

Discussion

We conclude that cultural differences in family ties shape immigrants’ intention to use certain LTC services. If policymakers aim at increasing the provision of specific LTC services or support to family caregivers, there should be a careful evaluation of demand-side factors in an increasingly culturally diverse society.
Further analyses of APRIL/APRIL-receptor/glycosaminoglycan interactions by biochemical assays linked to computational studies
Authors: Marcisz Mateusz , Huard Bertrand , Lipska Agnieszka G , Samsonov Sergey A
Published: February 2021

A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor superfamily. APRIL is quite unique in this superfamily for at least for two reasons: (i) it binds to glycosaminoglycans (GAGs) via its positively charged N-terminus; (ii) one of its signaling receptor, the transmembrane activator and CAML interactor (TACI), was also reported to bind GAGs. Here, as provided by biochemical evidences with the use of an APRIL deletion mutant linked to computational studies, APRIL–GAG interaction involved other regions than the APRIL N-terminus. Preferential interaction of APRIL with heparin followed by chondroitin sulfate E was confirmed by in silico analysis. Both computational and experimental approaches did not reveal the heparan sulfate binding to TACI. Together, computational results corroborated experiments contributing with atomistic details to the knowledge on this biologically relevant trimolecular system. Additionally, a high-throughput rigorous analysis of the free energy calculations data was performed to critically evaluate the applied computational methodologies.
Equity at a time of pandemic
Authors: Plamondon Katrina M
Published: February 2021

Health promotion has long aspired for a world where all people can live to their full potential. Yet, COVID-19 illuminates dramatically different consequences for populations bearing heavy burdens of systemic disadvantage within countries and between the Global South and Global North. Many months of pandemic is entrenching inequities that reveal themselves in the vastly differential distribution of hospitalization and mortality, for example, among racialized groups in the USA. Amplified awareness of the intimate relationship between health, social structures, and economy opens a window of opportunity to act on decades of global commitments to prioritize health equity. Choices to act (or not act) are likely to accelerate already vast inequities within and between countries as rapidly as the COVID-19 pandemic itself. Recognizing the inherently global nature of this pandemic, this article explores how determinants of equity are embedded in global responses to it, arguing that these determinants will critically shape our global futures. This article aims to stimulate dialogue about equity-centered health promoting action during a pandemic, using the Canadian Coalition for Global Health Research (CCGHR) Principles for Global Health Research to examine equity considerations at a time of pandemic. Attentiveness to power and the relationship between political economy and health are argued as central to identifying and examining issues of equity. This article invites dialogue about how equity-centered planning, decision-making and action could leverage this massive disruption to society to spark a more hopeful, just, and humane collective future.
Exome sequencing and functional studies in zebrafish identify WDR8 as the causative gene for isolated Microspherophakia in Indian families
Authors: Madhangi M , Dutta Debanjan , Show Sautan , Bhat Vishwanath K , Rather Mohammad I , Tiwari Ankana , Singh Nivedita , Duvvari Maheswara R , Murthy Gowri J , Kumar Arun , Nongthomba Upendra
Published: February 2021

Isolated Microspherophakia (MSP) is an autosomal recessive disorder characterized by a smaller than normal spherical lens. Till date, LTBP2 is the only gene shown to cause MSP. We used homozygosity mapping and whole-exome sequencing and identified a homozygous mutation, c.1148C > T (p.Pro383Leu), in the WDR8 (or WRAP73) gene in two Indian MSP families. In vitro experiments showed that the missense mutation renders the protein unstable. WDR8 is a centriolar protein that has important roles in centrosomal assembly, spindle pole formation and ciliogenesis. Co-immunoprecipitation experiments from HeLa cells indicated that the mutation interferes with the interaction of WDR8 with its binding partners. In zebrafish, both morpholino-mediated knockdown and CRISPR/Cas knockout of wdr8 resulted in decreased eye and lens size. The lack of wdr8 affected cell cycle progression in the retinal cells, causing a reduction in cell numbers in the retina and lens. The reduction in eye size and the cell cycle defects were rescued by exogenous expression of the human wild-type WDR8. However, the human mutant WDR8 (p.Pro383Leu) was unable to rescue the eye defects, indicating that the missense mutation abrogates WDR8 protein function. Thus, our zebrafish results suggested that WDR8 is the causative gene for MSP in these Indian families.
Preoperative risk factors influencing inter-stage mortality after the Norwood procedure
Authors: Ono Masamichi , Kido Takashi , Wallner Marie , Burri Melchior , Lemmer Julia , Ewert Peter , Strbad Martina , Cleuziou Julie , Hager Alfred , Hörer Jürgen
Published: February 2021

