bluuebunny/crossref_metadata_2025 huggingface dataset:
Adaptation of red rice farmers to long drought in Ponjong Districts Gunung Kidul Regency, Yogyakarta Indonesia
Authors: Rahayu Lestari , Rozaki Zuhud , Indardi  , Isdiana Ari
Published: April 2022

Adaptation of red rice farmers is an action taken by farmers to change crop cultivation during a prolonged drought, that cause by climate change. Adaptation consists of changes in planting patterns and crop cultivation. This study aims to describe the adaptation of red rice farmers and know the profile that influences the adaptation of red rice farmers to prolonged droughts. The study was conducted in three zones, including the northern zone (Umbulrejo Village), the central zone (Sumbergiri Village), and the southern zone (Sidorejo Village). This study was conducted in Ponjong Subdistrict purposively, on sampling conducted systematically random sampling with 200 respondents. The data were analyze using descriptive analysis, score analysis, and Spearman Rank correlation. The results showed that adaptations applied during prolonged droughts in all three zones were classified as “moderate.” The factors that affected adaptation in all three zones include age, number of family members, farming experience, income, land area, and agricultural ownership. In contrast, gender and education do not affect adaptation.
Coal combustion emission and corruption in ASEAN: Does government integrity plays moderation role?
Authors: Azzam Al Afif Rafiq , Daerobi Ahmad , Rizky Samudro Bhimo , Gravitiani Evi
Published: April 2022

Coal energy is a cheap and abundant source of electricity in ASEAN. Despite this, the reality of CO2 emissions from coal gets a red report card on the issue of climate change. In terms of the institutional economy, corruption is the main enemy in the issue of environmental pollution; the cleaner government agencies, the lower the environmental pollution. In particular, the research aims to find out the moderating effect of government integrity concerning corruption and CO2 emissions from coal in ASEAN. But to help construct the analysis, the paper also previously looked into the relationship between corruption and CO2 emissions from coal and found out whether economic development played a mediating effect in that relationship. Using ECM panel analysis with a sample of 9 ASEAN member states, the paper found that: (1) In the long and short term, the lower level of corruption will reduce CO2 emissions from coal. (2) FDI plays a mediating effect between corruption and CO2 emissions from coal. The scheme is that the lower the level of corruption, the FDI will decrease and reduce CO2 emissions. (3) Government integrity strengthens the relationship between corruption and CO2 emissions from coal, meaning that the more honest and non-corrupt the government will have an effect that can strengthen the relationship between corruption and CO2 emissions from coal. This study recommends that the government in ASEAN member states should be keeping public trust because it will decrease the level of corruption and can save climate change in the future.
Effectiveness of solar panel positioning and grid tie inverter (GTI) in generating solar energy in Indonesian houses
Authors: Siswantoro Dodik
Published: April 2022

In Indonesia, most electricity powers are based on non-renewable resources, which is not good for climate change. Therefore, the use of solar panels based on rooftops is an excellent alternative way to reduce electricity use. Thus, the objective of this paper is to analyze the effectiveness of solar panel positioning and Grid Tie Inverter (GTI) in generating solar energy for small- to medium-sized houses in Indonesia. Solar panel usage by residents living in the city may be limited, as the rooftop space in city houses is limited. GTIs can generate different types of power as they have different resources, this is good for climate change as no battery is needed In this research, two different solar panels with different positioning and angles, and connected to different types of GTI, were analyzed. The period of study was from 23rd July 2020 to 5th May 2021. The analysis was based on index comparison and movement of the sun during the said period. The result of the study indicates that the position and angle of solar panels affect the electricity generated by them. Solar panels placed in a horizontal position were observed to generate more power, and imported model inverters were observed to provide better electricity supply to homes.
Annual characteristics of gross primary productivity (GPP) in mangrove forest during 2016-2020 as revealed by Sentinel-2 remote sensing imagery
Authors: Sri Rahayu Romadhoni Linda , As-syakur Abd. Rahman , Hidayah Zainul , Budi Wiyanto Dwi , Safitri Rahma , Yusuf Satriyana Utama Raden , Made Sara Wijana I , Putra Anugrah Alfandy , Made Oka Guna Antara I
Published: April 2022

Carbon dioxide (CO2) is the most responsible gas in the phenomenon of global warming on earth because of its greatest concentration and longevity in the long atmosphere. Meanwhile mangrove is one of the blue carbon parameters that can take CO2 for photosynthesis and store it into biomass and sediment, so the existence of Mangrove plays a key role in the balance of the global carboncycle. Gross Primary Productivity (GPP) is one of the key variables in conducting a carboncycle study because the GPP values constitute the total value of carbon fixation by terrestrial ecosystem through vegetation photosynthesis. The aim of this study is to recognize the annual characteristics of GPP values in the mangrove ecosystem using remote sensing satellite Sentinel-2 during the period of 2016 to 2020 in TAHURA Ngurah Rai, Bali, Indonesia. The vegetation photosynthesis model (VPM) model is used to calculate annual GPP by using remote sensing indices of Enhanced Vegetation Index (EVI) and Land Surface Water Index (LSWI). Both remote sensing indices are supported by temperature and solar radiation data to determine photosynthesis fraction. The results of the current study indicated that the annual GPP values in the mangrove forest of TAHURA Ngurah Rai have decreased during the observation year. The total value of GPP in 2016 is reached to 28790 tC m−2 year−1, while the total amount of GPP value in 2020 decrease to 26223 tC m−2 year−1. The decline in GPP values may be due to changes of land cover and mangrove mortality that occurred around Benoa port in 2018.
Patterns of Tetragonula Laeviceps (Smith) colony activity in KHDTK Gunung Bromo UNS
Authors: Agustina Ana , Tanding Suryandari Retno , Rawidyo Putro Tetuko
Published: April 2022

