bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpretation of SNP combination effects on schizophrenia etiology based on stepwise deep learning with multi-precision data
Authors: Jo Yousang , Webster Maree J , Kim Sanghyeon , Lee Doheon
Published: September 2023

Schizophrenia genome-wide association studies (GWAS) have reported many genomic risk loci, but it is unclear how they affect schizophrenia susceptibility through interactions of multiple SNPs. We propose a stepwise deep learning technique with multi-precision data (SLEM) to explore the SNP combination effects on schizophrenia through intermediate molecular and cellular functions. The SLEM technique utilizes two levels of precision data for learning. It constructs initial backbone networks with more precise but small amount of multilevel assay data. Then, it learns strengths of intermediate interactions with the less precise but massive amount of GWAS data. The learned networks facilitate identifying effective SNP interactions from the intractably large space of all possible SNP combinations. We have shown that the extracted SNP combinations show higher accuracy than any single SNPs and preserve the accuracy in an independent dataset. The learned networks also provide interpretations of molecular and cellular interactions of SNP combinations toward schizophrenia etiology.
THGNCDA: circRNA–disease association prediction based on triple heterogeneous graph network
Authors: Guo Yuwei , Yi Ming
Published: September 2023

Circular RNAs (circRNAs) are a class of noncoding RNA molecules featuring a closed circular structure. They have been proved to play a significant role in the reduction of many diseases. Besides, many researches in clinical diagnosis and treatment of disease have revealed that circRNA can be considered as a potential biomarker. Therefore, understanding the association of circRNA and diseases can help to forecast some disorders of life activities. However, traditional biological experimental methods are time-consuming. The most common method for circRNA–disease association prediction on the basis of machine learning can avoid this, which relies on diverse data. Nevertheless, topological information of circRNA and disease usually is not involved in these methods. Moreover, circRNAs can be associated with diseases through miRNAs. With these considerations, we proposed a novel method, named THGNCDA, to predict the association between circRNAs and diseases. Specifically, for a certain pair of circRNA and disease, we employ a graph neural network with attention to learn the importance of its each neighbor. In addition, we use a multilayer convolutional neural network to explore the relationship of a circRNA–disease pair based on their attributes. When calculating embeddings, we introduce the information of miRNAs. The results of experiments show that THGNCDA outperformed the SOTA methods. In addition, it can be observed that our method gives a better recall rate. To confirm the significance of attention, we conducted extensive ablation studies. Case studies on Urinary Bladder and Prostatic Neoplasms further show THGNCDA’s ability in discovering known relationships between circRNA candidates and diseases.
HURTing: An Analysis of Service User and Carer Referrals to a UK Social Work Regulator
Authors: Hayes Davy
Published: September 2023

In the context of increasing regulation of social workers internationally, this study examines allegations made to a UK social work regulator, the Northern Ireland Social Care Council (NISCC), by service users and carers. A retrospective review of 134 records relating to such allegations during the ten-year period 2006–2015 was undertaken, representing just over one-third (36.4 per cent) of all allegations received. Allegations were made primarily about family and child-care social workers (91.0 per cent) and reflected the four inter-linking categories of concerns about the honesty of social workers, reports that service users/carers were treated unequally, allegations that social workers failed to demonstrate respect in their interactions with service users/carers, and concerns about technical aspects of social workers’ practice. The nature of these allegations forms the acronym HURT that describes both the experiences of service users/carers and the stressful context in which social workers practice. This article concludes that addressing the stress and HURT of both parties is important and makes suggestions regarding how the findings can strengthen the role of the regulator, influence social work practice and empower service users and carers.
m6A-modified circASXL1 promotes proliferation and migration of ovarian cancer through the miR-320d/RACGAP1 axis
Authors: Tian Qi , Mu Qingling , Liu Shuang , Huang Kui , Tang Yi , Zhang Pu , Zhao Jing , Shu Chuqiang
Published: September 2023