OBJECTIVES

With improvements in early survival after the stage I palliation (S1P) Norwood procedure for hypoplastic left heart syndrome (HLHS) and its variants, inter-stage death accounts for an increasing proportion of mortality. Our aim was to identify the risk factors for inter-stage mortality.

METHODS

The records of 322 neonates with HLHS or a variant who underwent the Norwood procedure at our centre between 2001 and 2019 were retrospectively analysed.

RESULTS

The diagnoses included 271 neonates with HLHS (84%) and 51 with variants (16%). Aortic atresia was observed in 138 (43%) patients, mitral atresia in 91 (28%), extracardiac anomalies in 42 (13%) and genetic disorder in 14 (4%). The median age and weight of the patients at the S1P Norwood procedure were 9 (interquartile range: 7–12) days and 3.2 (2.9–3.5) kg, respectively. The median cardiopulmonary bypass time was 137 (107–163) min. Modified Blalock–Taussig shunts were used in 159 (49%) and unvalved right ventricle-to-pulmonary artery shunts in 163 (51%) patients. The number of inter-stage deaths was as follows: between S1P and stage II palliation (S2P), 61 including 38 early (<30 days) and 23 late (>30 days) deaths, and between S2P and stage III palliation, 32 deaths. Low birth weight (<2.5 kg) (odds ratio 4.37, P = 0.020) and restrictive atrial septum (odds ratio 2.97, P = 0.013) were identified as risks for early mortality. Low birth weight [hazard ratio (HR) 0.99/g, P = 0.002] was a risk for inter-stage mortality between S1P and S2P. Extracardiac anomalies (HR 4.75, P = 0.049) and significant pre-S1P atrioventricular valve regurgitation (HR: 7.72, P = 0.016) were risks for inter-stage mortality between S2P and stage III palliation. Other anatomical variables including aortic atresia, anatomical subtypes and the diameter of the ascending aorta nor shunt type were not identified as risk factors for mortality during any inter-stage period.

CONCLUSIONS

The risk factors for inter-stage attrition after the Norwood procedure were different between each stage. Preoperative factors, including birth weight, restrictive atrial septum and extracardiac anomalies, adversely affected the inter-stage mortality.
Technical note: validation of the GreenFeed system for measuring enteric gas emissions from cattle
Authors: McGinn Sean M , Coulombe Jean-Franҫois , Beauchemin Karen A
Published: February 2021

There are knowledge gaps in animal agriculture on how to best mitigate greenhouse gas emissions while maintaining animal productivity. One reason for these gaps is the uncertainties associated with methods used to derive emission rates. This study compared emission rates of methane (CH4) and carbon dioxide (CO2) measured by a commercially available GreenFeed (GF) system with those from (1) a mass flow controller (MFC) that released known quantities of gas over time (i.e., emission rate) and (2) a respiration chamber (RC). The GF and MFC differed by only 1% for CH4 (P = 0.726) and 3% for CO2 (P = 0.013). The difference between the GF and RC was 1% (P = 0.019) for CH4 and 2% for CO2 (P = 0.007). Further investigation revealed that the difference in emission rate for CO2 was due to a small systematic offset error indicating a correction factor could be applied. We conclude that the GF system accurately estimated enteric CH4 and CO2 emission rates of cattle over a short measurement period, but additional factors would need to be considered in determining the 24-hr emission rate of an animal.
Optimization of a Diet for the Greater Wax Moth (Lepidoptera: Pyralidae) Using Full Factorial and Mixture Design
Authors: Hickin Mauri , Nadel Hannah , Schal Coby , Cohen Allen C
Published: February 2021