Due to climate change, many impacts occur on the sustainability of organisms, including the trigona bee. The occurrence of climate change not only affects decreasing honey production but also reduces the number of colonies. Presume that it can change the activity pattern of the trigona bee. This study aims to determine the pattern of activity demonstrated by Tetragonula laeviceps (Smith) colony in KHDTK Gunung Bromo UNS. This research was conducted in July 2021 at KHDTK Gunung Bromo UNS. The observation involved 128 colony boxes placed into four cages, namely cages A, B, C, and D. Observations on the activity of trigona bees starting from 06.00 WIB to 18.00 WIB, assuming trigona bee activity begins in the morning and end the activity outside the hive after sunset. The results showed that of the cages A, B, C, and D, the worker bees tend to be active in the morning (6-10 am) to collect nectars and resin. Before noon (10 to 12 noon), bee activities were decreasing. The activity of the worker bees increased between 12 to 2 pm and decreased again after that time slot. The food source most favored by trigona bees: Pinus merkusii (rp), Artocarpus heterophyllus (r), Spathiphyllum wallisii (np), and Xanthostemon chrysanthus (np). Resin extractions are very needed for bees as batumen materials, and this is due to natural enemies (lizards, ants, vespa wasps, and spiders) that appear around the cage.
A tunable quantum random number generator based on a fiber-optical Sagnac interferometer
Authors: Argillander Joakim , Alarcón Alvaro , Xavier Guilherme B
Published: April 2022

Quantum random number generators (QRNGs) are based on naturally random measurement results performed on individual quantum systems. Here, we demonstrate a branching-path photonic QRNG implemented using a Sagnac interferometer with a tunable splitting ratio. The fine-tuning of the splitting ratio allows us to maximize the entropy of the generated sequence of random numbers and effectively compensate for tolerances in the components. By producing single-photons from attenuated telecom laser pulses, and employing commercially-available components we are able to generate a sequence of more than 2 gigabytes of random numbers with an average entropy of 7.99 bits/byte directly from the raw measured data. Furthermore, our sequence passes randomness tests from both the NIST and Dieharder statistical test suites, thus certifying its randomness. Our scheme shows an alternative design of QRNGs based on the dynamic adjustment of the uniformity of the produced random sequence, which is relevant for the construction of modern generators that rely on independent real-time testing of its performance.
First-generation College Students Have Greater Systemic Inflammation than Continuing-Generation College Students Following the Initial College Transition: A Brief Report
Authors: Jones Emily J , Schreier Hannah M C
Published: April 2022

Background

First-generation college students (“first-gens”) are often at a disadvantage socially and academically; whether they are at risk physiologically is unknown despite the well-established link between greater education and better long-term health.

Purpose

To examine whether first-gens have higher levels of cardiovascular disease (CVD) risk markers relative to continuing-generation college students (“continuing-gens”).

Methods

A panel of CVD risk markers was assessed among 87 emerging adults (41 first-gens) twice over their first year of college.

Results

Compared to continuing-gens, first-gens had greater systemic inflammation (composite of averaged z-scores for C-reactive protein and interleukin-6; B = 0.515, SE = 0.171, p = .003) during the fall but not spring semester (p > .05). Associations were independent of family home ownership and childhood adversity, even though first-gens were more likely to live in rental homes and reported riskier home environments. Lower childhood subjective social status (SSS) accounted for greater systemic inflammation among first-gens as evidenced by an indirect effect of college generation status on systemic inflammation through childhood SSS (a1b1 = 0.261, bootstrapped SE = 0.103, 95% boot CI [0.078, 0.482]). There were no differences in metabolic risk and latent virus regulation by college generation status in either semester (p > .10).

Conclusions

This is the first study to find that first-gens have higher levels of systemic inflammation than continuing-gens following the college transition and that childhood SSS may be one explanatory pathway. First-gens may benefit from university resources that address social class differences, which should be provided early on so that first-gens can reap the health-relevant benefits of higher education, at least in the short term.
BAILA: A Randomized Controlled Trial of Latin Dancing to Increase Physical Activity in Spanish-Speaking Older Latinos
Authors: Marquez David X , Wilbur JoEllen , Hughes Susan , Wilson Robert , Buchner David M , Berbaum Michael L , McAuley Edward , Aguiñaga Susan , Balbim Guilherme M , Vásquez Priscilla M , Marques Isabela G , Wang Tianxiu , Kaushal Navin
Published: April 2022

Background

Latinos are the fastest growing minority group of the older adult population. Although physical activity (PA) has documented health benefits, older Latinos are less likely to engage in leisure time PA than older non-Latino whites. Dance, popular among Latinos, holds promise as a culturally relevant form of PA.