Ovarian cancer (OC) is one of the most common malignant tumors in women. Circular RNAs (circRNAs) can potentially regulate the development of OC. Therefore, this study investigated the role of circASXL1 in OC progression. Cell functions were assessed by MTT, colony formation, wound healing, and transwell assays. RIP and dual luciferase reporter assays confirmed the relationship between miR-320d and circASXL1 or RACGAP1. MeRIP was utilized to detect m6A levels. Xenograft tumor was established for in vivo experiments. CircASXL1 and RACGAP1 levels were increased in OC tissues and cells, whereas miR-320d expression was decreased. Upregulation of circASXL1 was associated with poor prognosis in OC patients. CircASXL1 silencing suppressed OC cell proliferation, migration and invasion in vitro and in vivo. Mechanistically, METTL3/IGF2BP1-mediated m6A modification maintained circASXL1 stability and upregulated its expression. CircASXL1 was a ceRNA that sequestrated miR-320d from RACGAP1, leading to increased RACGAP1 expression. CircASXL1 promoted OC cell proliferation, migration and invasion via the miR-320d/RACGAP1 axis. Therefore, m6A-modified circASXL1 acts as an oncogene in OC by targeting miR-320d and activating RACGAP1/PI3K/Akt pathway, which provides novel promising biomarkers for OC diagnosis.
State of the Management of Infections Caused by Multidrug-Resistant Gram-Negative Organisms
Authors: Yassin Arsheena , Huralska Mariya , Pogue Jason M , Dixit Deepali , Sawyer Robert G , Kaye Keith S
Published: September 2023

In the past decade, the prevalence of multidrug-resistant gram-negative (MDR-GN) bacterial infections has increased significantly, leading to higher rates of morbidity and mortality. Treating these infections poses numerous challenges, particularly when selecting appropriate empiric therapy for critically ill patients for whom the margin for error is low. Fortunately, the availability of new therapies has improved the treatment landscape, offering safer and more effective options. However, there remains a need to establish and implement optimal clinical and therapeutic approaches for managing these infections. Here, we review strategies for identifying patients at risk for MDR-GN infections, propose a framework for the choice of empiric and definitive treatment, and explore effective multidisciplinary approaches to managing patients in the hospital while ensuring a safe transition to outpatient settings.
Determining Herd Immunity Thresholds for Hepatitis A Virus Transmission to Inform Vaccination Strategies Among People Who Inject Drugs in 16 US States
Authors: Yang Judy , Lo Nathan C , Dankwa Emmanuelle A , Donnelly Christl A , Gupta Ribhav , Montgomery Martha P , Weng Mark K , Martin Natasha K
Published: September 2023

Background

Widespread outbreaks of person-to-person transmitted hepatitis A virus (HAV), particularly among people who inject drugs (PWID), continue across the United States and globally. However, the herd immunity threshold and vaccination coverage required to prevent outbreaks are unknown. We used surveillance data and dynamic modeling to estimate herd immunity thresholds among PWID in 16 US states.

Methods

We used a previously published dynamic model of HAV transmission calibrated to surveillance data from outbreaks involving PWID in 16 states. Using state-level calibrated models, we estimated the basic reproduction number (R0) and herd immunity threshold for PWID in each state. We performed a meta-analysis of herd immunity thresholds to determine the critical vaccination coverage required to prevent most HAV outbreaks among PWID.

Results

Estimates of R0 for HAV infection ranged from 2.2 (95% confidence interval [CI], 1.9–2.5) for North Carolina to 5.0 (95% CI, 4.5–5.6) for West Virginia. Corresponding herd immunity thresholds ranged from 55% (95% CI, 47%–61%) for North Carolina to 80% (95% CI, 78%–82%) for West Virginia. Based on the meta-analysis, we estimated a pooled herd immunity threshold of 64% (95% CI, 61%–68%; 90% prediction interval, 52%–76%) among PWID. Using the prediction interval upper bound (76%) and assuming 95% vaccine efficacy, we estimated that vaccination coverage of 80% could prevent most HAV outbreaks.