Diet optimization is an important process to increase the efficiency of rearing insects and can be used to develop high-quality insects with specific fitness and life-history traits. Galleria mellonella (L.), the greater wax moth, is widely used in research, microbiology assays, as pet food, and host for biological control agents. Although artificial diets for G. mellonella have been researched and optimized for decades, preliminary tests indicated that the predominantly utilized G. mellonella diet could be improved to yield larger larvae with a short development time. We used a design of experiments (DOE) approach that incorporated multiple full factorial designs and a final mixture design to test the qualitative and quantitative effects of ingredients and their interactions on larval mass and survival. Analysis of 17 ingredient variations in 35 diet formulations yielded an optimized diet that supported high survival and 2.4-fold greater larval body mass than the standard rearing diet. This study demonstrates the importance and efficiency of statistical DOE in guiding the optimization of insect diets to improve traits that represent the quality and fitness of the reared insects.
Susceptibility of Brazilian Populations of Anastrepha fraterculus, Ceratitis capitata (Diptera: Tephritidae), and Drosophila suzukii (Diptera: Drosophilidae) to Selected Insecticides
Authors: Morais Maíra C , Rakes Matheus , Padilha Aline C , Grützmacher Anderson D , Nava Dori E , Bernardi Oderlei , Bernardi Daniel
Published: February 2021

Anastrepha fraterculus (Wiedemann), Ceratitis capitata (Wiedemann), and Drosophila suzukii (Matsumura) are the main fruit pests in Brazil. Here, we evaluated the susceptibility of Brazilian populations of A. fraterculus, C. capitata, and D. suzukii to selected insecticides. In ingestion bioassays, adults from a laboratory susceptible population of each species were exposed to five different modes of action of insecticide. Then, field populations of each species were exposed to the diagnostic concentrations to evaluate possible changes in susceptibility. Our findings indicate that lambda-cyhalothrin, malathion, and spinosad had similar levels of toxicity against a susceptible laboratory population of A. fraterculus, with LC50 values of 6.34, 6.54, and 8.76 µg a.i./ml, respectively. Ceratitis capitata had similar susceptibilities to spinosad (1.30 µg a.i./ml), spinetoram (2.76 µg a.i./ml), and malathion (7.10 µg a.i./ml), but a lower susceptibility to lambda-cyhalothrin (76.55 µg a.i./ml). For D. suzukii, the LC50 values of deltamethrin (0.67 µg a.i./ml), malathion (3.30 µg a.i./mL), spinosad (4.16 µg a.i./ml), and spinetoram (4.75 µg a.i./ml) were lower than for abamectin (15.02 µg a.i./ml), acetamiprid (39.38 a.i./ml), and thiamethoxam (70.15 µg a.i./ml). The diagnostic concentrations, based on LC99 values of the insecticides, caused more than 99% mortality for most field populations of each species. For lambda-cyhalothrin the populations RS-1 (A. fraterculus) and SC (C. capitata) showed approximately 10% of live insects. These differences represent the natural variation in population susceptibility and not due to insecticide selection pressure. The diagnostic concentrations defined here should be used in future resistance monitoring programs in Brazil.
Implications of the germline variants of DNA damage response genes detected by cancer precision medicine for radiological risk communication and cancer therapy decisions
Authors: Hosoya Noriko , Miyagawa Kiyoshi
Published: February 2021