Purpose

To describe self-reported and device-assessed changes in PA as a result of a randomized controlled trial of BAILAMOS, a 4-month Latin dance program with a 4-month maintenance program, versus a health education control group.

Methods

Adults, aged 55+, Latino/Hispanic, Spanish speaking, with low PA levels at baseline, and risk for disability were randomized to the dance program (n = 167) or health education condition (n = 166). Data were analyzed using multilevel modeling with full information maximum likelihood.

Results

A series of multilevel models revealed significant time × group interaction effects for moderate-to-vigorous physical activity (MVPA), dance PA, leisure PA, and total PA. Exploring the interaction revealed the dance group to significantly increase their MVPA, dance PA, leisure PA, and total PA at months 4 and 8. Household PA and activity counts from accelerometry data did not demonstrate significant interaction effects.

Conclusions

The study supports organized Latin dance programs to be efficacious in promoting self-reported PA among older Latinos. Efforts are needed to make dancing programs available and accessible, and to find ways for older Latinos to add more PA to their daily lives.

Clinical Trial information

NCT01988233.
Psychosocial-Behavioral Phenotyping: A Novel Precision Health Approach to Modeling Behavioral, Psychological, and Social Determinants of Health Using Machine Learning
Authors: Burgermaster Marissa , Rodriguez Victor A
Published: April 2022

Background

The context in which a behavioral intervention is delivered is an important source of variability and systematic approaches are needed to identify and quantify contextual factors that may influence intervention efficacy. Machine learning-based phenotyping methods can contribute to a new precision health paradigm by informing personalized behavior interventions. Two primary goals of precision health, identifying population subgroups and highlighting behavioral intervention targets, can be addressed with psychosocial-behavioral phenotypes. We propose a method for psychosocial-behavioral phenotyping that models social determinants of health in addition to individual-level psychological and behavioral factors.

Purpose

To demonstrate a novel application of machine learning for psychosocial-behavioral phenotyping, the identification of subgroups with similar combinations of psychosocial characteristics.

Methods

In this secondary analysis of psychosocial and behavioral data from a community cohort (n = 5,883), we optimized a multichannel mixed membership model (MC3M) using Bayesian inference to identify psychosocial-behavioral phenotypes and used logistic regression to determine which phenotypes were associated with elevated weight status (BMI ≥ 25kg/m2).

Results

We identified 20 psychosocial-behavioral phenotypes. Phenotypes were conceptually consistent as well as discriminative; most participants had only one active phenotype. Two phenotypes were significantly positively associated with elevated weight status; four phenotypes were significantly negatively associated. Each phenotype suggested different contextual considerations for intervention design.

Conclusions

By depicting the complexity of psychological and social determinants of health while also providing actionable insight about similarities and differences among members of the same community, psychosocial-behavioral phenotypes can identify potential intervention targets in context.
Kinship, Migration, and the Chinese American Immigrant Family Narrative
Authors: Lee Christopher
Published: April 2022

The Asian American immigrant family narrative has been extensively discussed in relation to white domesticity and assimilation by critics who emphasize the unique conditions of Asian racialization in North America. Departing from this approach, this essay considers how the immigrant family narrative depicts kinship structures that were instrumental in sustaining the lifeworld of Chinese migrants during and in the aftermath of the exclusion period (1882–1943). Drawing on theories of racial capitalism, I argue that the appropriation of pre-existing kinship structures played a crucial role in the exploitation of Chinese migrants by sustaining a transnational remittance economy that tied migrants to their locations of origin. Through an extended reading of the opening chapter of Maxine Hong Kingston’s The Woman Warrior (1975), I trace how the text depicts the communal and intimate consequences of this social structure. Kingston’s detailed knowledge of migrant kinship relations stands in contrast with her professed confusion about Chinese culture and identity, a tension that underscores the text’s combination of speculative narrative and historical realism.

… the immigrant family narrative conveys the global operations of capital even if, or more precisely because, it subordinates depictions of recognizably “economic” tropes—labor, wages, remittances, and so on—to the ostensibly private realm of family relations.
Hierarchy of fear: experimentally testing ungulate reactions to lion, African wild dog and cheetah
Authors: Rigoudy Noa L A , Clinchy Michael , Peel Mike J S , Huebner Sarah , Packer Craig , Zanette Liana Y
Published: April 2022