Conclusions

Hepatitis A vaccination programs in the United States may need to achieve vaccination coverage of at least 80% among PWID in order to prevent most HAV outbreaks among this population.
Are Contact Precautions “Essential” for the Prevention of Healthcare-associated Methicillin-Resistant Staphylococcus aureus?
Authors: Diekema Daniel J , Nori Priya , Stevens Michael P , Smith Matthew W , Coffey K C , Morgan Daniel J
Published: September 2023

The recently updated Society for Healthcare Epidemiology of America, the Infectious Diseases Society of America, and the Association of Professionals in Infection Control practice recommendations for methicillin-resistant Staphylococcus aureus (MRSA) prevention in acute care facilities list contact precautions (CPs) for patients known to be infected or colonized with MRSA as an “essential practice,” meaning that it should be adopted in all acute care facilities. We argue that existing evidence on benefits and harms associated with CP do not justify this recommendation. There are no controlled trials that support broad use of CP for MRSA prevention. Data from hospitals that have discontinued CP for MRSA have found no impact on MRSA acquisition or infection. The burden and harms of CP remain concerning, including the environmental impact of increased gown and glove use. We suggest that CP be included among other “additional approaches” to MRSA prevention that can be implemented under specific circumstances (eg outbreaks, evidence of ongoing transmission despite application of essential practices).
Learning from architectural theory about how cities work as complex and evolving spatial systems
Authors: Froy Francesca
Published: September 2023

This article seeks to advance a key element of the methodological framework for evolutionary economic geography (EEG)—the conceptualisation of ‘urban space’. Drawing on recent theories from architecture and urban data science, it argues that the networked and topological qualities of urban built environments have been neglected in the EEG discipline, and yet they play an important role in how cities work as ‘complex evolving systems’. The article explores different ways in which the spatial configuration of cities influences urban economic evolution, drawing on Bill Hillier’s theory of space syntax and a case study from Greater Manchester. It concludes that when urban street systems are disrupted this can potentially become one contributing factor in why places become economically ‘left behind’.
Cryptanalysis Of A Type Of White-Box Implementations Of The SM4 Block Cipher
Authors: Lu Jiqiang , Li Jingyu , Chen Zexuan , Li Yanan
Published: September 2023

The SM4 block cipher is a Chinese national standard and an ISO international standard. Since white-box cryptography has many real-life applications nowadays, a few white-box implementations of SM4 has been proposed, among which a type of constructions is dominated, which uses a linear or affine diagonal block encoding to protect the original three 32-bit branches entering a round function and uses its inverse as the input encoding to the S-box layer. In this paper, we analyse the security of this type of constructions against Lepoint et al.’s collision-based attack method. Our experiment under a small fraction of (encodings, round key) combinations shows that the rank of the concerned linear system is much less than the number of the involved unknowns, meaning these white-box SM4 implementations should resist Lepoint et al.’s method, but we leave it as an open problem whether there are such encodings that the rank of the corresponding linear system is slightly less than the number of the involved unknowns, in which scenario Lepoint et al.’s method may be used to recover a round key for the case with linear encodings and to remove most white-box operations until mainly some Boolean masks for the case with affine encodings.
The X chromosome of insects likely predates the origin of class Insecta
Authors: Toups Melissa A , Vicoso Beatriz
Published: September 2023

Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.
Maternal ancestry and lineages diversity of the Santander population from Colombia
Authors: Castillo Adriana , Rondón Fernando , Mantilla Gerardo , Gusmão Leonor , Simão Filipa
Published: September 2023

Santander, located in the Andean region of Colombia, is one of the 32 departments of the country. Its population was shaped by intercontinental admixture between autochthonous native Americans, European settlers, and African slaves. To establish forensic databases of haplotype frequencies, the evaluation of population substructure is crucial to capture the genetic diversity in admixed populations. Total control region mitochondrial deoxyribonucleic acid haplotypes were determined for 204 individuals born in the seven provinces across the department. The maternal native heritage is highly preserved in Santander genetic background, with 90% of the haplotypes belonging to haplogroups inside A2, B4, C1, and D. Most native lineages are found broadly across the American continent, while some sub-branches are concentrated in Central America and north South America. Subtle European (6%) and African (4%) input was detected. In pairwise comparisons between provinces, relatively high FST values were found in some cases, although not statistically significant. Nonetheless, when provinces were grouped according to the principal component analysis results, significant differences were detected between groups. The database on mitochondrial deoxyribonucleic acid control region haplotype frequencies established here can be further used for populational and forensic purposes.
Cardiovascular Disorders and Falls Among Older Adults: A Systematic Review and Meta-Analysis
Authors: Bourke Robbie , Doody Paul , Pérez Sergio , Moloney David , Lipsitz Lewis A , Kenny Rose Anne
Published: September 2023