Large-scale cancer-associated gene testing is now being rapidly incorporated into clinical settings, and is leading to incidental identification of the germline variants present in cancer patients. Because many cancer susceptibility genes are related to DNA damage response and repair, the variants may reflect not only the susceptibility to cancer but also the genetically defined radiation sensitivity of the patients and their relatives. When the presence of a certain germline variant increases the risk for developing radiation toxicity or radiation-induced secondary cancers, it will greatly influence the clinical decision-making. In order to achieve optimal radiological risk communication and to select the best cancer management for a given patient based on information from gene testing, healthcare professionals including genetic counselors, risk communicators and clinicians need to increase their knowledge of the health effects of various genetic variants. While germline loss-of-function mutations in both of the alleles of the DNA damage response genes cause rare hereditary diseases characterized by extreme hypersensitivity to radiation, the health effects of the carriers who have germline variants in one allele of such genes would be a matter of debate, especially when the significance of the variants is currently unknown. In this review, we describe the clinical significance of the genetic variants of the important DNA damage response genes, including ATM and TP53, and discuss how we can apply current knowledge to the management of cancer patients and their relatives from a radiological point of view.
Testing the turbulent origin of the stellar initial mass function
Authors: Nam Donghee G , Federrath Christoph , Krumholz Mark R
Published: February 2021

Supersonic turbulence in the interstellar medium (ISM) is closely linked to the formation of stars; hence, many theories connect the stellar initial mass function (IMF) with the turbulent properties of molecular clouds. Here, we test three turbulence-based IMF models (by Padoan and Nordlund, Hennebelle and Chabrier, and Hopkins) that predict the relation between the high-mass slope (Γ) of the IMF, dN/d log M ∝ MΓ, and the exponent n of the velocity power spectrum of turbulence, Ev(k) ∝ k−n, where n ≈ 2 corresponds to typical ISM turbulence. Using hydrodynamic simulations, we drive turbulence with an unusual index of n ≈ 1, measure Γ, and compare the results with n ≈ 2. We find that reducing n from 2 to 1 primarily changes the high-mass region of the IMF (beyond the median mass), where we measure high-mass slopes within the 95 per cent confidence interval of −1.5 < Γ < −1 for n ≈ 1 and −3.7 < Γ < −2.4 for n ≈ 2, respectively. Thus, we find that n = 1 results in a significantly flatter high-mass slope of the IMF, with more massive stars formed than for n ≈ 2. We compare these simulations with the predictions of the three IMF theories. We find that while the theory by Padoan and Nordlund matches our simulations with fair accuracy, the other theories either fail to reproduce the main qualitative outcome of the simulations or require some modifications. We conclude that turbulence plays a key role in shaping the IMF, with a shallower turbulence power spectrum producing a shallower high-mass IMF, and hence more massive stars.
Infrared emission of z ∼ 6 galaxies: AGN imprints
Authors: Di Mascia F , Gallerani S , Behrens C , Pallottini A , Carniani S , Ferrara A , Barai P , Vito F , Zana T
Published: February 2021

We investigate the infrared (IR) emission of high-redshift (z ∼ 6), highly star-forming (${{\rm SFR}\gt 100\,{\rm M}_{\odot }\, {\rm yr}^{-1}}$) galaxies, with/without active galactic nuclei (AGN), using a suite of cosmological simulations featuring dust radiative transfer. Synthetic spectral energy distributions (SEDs) are used to quantify the relative contribution of stars/AGN to dust heating. In dusty (Md ≳ 3 × 107 M⊙) galaxies, ≳50–90 per cent of the ultraviolet (UV) radiation is obscured by dust inhomogeneities on scales ≳100 pc. In runs with AGN, a clumpy, warm (≈250 K) dust component coexists with a colder (≈60 K) and more diffuse one, heated by stars. Warm dust provides up to ${50 {{\ \rm per\ cent}}}$ of the total infrared (IR) luminosity, but only ${\lesssim}0.1 {{\ \rm per\ cent}}$ of the total mass content. The AGN boosts the MIR flux by 10–100 times with respect to star-forming galaxies, without significantly affecting the far-IR. Our simulations successfully reproduce the observed SED of bright (MUV ∼ −26) z ∼ 6 quasars, and show that these objects are part of complex, dust-rich merging systems, containing multiple sources (accreting black holes and/or star-forming galaxies) in agreement with recent HST and ALMA observations. Our results show that the proposed ORIGINS missions will be able to investigate the mid-IR (MIR) properties of dusty star-forming galaxies and to obtain good-quality spectra of bright quasars at z ∼ 6. Finally, the MIR-to-FIR flux ratio of faint (MUV ∼ −24) AGN is >10 times higher than for normal star-forming galaxies. This implies that combined JWST/ORIGINS/ALMA observations will be crucial to identify faint and/or dust-obscured AGN in the distant Universe.
KERA: analysis tool for multi-process, multi-state single-molecule data
Authors: Tibbs Joseph , Ghoneim Mohamed , Caldwell Colleen C , Buzynski Troy , Bowie Wayne , Boehm Elizabeth M , Washington M Todd , Tabei S M Ali , Spies Maria
Published: February 2021