Experiments have begun demonstrating that the fear (antipredator behavioral responses) large carnivores inspire in ungulates can shape ecosystem structure and function. Most such experiments have focused on the impacts of either just one large carnivore, or all as a whole, rather than the different impacts different large carnivores may have in intact multi-predator-prey systems. Experimentally testing the relative fearfulness ungulates demonstrate toward different large carnivores is a necessary first step in addressing these likely differing impacts. We tested the fearfulness ungulates demonstrated to playbacks of lion (Panthera leo), African wild dog (Lycaon pictus), cheetah (Acinonyx jubatus) or non-predator control (bird) vocalizations, in Greater Kruger National Park, South Africa. Ungulates ran most to lions, then wild dogs, and then cheetahs, demonstrating a very clear hierarchy of fear. Those that did not run looked toward the sound more on hearing large carnivores than controls, looking most on hearing lions. Notably, prey species-specific population level kill rates by each predator did not predict the patterns observed. Our results demonstrate that different large carnivores inspire different levels of fear in their ungulate prey, pointing to differing community-level impacts, which we discuss in relation to the ongoing worldwide decline and loss of large carnivores.
Ecological adaptation and birdsong: how body and bill sizes affect passerine sound frequencies
Authors: Friis Jakob Isager , Sabino Joana , Santos Pedro , Dabelsteen Torben , Cardoso Gonçalo C
Published: April 2022

The avian bill is finely adjusted to foraging ecology and, as part of the vocal tract, it may also affect sexual signals such as songs. Acoustic theory predicts that larger bills lower the resonant frequency of vocal tracts, allowing larger-billed species to emphasize lower sound frequencies. Theory also predicts that identical changes in bill gape allow singing over a wider frequency bandwidth in larger-billed species. We tested these associations between bill size and sound frequencies of song, controlling for body mass, across ca. 1000 taxonomically-diverse passerines. Phylogenetically informed analyses indicated that both bill and body sizes are negatively related to the sound frequency of songs, with additive effects of similar strength. Analyses of reduced datasets, to decrease bill-body size associations, indicated that the effect of bill size remains identical and is thus not an artefact of its covariation with body size. Sound frequency bandwidth was only related to body size but not bill size, perhaps because large bills may allow greater modulation of frequency but also hinder fast bill movement. Since the bill has a major role explaining species differences in birdsong sound frequency, it can be a magic trait that promotes reproductive isolation as a consequence of ecological divergence.
Dysregulated ligand–receptor interactions from single-cell transcriptomics
Authors: Liu Qi , Hsu Chih-Yuan , Li Jia , Shyr Yu
Published: April 2022

Motivation

Intracellular communication is crucial to many biological processes, such as differentiation, development, homeostasis and inflammation. Single-cell transcriptomics provides an unprecedented opportunity for studying cell-cell communications mediated by ligand–receptor interactions. Although computational methods have been developed to infer cell type-specific ligand–receptor interactions from one single-cell transcriptomics profile, there is lack of approaches considering ligand and receptor simultaneously to identifying dysregulated interactions across conditions from multiple single-cell profiles.

Results

We developed scLR, a statistical method for examining dysregulated ligand–receptor interactions between two conditions. scLR models the distribution of the product of ligands and receptors expressions and accounts for inter-sample variances and small sample sizes. scLR achieved high sensitivity and specificity in simulation studies. scLR revealed important cytokine signaling between macrophages and proliferating T cells during severe acute COVID-19 infection, and activated TGF-β signaling from alveolar type II cells in the pathogenesis of pulmonary fibrosis.

Availability and implementation

scLR is freely available at https://github.com/cyhsuTN/scLR.

Supplementary information

Supplementary data are available at Bioinformatics online.
GC-MS Based Metabolomics Analysis to Evaluate Short-Term Effect of Tumor Removal on Patients with Early-Stage Breast Cancer
Authors: Beksac Kemal , Reçber Tuba , Çetin Bahadır , Alp Orkun , Kaynaroğlu Volkan , Kır Sedef , Nemutlu Emirhan
Published: April 2022

In this study, it was aimed to demonstrate the short-term effect of breast cancer surgery and tumor removal on the metabolomic profiles of patients with early-stage breast cancer. This cohort consisted of 18 early-stage breast carcinoma patients who had breast cancer surgery to remove tumor and surrounding tissues. The blood samples obtained preoperatively and 24 h after surgery were used in this investigation. Gas chromatography–mass spectrometry (GC–MS) based metabolomic analysis was performed to determine the metabolites. The GC–MS-based metabolomics profile enabled the identification of 162 metabolites in the plasma samples. Postoperatively, glyceric acid, phosphoric acid, O-phosphocolamine, 2-hydroxyethyliminodiacetic acid, N-acetyl-D-mannosamine, N-acetyl-5-hydroxytryptamine, methyl stearate, methyl oleate, iminodiacetic acid, glycerol 1-phosphate, β-glycerol phosphate and aspartic acid were found to be significantly increased (P < 0.05 for all), whereas saccharic acid, leucrose, gluconic acid, citramalic acid and acetol were significantly decreased (P < 0.05 for all). Breast cancer surgery and tumor removal has an impact on the metabolomic profiles of patients with early-stage breast cancer. These findings can be used for understanding the pathogenesis of breast cancer biology and screening the success of the surgery.
Scotland’s Last Blasphemy Trials: Popular Unbelief and its Opponents, 1819–1844
Authors: Loughlin Felicity
Published: April 2022