Background

Falls are a common cause of injury, hospitalization, functional decline, and residential care admission among older adults. Cardiovascular disorders are recognized risk factors for falls. This systematic review assesses the association between cardiovascular disorders and falls in older adults.

Methods

Systematic searches were conducted on MEDLINE and Embase, encompassing all literature published prior to December 31, 2022. Included studies addressed persons aged 50 years and older, and assessed the association between cardiovascular disorders and falls or the efficacy of cardiovascular-based interventions to reduce falls. Two reviewers independently extracted data and assessed study quality utilizing a modified Newcastle–Ottawa scale for observational studies, and the Cochrane Risk of Bias 2 tool for interventional studies. A systematic narrative analysis of all cardiovascular outcomes, and meta-analyses of unadjusted odds ratios (ORs) were performed.

Results

One hundred and eighty-four studies were included: 181 observational and 3 interventional. Several cardiovascular disorders, including stroke, coronary artery disease, valvular heart disease, arterial stiffness, arrhythmia, orthostatic hypotension, and carotid sinus hypersensitivity, were consistently associated with falls. In meta-analysis of unadjusted ORs, the largest positive pooled associations with falls during a 12-month reporting interval were for stroke (OR: 1.90, 95% confidence interval [CI]: 1.70–2.11), peripheral arterial disease (OR: 1.82, 95% CI: 1.12–2.95), atrial fibrillation (OR: 1.52, 95% CI: 1.27–1.82), and orthostatic hypotension (OR: 1.39, 95% CI: 1.18–1.64).

Conclusions

Several cardiovascular disorders are associated with falls. These results suggest the need to incorporate cardiovascular assessments for patients with falls. This review informed the cardiovascular recommendations in the new World Guidelines for falls in older adults.

Clinical Trials Registration Number: CRD42021272245
The Triple Alliance: Microbiome, Mitochondria, and Metabolites in the Context of Age-Related Cognitive Decline and Alzheimer’s Disease
Authors: Prajapati Santosh K , Shah Ria , Alford Nicholas , Mishra Sidharth P , Jain Shalini , Hansen Barbara , Sanberg Paul , Molina Anthony J A , Yadav Hariom
Published: September 2023

Alzheimer’s disease (AD) is a progressive, age-related neurodegenerative disorder that affects a large proportion of the older population. It currently lacks effective treatments, placing a heavy burden on patients, families, health care systems, and society. This is mainly due to our limited comprehension of the pathophysiology of AD progression, as well as the lack of effective drug targets and intervention timing to address the underlying pathology. AD is a multifactorial condition, and emerging evidence suggests that abnormalities in the gut microbiota play a significant role as environmental and multifaceted contributors to AD, although the exact mechanisms are yet to be fully explored. Changes in the composition of microbiota influence host neuronal health through their metabolites. These metabolites regulate intestinal epithelia, blood-brain barrier permeability, and neuroinflammation by affecting mitochondrial function. The decline in the proportion of beneficial microbes and their essential metabolites during aging and AD is directly linked to poor mitochondrial function, although the specific mechanisms remain unclear. In this review, we discuss recent developments in understanding the impact of the microbiome and its metabolites on various cell types, their influence on the integrity of the gut and blood-brain barriers, systemic and brain inflammation, and cell-specific effects in AD pathology. This information is expected to pave the way for a new understanding of the interactions between microbiota and mitochondria in AD, providing a foundation for the development of novel treatments for AD.
Family Ties and Older Adult Well-Being: Incorporating Social Networks and Proximity
Authors: Patterson Sarah E , Margolis Rachel
Published: September 2023

Objectives

This paper examines the family ties of older adults in the United States and how they are associated with mental health and social activity. We compare older adults with 4 types of family ties: adults “close” to family in proximity and social network, “kinless” older adults without a partner or children, “distanced” adults who live far from close kin, and “disconnected” older adults who do not report kin in their social network or do not report a location for some kin.