Molecular machines within cells dynamically assemble, disassemble and reorganize. Molecular interactions between their components can be observed at the single-molecule level and quantified using colocalization single-molecule spectroscopy, in which individual labeled molecules are seen transiently associating with a surface-tethered partner, or other total internal reflection fluorescence microscopy approaches in which the interactions elicit changes in fluorescence in the labeled surface-tethered partner. When multiple interacting partners can form ternary, quaternary and higher order complexes, the types of spatial and temporal organization of these complexes can be deduced from the order of appearance and reorganization of the components. Time evolution of complex architectures can be followed by changes in the fluorescence behavior in multiple channels. Here, we describe the kinetic event resolving algorithm (KERA), a software tool for organizing and sorting the discretized fluorescent trajectories from a range of single-molecule experiments. KERA organizes the data in groups by transition patterns, and displays exhaustive dwell time data for each interaction sequence. Enumerating and quantifying sequences of molecular interactions provides important information regarding the underlying mechanism of the assembly, dynamics and architecture of the macromolecular complexes. We demonstrate KERA’s utility by analyzing conformational dynamics of two DNA binding proteins: replication protein A and xeroderma pigmentosum complementation group D helicase.
Inpatient palliative care utilization for patients with brain metastases
Authors: Price Meghan , Howell Elizabeth P , Dalton Tara , Ramirez Luis , Howell Claire , Williamson Theresa , Fecci Peter E , Anders Carey K , Check Devon K , Kamal Arif H , Goodwin C Rory
Published: February 2021

Introduction

Given the high symptom burden and complex clinical decision making associated with a diagnosis of brain metastases (BM), specialty palliative care (PC) can meaningfully improve patient quality of life. However, no prior study has formally evaluated patient-specific factors associated with PC consultation among BM patients.

Methods

We examined the rates of PC consults in a cohort of 1303 patients with BM admitted to three tertiary medical centers from October 2015 to December 2018. Patient demographics, surgical status, 30-day readmission, and death data were collected via retrospective chart review. PC utilization was assessed by identifying encounters for which an inpatient consult to PC was placed. Statistical analyses were performed to compare characteristics and outcomes between patients who did and did not receive PC consults.

Results

We analyzed 1303 patients admitted to the hospital with BM. The average overall rate of inpatient PC consultation was 19.6%. Rates of PC utilization differed significantly by patient race (17.5% in White/Caucasian vs 26.0% in Black/African American patients, P = .0014). Patients who received surgery during their admission had significantly lower rates of PC consultation (3.9% vs 22.4%, P < .0001). Patients who either died during their admission or were discharged to hospice had significantly higher rates of PC than those who were discharged home or to rehabilitation (P < .0001).

Conclusions

In our dataset, PC consultation rates varied by patient demographic, surgical status, discharging service, and practice setting. Further work is needed to identify the specific barriers to optimally utilizing specialty PC in this population.
The complexities of approaching nutrition in inflammatory bowel disease: current recommendations and future directions
Authors: Russell Lindsey A , Balart Maria Teresa , Serrano Pablo , Armstrong David , Pinto-Sanchez Maria Ines
Published: February 2021