This article provides the first detailed historical analysis of Scotland’s last blasphemy trials (1819–1844). During this period, numerous booksellers and publishers were convicted for selling printed works that denied, ridiculed and vilified the scriptures and the Christian religion. Despite their significance as the last cases of their kind in Scottish history, these trials are almost entirely absent from the existing scholarship. The article positions them as a response to the unprecedented rise of popular unbelief in the Scottish religious landscape, a phenomenon that has itself been overlooked or dismissed by historians. In doing so, it demonstrates their significance in the campaign to extend religious toleration to unbelievers and identifies the early nineteenth century as an important transitional period, in which public attitudes towards the right of unbelievers to express openly their disavowal of Christianity underwent a significant transformation. As the article shows, debates over Scottish blasphemy legislation intersected with wider debates between Scottish Christians over the validity of an established church protected by law, and with contemporary campaigns from English unbelievers and their liberal supporters for the unfettered freedom of opinion. By 1844, conflicting attitudes over the desirability, utility and legitimacy of policing unbelief deepened divisions between different groups of Scottish Christians, while opening new areas of common ground between certain kinds of Christians and unbelievers.
Evolution of Complex Regulation for Cell-Cycle Control
Authors: von der Dunk Samuel H. A. , Snel Berend , Hogeweg Paulien
Published: April 2022

Many questions remain about the interplay between adaptive and neutral processes leading to genome expansion and the evolution of cellular complexity. Genome size appears to be tightly linked to the size of the regulatory repertoire of cells (van Nimwegen E. 2003. Scaling laws in the functional content of genomes. Trends Gen. 19(9):479–484). In the context of gene regulation, we here study the interplay between adaptive and nonadaptive forces on genome and regulatory network in a computational model of cell-cycle adaptation to different environments. Starting from the well-known Caulobacter crescentus network, we report on ten replicate in silico evolution experiments where cells evolve cell-cycle control by adapting to increasingly harsh spatial habitats.

We find adaptive expansion of the regulatory repertoire of cells. Having a large genome is inherently costly, but also allows for improved cell-cycle behavior. Replicates traverse different evolutionary trajectories leading to distinct eco-evolutionary strategies. In four replicates, cells evolve a generalist strategy to cope with a variety of nutrient levels; in two replicates, different specialist cells evolve for specific nutrient levels; in the remaining four replicates, an intermediate strategy evolves. These diverse evolutionary outcomes reveal the role of contingency in a system under strong selective forces.

This study shows that functionality of cells depends on the combination of regulatory network topology and genome organization. For example, the positions of dosage-sensitive genes are exploited to signal to the regulatory network when replication is completed, forming a de novo evolved cell cycle checkpoint. Our results underline the importance of the integration of multiple organizational levels to understand complex gene regulation and the evolution thereof.
Frailty and COVID-19 mRNA Vaccine Antibody Response in the COVID-19 Community Research Partnership
Authors: Semelka Charles T , DeWitt Michael E , Callahan Kathryn E , Herrington David M , Alexander-Miller Martha A , Yukich Joshua O , Munawar Iqra , McCurdy Lewis H , Gibbs Michael A , Weintraub William S , Sanders John W
Published: April 2022

Background

COVID-19 has disproportionately affected older adults. Frailty has been associated with impaired vaccine response in other vaccine types, but the impact of frailty on mRNA vaccine response is undefined.

Methods

Observational study of adults aged 55 and older from 1 U.S. health care system between January 22, 2021 and September 16, 2021 with self-reported Moderna or Pfizer COVID-19 mRNA vaccine and an electronic frailty index (eFI) score from their medical record (n = 1 677). Participants’ frailty status was compared with positive antibody detection (seroconversion) following full vaccination and subsequent loss of positive antibody detection (seroreversion) using logistic regression models.

Results

Of 1 677 older adults with median (interquartile range) age, 67 (62 and 72) years, and frailty status (nonfrail: 879 [52%], prefrail: 678 [40%], and frail: 120 [7.2%]), seroconversion was not detected in 23 (1.4%) over 60 days following full vaccination. Frail individuals were less likely to seroconvert than nonfrail individuals, adjusted odds ratio (OR) 3.75, 95% confidence interval (CI; 1.04, 13.5). Seroreversion was detected in 50/1 631 individuals (3.1%) over 6 months of median follow-up antibody testing. Frail individuals were more likely to serorevert than nonfrail individuals, adjusted OR 3.02, 95% CI (1.17, 7.33).

Conclusion

Overall antibody response to COVID-19 mRNA vaccination was high across age and frailty categories. While antibody detection is an incomplete descriptor of vaccine response, the high sensitivity of this antibody combined with health-system data reinforce our conclusions that frailty is an independent predictor of impaired antibody response to the COVID-19 mRNA vaccines. Frailty should be considered in vaccine studies and prevention strategies.
Trajectories of Loneliness Among Older Women and Men: Variation by Sexual Identity?
Authors: Lam Jack , Campbell Alice
Published: April 2022

Background and Objectives

The aim of this study is to contribute to the literature on variation in later-life outcomes by sexual identity. Drawing on the Iridescent Life Course framework, we examined differences in loneliness trajectories, and tested the roles of social connectedness and support, and socioeconomic and health statuses in explaining any observed disparities.

Research Design and Methods

Using growth models, we analyzed 19 years of data (2001–2019) from adults aged 50 years and older from the Household, Income and Labour Dynamics in Australia Survey (n = 5,500 individuals), where a question on sexual identity was asked twice in the study.