Methods

Using pooled data from the National Health and Aging Trends Study 2015–2019 for older adults aged 70 and older (N = 24,818 person-waves), we examine how family ties are associated with mental health and social activity, and whether lacking family is tied to poor well-being because older adults’ needs are not being met.

Results

Kinless older adults and disconnected older adults have poorer outcomes (lower mental health scores and less social activity), compared to those close to their family. These findings suggest that both the presence and quality of the connection, as measured here via both location and social network, are critical for understanding which older adults are “at risk.” Older adults who were not geographically proximate to their close kin (i.e., distanced) were not disadvantaged relative to those close to their families. Unmet needs do not help explain these patterns.

Discussion

Our results highlight that family ties are important for older adults well-being, not just through their existence but also their quality and strength.
The Impact of Cat Fostering on Older Adult Well-Being and Loneliness: A Feasibility Study
Authors: Sanderson Sherry L , Emerson Kerstin G , Scott Donald W , Vidrine Maureen , Hartzell Diane L , Keys Deborah A
Published: September 2023

Objectives

This feasibility study explored the impact of fostering a shelter cat on loneliness and well-being in older adults living alone without a pet. The study also examined the effect of cat fostering on older adults’ interest in cat adoption when perceived barriers to adoption were removed.

Methods

A total of 29 adults (age ≥60) were paired with a cat and asked to foster for a minimum of 4 months (with an option to adopt). Participants completed surveys before placement with cats, with a follow-up at 1 and 4 months postplacement and 12 months if they adopted their cat. The survey included scales of loneliness, physical and mental health, self-efficacy, positive and negative affect, and comfort from a companion animal. Scores were compared across time using a Multivariable Linear Mixed Model.

Results

A total of 23 of 29 (79.3%) participants remained in the study for at least 4 months, and a majority (95.7%) adopted their cat. Differences in marginal means (adjusted for physical health) showed a significant improvement in loneliness from baseline to 4 months (p = .029). A similar 4-month improvement that approached statistical significance (adjusted p = .079) was observed for mental health. No other scales showed statistically significant changes across time.

Discussion

Fostering a shelter cat with the option for adoption may be an effective solution for alleviating loneliness and improving mental health in older adults. Interest in adopting foster cats was high when perceived barriers to adoption were removed.
6. Confidentiality
Authors: Herring Jonathan
Published: September 2023

This chapter discusses the principle of confidentiality. It explains the protection of lawyer–client communications and it discusses professional guidance on confidentiality. It is clear that the duty of confidence is not an absolute one and there are circumstances in which it is appropriate, indeed even required, for a lawyer to disclose confidential information. The chapter explores when these exceptions to the general principle of protection of confidence arise. It goes on to examine the rule of legal professional privilege and the circumstances in which lawyers have a duty to disclose. The chapter discusses when a lawyer is permitted to breach confidence. In doing so, it looks at the broader ethical foundation for the duty of confidence.
12. Third parties
Authors: Herring Jonathan
Published: September 2023

This chapter explores how lawyers can balance their obligations to promote their clients’ interests and their obligations to third parties. While there are circumstances in which duties are owed to third parties, these are limited. The law and ethical codes struggle to ensure that, even when these duties are imposed, they are not used to undermine the relationship between lawyer and client. The regulations ensure that the lawyer never acts against the best interests of the client. The chapter explores the guidance issued by the professional codes of practice. It also looks at the practice of giving an undertaking, which is an important aspect of some lawyer’s work.
Divergent phenotypes in constitutive versus conditional mutant mouse models of Sifrim-Hitz-Weiss syndrome
Authors: Larrigan Sarah , Joshi Shrilaxmi V , Mattar Pierre
Published: September 2023