Inflammatory bowel diseases (IBDs), including Crohn's disease and ulcerative colitis predispose patients to malnutrition due to a combination of increased basal metabolic rate, decreased oral intake, and increased nutritional losses and malabsorption. Malnutrition is common, affecting up to 75% of patients with Crohn's disease and 62% of patients with ulcerative colitis, and is associated with worse disease prognosis, higher complication rates, decreased quality of life, and increased mortality risk. It is imperative to screen patients with IBD for malnutrition to assess those at increased risk and treat accordingly to prevent progression and complications. This literature review provides an overall approach to optimizing nutrition in IBD, focusing on the assessment for the diagnosis of malnutrition, management of macro- and micronutrient deficiencies, and identification of areas for future study.
Seven computations of the social brain
Authors: Molapour Tanaz , Hagan Cindy C , Silston Brian , Wu Haiyan , Ramstead Maxwell , Friston Karl , Mobbs Dean
Published: February 2021

The social environment presents the human brain with the most complex information processing demands. The computations that the brain must perform occur in parallel, combine social and nonsocial cues, produce verbal and nonverbal signals and involve multiple cognitive systems, including memory, attention, emotion and learning. This occurs dynamically and at timescales ranging from milliseconds to years. Here, we propose that during social interactions, seven core operations interact to underwrite coherent social functioning; these operations accumulate evidence efficiently—from multiple modalities—when inferring what to do next. We deconstruct the social brain and outline the key components entailed for successful human–social interaction. These include (i) social perception; (ii) social inferences, such as mentalizing; (iii) social learning; (iv) social signaling through verbal and nonverbal cues; (v) social drives (e.g. how to increase one’s status); (vi) determining the social identity of agents, including oneself and (vii) minimizing uncertainty within the current social context by integrating sensory signals and inferences. We argue that while it is important to examine these distinct aspects of social inference, to understand the true nature of the human social brain, we must also explain how the brain integrates information from the social world.
Bedtimes, bedtime routines, and children’s sleep across the first 2 years of life
Authors: Fiese Barbara H , Cai Tianying , Sutter Carolyn , Bost Kelly K
Published: February 2021

Study Objectives

The first objective of this study was to determine whether establishing bedtime routines in the first year of life predicts better sleep outcomes (i.e. longer sleep duration, less nighttime waking, earlier bedtime, shorter sleep latency, fewer sleep problems) across the first 2 years of life. The second objective was to determine whether specific adaptive bedtime activities (e.g. book reading) were associated with sleep outcomes. The third objective was to describe changes in adaptive bedtime activities (hug/kiss caregiver, say goodnight to family) across the first 2 years of life.

Methods

Parents of 468 children from the STRONG Kids 2 birth cohort were surveyed about bedtime and bedtime routines, their child’s sleep duration, nighttime waking, sleep latency, and sleep problems at 3, 12, 18, and 24 months of age.

Results

Cross-lagged panel models revealed partial evidence for reciprocal associations between bedtime routine consistency and adaptive bedtime activities and better sleep outcomes over time. Specifically, more bedtime routine consistency predicted less nighttime waking and sleep problems, and more bedtime adaptive activities predicted longer sleep duration and fewer sleep problems.

Discussion

The findings are discussed from a developmental perspective to highlight how consistency of bedtime routines established as early as 3 months of age may affect sleep outcomes and that the adaptive activities associated with these routines may increase in frequency over the first 2 years of life.
More than Recruitment: How Social Ties Support Protest Participation
Authors: Walgrave Stefaan , Wouters Ruud
Published: February 2021

Social movement scholars have frequently pointed to individuals’ personal networks to explain protest participation. While the recruitment function of micro networks has been explored in depth, the support effect of networks has received only scant attention. The study explores how and to what extent social support and social constraints in people’s personal networks explain differential protest participation. Three dimensions of support are distinguished: the politicization of a person’s network, the political agreement about the protest topic within a person’s network, and the social approval of protest participation within a person’s network. Drawing on panel survey data (N=1,684) of a large protest in Belgium including both participants and non-participants, we test whether the support effects of networks play a role on top of the recruitment effect. We find evidence that two functions of social networks (politicization and social approval) affect protest participation. Additionally, we find differences in support-effects across types of social ties. Co-members of an organization exert influence on protest participation across a variety of support functions. The most intimate ties prospective participants have (partners), in contrast, matter only in so far as they approve of participation.
Pain in the Developing Brain: Early Life Factors Alter Nociception and Neurobiological Function in Adolescent Rats
Authors: Salberg Sabrina , Yamakawa Glenn R , Griep Yannick , Bain Jesse , Beveridge Jaimie K , Sun Mujun , McDonald Stuart J , Shultz Sandy R , Brady Rhys D , Wright David K , Noel Melanie , Mychasiuk Richelle
Published: February 2021