Results

One percent of our sample reported a change in their sexual identity, which we grouped with individuals who reported as bisexual. Our sample comprised of 45.3% heterosexual men, 52.2% heterosexual women, 0.6% gay men, 0.6% lesbian women, 0.6% bisexual-plus men, and 0.6% bisexual-plus women. We found bisexual-plus men were vulnerable to loneliness as they aged. This group had the highest levels of loneliness at age 50, and differences compared with heterosexual men persisted over time. Loneliness of bisexual-plus men increased steeply from age 70. Socioeconomic and health statuses did not explain the increased loneliness of older bisexual-plus men. Lower social support and connectedness partly accounted for these disparities.

Discussion and Implications

Findings are discussed with regards to existing research and theories on social disadvantage and resilience over the life course. We expand knowledge on factors explaining loneliness and how it varies in women and men by sexual identity.
Evaluations of effective coverage of maternal and child health services: A systematic review
Authors: Ferede Gebremedhin Aster , Dawson Angela , Hayen Andrew
Published: April 2022

Conventionally used coverage measures do not reflect the quality of care. Effective coverage (EC) assesses the extent to which health care services deliver potential health gains to the population by integrating concepts of utilization, need and quality. We aimed to conduct a systematic review of studies evaluating EC of maternal and child health services, quality measurement strategies and disparities across wealth quantiles. A systematic search was performed in six electronic databases [MEDLINE, EMBASE, Cumulative Index of Nursing and Allied Health (CINAHL), Scopus, Web of Science and Maternity and Infant Care] and grey literature. We also undertook a hand search of references. We developed search terms having no restrictions based on publication period, country or language. We included studies which reported EC estimates based on the World Health Organization framework of measuring EC. Twenty-seven studies, all from low- and middle-income settings (49 countries), met the criteria and were included in the narrative synthesis of the results. Maternal and child health intervention(s) and programme(s) were assessed either at an individual level or as an aggregated measure of health system performance or both. The EC ranged from 0% for post-partum care to 95% for breastfeeding. When crude coverage measures were adjusted to account for the quality of care, the EC values turned lower. The gap between crude coverage and EC was as high as 86%, and it signified a low quality of care. The assessment of the quality of care addressed structural, process and outcome domains individually or combined. The wealthiest 20% had higher EC of services than the poorest 20%, an inequitable distribution of coverage. More efforts are needed to improve the quality of maternal and child health services and to eliminate the disparities. Moreover, considering multiple dimensions of quality and the use of standard measurements are recommended to monitor coverage effectively.
Hippocampals neurogenesis is impaired in mice with a deletion in the coiled coil domain of Talpid3—implications for Joubert syndrome
Authors: Bashford Andrew L , Subramanian Vasanta
Published: April 2022

Mutations in Talpid3, a basal body protein essential for the assembly of primary cilia, have been reported to be causative for Joubert Syndrome (JS). Herein, we report prominent developmental defects in the hippocampus of a conditional knockout mouse lacking the conserved exons 11 and 12 of Talpid3. At early postnatal stages, the Talpid3 mutants exhibit a reduction in proliferation in the dentate gyrus and a disrupted glial scaffold. The occurrence of mis-localized progenitors in the granule cell layer suggests a role for the disrupted glial scaffold in cell migration resulting in defective subpial neurogenic zone-to-hilar transition. Neurospheres derived from the hippocampus of Talpid3fl/flUbcCre mouse, in which Talpid3 was conditionally deleted, lacked primary cilia and were smaller in size. In addition, neurosphere cells showed a disrupted actin cytoskeleton and defective migration. Our findings suggest a link between the hippocampal defects and the learning/memory deficits seen in JS patients.
Emulating a target trial of intensive nurse home visiting in the policy-relevant population using linked administrative data
Authors: Moreno-Betancur Margarita , Lynch John W , Pilkington Rhiannon M , Schuch Helena S , Gialamas Angela , Sawyer Michael G , Chittleborough Catherine R , Schurer Stefanie , Gurrin Lyle C
Published: April 2022

Background

Populations willing to participate in randomized trials may not correspond well to policy-relevant target populations. Evidence of effectiveness that is complementary to randomized trials may be obtained by combining the ‘target trial’ causal inference framework with whole-of-population linked administrative data.

Methods

We demonstrate this approach in an evaluation of the South Australian Family Home Visiting Program, a nurse home visiting programme targeting socially disadvantaged families. Using de-identified data from 2004–10 in the ethics-approved Better Evidence Better Outcomes Linked Data (BEBOLD) platform, we characterized the policy-relevant population and emulated a trial evaluating effects on child developmental vulnerability at 5 years (n = 4160) and academic achievement at 9 years (n = 6370). Linkage to seven health, welfare and education data sources allowed adjustment for 29 confounders using Targeted Maximum Likelihood Estimation (TMLE) with SuperLearner. Sensitivity analyses assessed robustness to analytical choices.

Results

We demonstrated how the target trial framework may be used with linked administrative data to generate evidence for an intervention as it is delivered in practice in the community in the policy-relevant target population, and considering effects on outcomes years down the track. The target trial lens also aided in understanding and limiting the increased measurement, confounding and selection bias risks arising with such data. Substantively, we did not find robust evidence of a meaningful beneficial intervention effect.