Chromatin remodellers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), however, their functions during brain development are not fully understood. Here, we focused on Sifrim-Hitz-Weiss Syndrome (SIHIWES)—an intellectual disability disorder caused by mutations in the CHD4 chromodomain helicase gene. We utilized mouse genetics to excise the Chd4 ATPase/helicase domain—either constitutively, or conditionally in the developing telencephalon. Conditional heterozygotes exhibited no change in cortical size and cellular composition, and had only subtle behavioral phenotypes. Telencephalon-specific conditional knockouts had marked reductions in cortical growth, reduced numbers of upper-layer neurons, and exhibited alterations in anxiety and repetitive behaviors. Despite the fact that whole-body heterozygotes exhibited comparable growth defects, they were unaffected in these behaviors, but instead exhibited female-specific alterations in learning and memory. These data reveal unexpected phenotypic divergence arising from differences in the spatiotemporal deployment of loss-of-function manipulations, underscoring the importance of context in chromatin remodeller function during neurodevelopment.
Abundant Neutrophil-Initiated Acute Myocardial Injury Following Coxsackievirus A6 Infection
Authors: Zhang Yu , Chen Shuaiyin , Sun Tiantian , Duan Guangcai , Yang Haiyan , Feng Huifen , Jiang Wenjie , Li Dong , Ji Wangquan , Zhu Peiyu , Jin Yuefei
Published: September 2023

Coxsackievirus A6 (CVA6) is currently considered as a predominant pathogen of hand, foot, and mouth disease (HFMD), and is occasionally linked to myocardial injury. We first established a mouse model of CVA6-induced myocardial injury. Next, we analyzed the immune cell phenotypes CVA6-infected mice hearts by fluorescence-activated cell sorting, and found that CVA6 led to massive neutrophils infiltration, suggesting their potential link with the occurrence of myocardial injury. We further used either αGr-1 or αLy6G antibody to deplete neutrophils, and found that neutrophil-depleted animals showed decreased cardiac enzymes, lower degree of pathology in hearts, and reduced inflammatory cytokine production compared to isotype controls. Finally, we confirmed the involvement of neutrophils in myocardial injury of clinical patients with severe HFMD. Our study suggests that excessive neutrophils contribute to myocardial injury caused by CVA6 infection, which provides new insights into myocardial injury during the development of HFMD severity and the outcome of immune cell-mediated therapies.
Susceptibility and diagnostic concentration for Bacillus thuringiensis toxins and newer chemical insecticides in Spodoptera frugiperda (Lepidoptera: Noctuidae) from China
Authors: Guan Fang , Zhang Zheng , Lin Yuhang , Liu Xiangjie , Wang Xingliang , Yang Yihua , Carrière Yves , Wu Yidong
Published: September 2023

The fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), is a cosmopolitan pest that exploits more than 350 host plants, including economically important crops such as corn, cotton and rice. Control of S. frugiperda largely relies on transgenic crops producing insecticidal proteins from Bacillus thuringiensis (Bt) and spraying synthetic insecticides. Here, we established the susceptibility and diagnostic concentration for 2 Bt toxins and 5 newer insecticides in invasive populations of S. frugiperda from southeastern China. Concentrations causing 50% mortality (LC50) in ten field populations sampled in 2022 ranged from 2.13 to 19.29 and 22.43 to 71.12 ng/cm2 for Cry1Fa and Vip3Aa, and 0.83 to 5.30, 2.83 to 9.94, 0.04 to 0.23, 4.59 to 8.40, and 1.49 to 6.79 mg/liter for chlorantraniliprole, chlorfenapyr, emamectin benzoate, indoxacarb, and spinosad, respectively. Relative to the susceptible strain YJ-19, the largest resistance ratio in the field populations was 5.1, 1.6, 6.2, 3.9, 4.6, 2.2, and 3.6 for Cry1Fa, Vip3Aa, chlorantraniliprole, chlorfenapyr, emamectin benzoate, indoxacarb, and spinosad, respectively, indicating that the field populations were generally susceptible to these Bt toxins and insecticides. Based on the pooled response of the field populations, the diagnostic concentration for resistance monitoring, estimated as ca. twice the LC99, was 400 and 1,500 ng/cm2 for Cry1Fa and Vip3Aa, and 2, 40, 60, 60, and 100 mg/liter for emamectin benzoate, chlorantraniliprole, chlorfenapyr, spinosad, and indoxacarb, respectively. These results provide useful information for monitoring resistance to key Bt toxins and insecticides for the control of S. frugiperda in China.
A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides
Authors: Schiebelhut Lauren M , DeBiasse Melissa B , Gabriel Lars , Hoff Katharina J , Dawson Michael N
Published: September 2023

Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses—as well as their integration across scales—of SSW and environmental stressors.
Characterization of the swarming behavior of Anopheles coluzzii and Anopheles gambiae (Diptera: Culicidae) populations in a hybrid zone of Senegal
Authors: Gueye Oumou Kalsom , Niang Abdoulaye , Faye Mouhamed Bassir , Dia Abdoulaye Kane , Ahmed Amblat Ali , Sy Ousmane , Tripet Frederic , Konaté Lassana , Dia Ibrahima , Wondji Charles Sinclair , Gaye Oumar , Faye Ousmane , Diabate Abdoulaye , Niang El Hadji Amadou
Published: September 2023

Anopheles gambiae and Anopheles coluzzii, often found in sympatry and synchronous, have undergone a premating reproductive isolation across their distribution range. However, in the Western coast of Africa, unexpected hybridization zones have been observed, and little is known about swarming behavior of these cryptic taxa. Here, we characterized the swarming behavior of An. coluzzii and An. gambiae to investigate its role in the high hybridization level in Senegal. The study was conducted in the south and central Senegal during the 2018 rainy season. Mating swarms of malaria vectors were surveyed at sunset and collected using an insect net. Meanwhile, indoor resting populations of malaria vectors were collected by pyrethrum spray catches. Upon collection, specimens were identified morphologically, and then members of the An. gambiae complex were identified at the species level by polymerase chain reaction (PCR). An. gambiae swarmed mainly over bare ground, whereas An. coluzzii were found swarming above various objects creating a dark–light contrast with the bare ground. The swarms height varied from 0.5 to 2.5 m. Swarming starting time was correlated with sunset whatever the months for both species, and generally lasted about 10 min. No mixed swarm of An. gambiae and An. coluzzii was found even in the high hybridization area. These results indicated a premating isolation between An. coluzzii and An. gambiae. However, the high hybridization rate in the sympatric area suggests that heterogamous mating is occurring, thus stressing the need for further extensive studies.
Mapping current and future risk of scorpion sting from a species with low medical concern, Mesobuthus phillipsii (Scorpiones: Buthidae) in Iran
Authors: Kafash Anooshe , Hanafi-Bojd Ahmad Ali , Mohammadi Bavani Mulood , Shahi Mehran , Akbari Morteza , Rafinejad Javad , Bozorg Omid Faramarz , Hassanpour Gholamreza
Published: September 2023

Scorpion stings are one of the most important health challenges and high priority research topic in public health. In this study, we aimed to model habitat suitability of the Mesobuthus phillipsii (Pocock 1889), a species with low medical concern, under current and future climatic conditions in Iran. We also identified vulnerable populations to scorpion stings in the country. Scorpion sting risk modeling was done using an ensemble approach by considering two species distribution modeling methods: MaxEnt and Random Forest methods. Distribution modeling was performed using the sdm R package. The results showed that due to climate change in 2070, the high-risk areas will increase from 20,839 to 79,212 km2. Habitats with a moderate risk of scorpion stings will also increase from 139,347 to 222,833 km2. Consequently, the number of villages in high-risk areas of scorpion stings will increase from 2,870 to 7,017, while this number will increase from 12,759 to 20,104 in the case of medium-risk villages. The results of this study can be used for scorpion stings management in Iran. This study can be used as an example for similar studies on scorpions with high medical emergency.
A Scoping Review of the Complementary Feeding Practices and Early Eating Experiences of Children With Down Syndrome
Authors: Hielscher Laura , Irvine Karen , Ludlow Amanda K , Rogers Samantha , Mengoni Silvana E
Published: September 2023

Objective

Children with Down syndrome may experience more challenges in their early feeding and may be introduced to complementary foods comparatively later than typically developing (TD) children. This scoping review aimed to identify and synthesize the existing literature that describes feeding problems and early eating experiences relating to the period of complementary feeding for children with Down syndrome.