Although adverse early experiences prime individuals to be at increased risk for chronic pain, little research has examined the trauma–pain relationship in early life or the underlying mechanisms that drive pathology over time. Given that early experiences can potentiate the nociceptive response, this study aimed to examine the effects of a high-fat, high-sugar (HFHS) diet and early life stress (maternal separation [MS]) on pain outcomes in male and female adolescent rats. Half of the rats also underwent a plantar-incision surgery to investigate how the pain system responded to a mildly painful stimuli in adolescence. Compared with controls, animals that were on the HFHS diet, experienced MS, or had exposure to both, exhibited increased anxiety-like behavior and altered thermal and mechanical nociception at baseline and following the surgery. Advanced magnetic resonance imaging demonstrated that the HFHS diet and MS altered the maturation of the brain, leading to changes in brain volume and diffusivity within the anterior cingulate, amygdala, corpus callosum, nucleus accumbens, and thalamus, while also modifying the integrity of the corticospinal tracts. The effects of MS and HFHS diet were often cumulative, producing exacerbated pain sensitivity and increased neurobiological change. As early experiences are modifiable, understanding their role in pain may provide targets for early intervention/prevention.
Integrative taxonomy of calcareous sponges (Porifera: Calcarea) from Réunion Island, Indian Ocean
Authors: Klautau Michelle , Lopes Matheus Vieira , Tavares Gabriela , Pérez Thierry
Published: February 2021

The Western Indian Ocean Province is reckoned for its rich marine diversity; however, sponges of the Mascarene Islands ecoregion are still poorly known. In La Réunion, only three species of class Calcarea have been registered. Hence, calcareous sponges were searched in seven sites representing various habitats of the Western coast of La Réunion, but found in only three of them. A total of 23 sponge samples was identified using morphological and molecular taxonomy. This sampling represents 11 species, all new records for the region, and seven of them are new to science: Ascandra mascarenica sp. nov., A. oceanusvitae sp. nov., Janusya indica gen. et sp. nov., Leucascus tenuispinae sp. nov., Lelapiella tertia sp. nov., Soleneiscus intermedius sp. nov. and Leucandra ornata sp. nov.; and a new genus, Janusya gen. nov.. Based on results from this and from previous studies, we propose the synonymization of the order Murrayonida with Clathrinida. A very low sampling effort has thus increased the number of calcareous sponge species from the Mascarenes Islands ecoregion by 69 % and from La Réunion by 367%.
Eight Species of Poaceae Are Hosting Different Genetic and Pathogenic Strains of Sugarcane Mosaic Virus in the Everglades Agricultural Area
Authors: Hincapie Martha , Sood Sushma , Mollov Dimitre , Odero D. Calvin , Grisham Michael , Rott Philippe
Published: February 2021