Conclusions

This approach could be a valuable avenue for generating high-quality, policy-relevant evidence that is complementary to trials, particularly when the target populations are multiply disadvantaged and less likely to participate in trials.
Herpes Simplex Virus-2 Variation Contributes to Neurovirulence During Neonatal Infection
Authors: Hayes Cooper K , Villota Christopher K , McEnany Fiona B , Cerón Stacey , Awasthi Sita , Szpara Moriah L , Friedman Harvey M , Leib David A , Longnecker Richard , Weitzman Matthew D , Akhtar Lisa N
Published: April 2022

Herpes simplex virus (HSV) infection of the neonatal brain causes severe encephalitis and permanent neurologic deficits. However, infants infected with HSV at the time of birth follow varied clinical courses, with approximately half of infants experiencing only external infection of the skin rather than invasive neurologic disease. Understanding the cause of these divergent outcomes is essential to developing neuroprotective strategies. To directly assess the contribution of viral variation to neurovirulence, independent of human host factors, we evaluated clinical HSV isolates from neonates with different neurologic outcomes in neurologically relevant in vitro and in vivo models. We found that isolates taken from neonates with encephalitis are more neurovirulent in human neuronal culture and mouse models of HSV encephalitis, as compared to isolates collected from neonates with skin-limited disease. These findings suggest that inherent characteristics of the infecting HSV strain contribute to disease outcome following neonatal infection.
On the misuse of regressions of price on the HHI in merger review
Authors: Miller Nathan , Berry Steven , Scott Morton Fiona , Baker Jonathan , Bresnahan Timothy , Gaynor Martin , Gilbert Richard , Hay George , Jin Ginger , Kobayashi Bruce , Lafontaine Francine , Levinsohn James , Marx Leslie , Mayo John , Nevo Aviv , Pakes Ariel , Rose Nancy , Rubinfeld Daniel , Salop Steven , Schwartz Marius , Seim Katja , Shapiro Carl , Shelanski Howard , Sibley David , Sweeting Andrew , Wosinska Marta
Published: April 2022

The article explains why regressions of price on HHI should not be used in merger review. Both price and HHI are equilibrium outcomes determined by demand, supply, and the factors that drive them. Thus, a regression of price on the HHI does not recover a causal effect that could inform the likely competitive effects of a merger. Nonetheless, economic theory is consistent with the legal presumption that a merger is likely to have adverse competitive effects if it occurs in a concentrated market and makes that market more concentrated.
Growth and nitrogen status of cotton (Gossypium hirsutum L.) under salt stress revealed using 15N-labeled fertilizer
Authors: Heng Tong , He Xin-Lin , Yang Guang , Tian Li-Jun , Li Fa-Dong , Yang Li-Li , Zhao Li , Feng Yue , Xu Xuan
Published: April 2022

Salt stress is a vital factor limiting nitrogen uptake and cotton growth in arid regions. The mechanisms underlying salt stress tolerance in cotton plants under high soil salinity have not been fully elucidated. Therefore, the aim of this study was to examine the proportion and mechanism of cotton nitrogen uptake under salt stress using the 15N isotope labeling technique. Cotton plants were grown in four undisturbed saline soils (1, 3, 6 and 9 dS m−1), and the experiment was designed using the ENVIRO-GRO (E-G) model. The results showed that the dry matter of roots, stems and leaves of the cotton parts in slightly saline soil (C2, 3 dS m−1) was not significant compared with the non-saline soil (C1, 1 dS m−1). The cotton fruit grown in low-salinity soil (C2, 3 dS m−1) had significantly higher dry matter than that grown in the other treatments, implying that cotton plants grown in 3 dS m−1 soil have the best nitrogen uptake and salt tolerance. Cotton plants grown in weakly (C3, 6 dS m−1) and moderately (C4, 9 dS m−1) saline soils exhibited premature senescence. The distribution of total nitrogen and nitrate content in cotton was the best explanatory variable of total 15N recovery, of which cotton 15N recovery was between 26.1% and 47.2%, and soil 15N recovery was between 7.7% and 14.9%. Our findings provide guidance for further exploitation and utilization of saline soil resources and sustainable development of the agricultural soil ecosystem in arid regions.
Child Posttraumatic Stress after Parental Cancer: Associations with Individual and Family Factors
Authors: Egberts Marthe R , Verkaik Dineke , van Baar Anneloes L , Mooren Trudy T M , Spuij Mariken , de Paauw-Telman Liesbeth G E , Boelen Paul A
Published: April 2022

Objective

This study aimed to examine the severity of posttraumatic stress disorder (PTSD) symptoms in children of parents with cancer and to identify individual and family factors associated with these symptoms.

Methods

The sample consisted of 175 children (52% girls, aged M = 11.98, SD = 3.20, range = 6–20 years) from 92 families, of which 90 parents with a current or past cancer diagnosis and 71 healthy co-parents also completed questionnaires. Children reported on PTSD symptoms, trauma-related cognitions, emotion regulation difficulties, general family functioning, and family communication. Both parents reported on their own PTSD symptoms. Associations were investigated using multilevel regression.

Results

Twenty-seven percentage of the children showed clinically relevant PTSD symptoms. Intraclass correlations indicated that children from the same family showed little overlap in these symptoms. Multilevel analyses showed that child trauma-related cognitions and emotion regulation difficulties were related to higher levels of PTSD symptoms at the individual level. General family functioning was only related to child PTSD symptoms at the family level. Child PTSD severity was unrelated to parental PTSD symptoms and family communication at the family level when taking into account the other factors.

Conclusions

The current study highlights the psychological impact of parental cancer on children. Individual factors contributed more strongly to child PTSD symptoms than family factors. Trauma-related cognitions and emotion regulation difficulties might be targeted through specific psychoeducation for children and parents, family-oriented support and interventions, and evidence-based treatments for child PTSD.
SETDB1 fuels the lung cancer phenotype by modulating epigenome, 3D genome organization and chromatin mechanical properties
Authors: Zakharova Vlada V , Magnitov Mikhail D , Del Maestro Laurence , Ulianov Sergey V , Glentis Alexandros , Uyanik Burhan , Williart Alice , Karpukhina Anna , Demidov Oleg , Joliot Veronique , Vassetzky Yegor S , Mège René-Marc , Piel Matthieu , Razin Sergey V , Ait-Si-Ali Slimane
Published: April 2022

Imbalance in the finely orchestrated system of chromatin-modifying enzymes is a hallmark of many pathologies such as cancers, since causing the affection of the epigenome and transcriptional reprogramming. Here, we demonstrate that a loss-of-function mutation (LOF) of the major histone lysine methyltransferase SETDB1 possessing oncogenic activity in lung cancer cells leads to broad changes in the overall architecture and mechanical properties of the nucleus through genome-wide redistribution of heterochromatin, which perturbs chromatin spatial compartmentalization. Together with the enforced activation of the epithelial expression program, cytoskeleton remodeling, reduced proliferation rate and restricted cellular migration, this leads to the reversed oncogenic potential of lung adenocarcinoma cells. These results emphasize an essential role of chromatin architecture in the determination of oncogenic programs and illustrate a relationship between gene expression, epigenome, 3D genome and nuclear mechanics.
TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure
Authors: Poszewiecka Barbara , Pienkowski Victor Murcia , Nowosad Karol , Robin Jérôme D , Gogolewski Krzysztof , Gambin Anna
Published: April 2022

In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
ICARUS, an interactive web server for single cell RNA-seq analysis
Authors: Jiang Andrew , Lehnert Klaus , You Linya , Snell Russell G
Published: April 2022

Here we present ICARUS, a web server to enable users without experience in R to undertake single cell RNA-seq analysis. The focal point of ICARUS is its intuitive tutorial-style user interface, designed to guide logical navigation through the multitude of pre-processing, analysis and visualization steps. ICARUS is easily accessible through a dedicated web server (https://launch.icarus-scrnaseq.cloud.edu.au/) and avoids installation of software on the user's computer. Notable features include the facility to apply quality control thresholds and adjust dimensionality reduction and cell clustering parameters. Data is visualized through 2D/3D UMAP and t-SNE plots and may be curated to remove potential confounders such as cell cycle heterogeneity. ICARUS offers flexible differential expression analysis with user-defined cell groups and gene set enrichment analysis to identify likely affected biological pathways. Eleven organisms including human, dog, mouse, rat, zebrafish, fruit fly, nematode, yeast, cattle, chicken and pig are currently supported. Visualization of multimodal data including those generated by CITE-seq and the 10X Genomics Multiome kit is included. ICARUS incorporates a function to save the current state of analysis avoiding computationally intensive steps during repeat analysis. The complete analysis of a typical single cell RNA-seq dataset by inexperienced users may be achieved in 1–2 h.
SigCom LINCS: data and metadata search engine for a million gene expression signatures
Authors: Evangelista John Erol , Clarke Daniel J B , Xie Zhuorui , Lachmann Alexander , Jeon Minji , Chen Kerwin , Jagodnik Kathleen M , Jenkins Sherry L , Kuleshov Maxim V , Wojciechowicz Megan L , Schürer Stephan C , Medvedovic Mario , Ma’ayan Avi
Published: April 2022

Millions of transcriptome samples were generated by the Library of Integrated Network-based Cellular Signatures (LINCS) program. When these data are processed into searchable signatures along with signatures extracted from Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO), connections between drugs, genes, pathways and diseases can be illuminated. SigCom LINCS is a webserver that serves over a million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. SigCom LINCS is built with Signature Commons, a cloud-agnostic skeleton Data Commons with a focus on serving searchable signatures. SigCom LINCS provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term. Additionally, users of SigCom LINCS can perform a metadata search to find and analyze subsets of signatures and find information about genes and drugs. SigCom LINCS is findable, accessible, interoperable, and reusable (FAIR) with metadata linked to standard ontologies and vocabularies. In addition, all the data and signatures within SigCom LINCS are available via a well-documented API. In summary, SigCom LINCS, available at https://maayanlab.cloud/sigcom-lincs, is a rich webserver resource for accelerating drug and target discovery in systems pharmacology.