Sugarcane mosaic virus (SCMV) was detected by reverse transcription polymerase chain reaction in eight different species of the Poaceae family in the Everglades Agricultural Area (EAA) of south Florida: broadleaf signalgrass (Urochloa platyphylla), Columbus grass (Sorghum almum), goosegrass (Eleusine indica), maize (Zea mays), sorghum (Sorghum bicolor), St. Augustine grass (Stenotaphrum secundatum), southern crabgrass (Digitaria ciliaris), and sugarcane (Saccharum interspecific hybrids). Based on their coat protein (CP) gene sequence, 62 isolates of SCMV from Florida and 29 worldwide isolates representing the known genetic diversity of this virus were distributed into eight major phylogenetic groups. SCMV isolates infecting Columbus grass, maize, and sorghum in Florida formed a unique group, whereas virus isolates infecting sugarcane in the United States (Florida and Louisiana) clustered with isolates from other countries. Based on the entire genome coding region, SCMV isolates infecting sugarcane in Florida were closest to virus isolates infecting sorghum species or St. Augustine grass. Virus isolates from Columbus grass, St. Augustine grass, and sugarcane showed different virulence patterns after mechanical inoculation of Columbus grass, St. Augustine grass, and sugarcane plants, thus proving that these isolates were different pathogenic strains. Sugarcane was symptomless and tested negative for SCMV by tissue blot immunoassay after inoculation with crude sap from SCMV-infected Columbus grass, indicating that Columbus grass was not a reservoir for SCMV infecting sugarcane in the EAA. Close CP sequence identity between isolates of SCMV from Columbus grass, maize, and sorghum suggested that the same virus strain was naturally spreading between these three plants in south Florida.
Gender Bias: Another Rising Curve to Flatten?
Authors: Lewiss Resa E. , Jagsi Reshma
Published: February 2021

The COVID-19 pandemic and the upheaval it is causing may be leading to novel manifestations of the well-established mechanisms by which women have been marginalized in professional roles, robbing the field of the increased collective intelligence that exists when diverse perspectives are embraced. Unconscious bias, gendered expectations, and overt hostility minimize the contributions of women in academic medicine to the detriment of all. The current environment of heightened stress and new socially distant forms of communication may be exacerbating these well-recognized obstacles to women contributing to the field. Of note, none of these actions requires ill intent; all they require is the activation of unconscious biases and almost instinctive preferences and behaviors that favor the comfortable and familiar leadership of men in a time of extreme stress.

The authors argue that it is time to investigate the frequency of behaviors that limit both the recognition and the very exercise of women’s leadership during this pandemic, which is unprecedented but nevertheless may recur in the future. Leaders in health care must pay attention to equity, diversity, and inclusion given increases in undermining and harassing behaviors toward women during this crisis. The longer-term consequences of marginalizing women may hamper efforts to combat the next pandemic, so the time to flatten the rising gender bias curve in academic medicine is now.
Optimizing Surgeon Well-Being
Authors: Vitous C. Ann , Dinh Duyhoang Q. , Jafri Sara M. , Bennett Olivia M. , MacEachern Mark , Suwanabol Pasithorn A.
Published: February 2021

Objective:

Through a systematic review and mixed-methods meta-synthesis of the existing literature on surgeon well-being, we sought to identify the specific elements of surgeon well-being, examine factors associated with suboptimal well-being, and highlight opportunities to promote well-being.

Background:

Suboptimal surgeon well-being has lasting and substantial impacts to the individual surgeon, patients, and to society as a whole. However, most of the existing literature focuses on only 1 aspect of well-being—burnout. While undoubtedly a crucial component of overall well-being, the mere absence of burnout does not fully consider the complexities of being a surgeon.

Methods:

We performed a literature search within Ovid Medline, Elsevier Excerpta Medica dataBASE, EBSCOhost Cumulative Index to Nursing and Allied Health Literature, and Clarivate Web of Science from inception to May 7, 2020, in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Studies with primary data examining surgeon well-being were included. Using a predetermined instrument, data were abstracted from each study and compared using thematic analysis.

Results:

A total of 5369 abstracts were identified and screened, with 184 full articles (172 quantitative, 3 qualitative, 9 mixed methods) selected for analysis. Among these, 91 articles measured burnout, 82 examined career satisfaction, 95 examined work-related stressors, 44 explored relationships and families, and 85 assessed emotional and physical health. Thematic analysis revealed 4 themes: professional components, personal components, work-life balance, and impacts to well-being.

Conclusions:

Surgeon well-being is complex and multifaceted. This nuanced examination of surgeon well-being highlights the critical need to develop and provide more long-term support to surgeons—with interventions being tailored based on individual, institutional, and systemic factors.