Methods

Scopus, PubMed, Medline, Web of Science, and PsycInfo were searched. Journal articles published between January 1991 and June 2022 that reported on the complementary feeding period with children with Down syndrome were included.

Results

Eighteen journal articles met the inclusion criteria. Children with Down syndrome were introduced to complementary foods later than TD children and progressed to more challenging food textures at a slower rate. Gross and fine motor skill delays and sensory difficulties contributed to secondary feeding problems such as difficulties chewing, biting, and reduced awareness of food on lips and tongue. Parents of children with Down syndrome reported exercising more caution and employing more controlling feeding practices compared to TD and had higher levels of concern regarding their child’s weight.

Conclusions

Guidelines and early feeding support specific to children with Down syndrome should be available before the first complementary foods are introduced and throughout this period. Feeding support should aim to address parental concerns and provide assistance when feeding problems occur, to minimize delays and encourage the optimum development of eating abilities. Future research should address the development of feeding problems during this period and explore possible interventions.
Sucrose phosphate synthase 8 is required for the remobilization of carbon reserves in rice stems during grain filling
Authors: Ma Mingyang , Zhu Tong , Cheng Xiuyue , Li Mengyu , Yuan Guoliang , Li Changbao , Zhang Aihong , Lu Congming , Fang Ying , Zhang Yi
Published: September 2023

Carbon reserve remobilization in stems is closely related to rice grain filling. Sucrose phosphate synthase (SPS) is highly associated with carbon reserve remobilization. In this study, we investigated the expression pattern of SPS genes in various rice tissues, and found that SPS8 is the major SPS isoform in rice stems during the grain-filling stage. We then constructed sps8 mutants using the CRISPR/Cas9 system. The SPS activity of the sps8 mutants was markedly reduced in the stems. In addition, the sps8 mutants exhibited significant starch accumulation in stems. 14C-labelling experiments revealed that the remobilization of non-structural carbohydrates from rice stems to grains was impaired in the sps8 mutants. In the sps8 mutants, grain filling was delayed and yield decreased by 15% due to a reduced percentage of ripened grains. RNA sequencing and quantitative PCR analyses indicated that the genes involved in starch synthesis and degradation were up-regulated in the sps8 mutant stems. In addition, the activity of the enzymes involved in starch synthesis and degradation was increased in the sps8 stems. These results demonstrate that SPS8 is required for carbon reserve remobilization from rice stems to grains, and that its absence may enhance ‘futile cycles’ of starch synthesis and degradation in rice stems.
The BarYon Cycle project (ByCycle): identifying and localizing Mg ii metal absorbers with machine learning
Authors: Szakacs Roland , Péroux Céline , Nelson Dylan , Zwaan Martin A , Grün Daniel , Weng Simon , Fresco Alejandra Y , Bollo Victoria , Casavecchia Benedetta
Published: September 2023

The upcoming ByCycle project on the VISTA/4MOST multi-object spectrograph will offer new prospects of using a massive sample of ∼1 million high spectral resolution (R = 20 000) background quasars to map the circumgalactic metal content of foreground galaxies (observed at R = 4000–7000), as traced by metal absorption. Such large surveys require specialized analysis methodologies. In the absence of early data, we instead produce synthetic 4MOST high-resolution fibre quasar spectra. To do so, we use the TNG50 cosmological magnetohydrodynamical simulation, combining photo-ionization post-processing and ray tracing, to capture Mg ii (λ2796, λ2803) absorbers. We then use this sample to train a convolutional neural network (CNN) which searches for, and estimates the redshift of, Mg ii absorbers within these spectra. For a test sample of quasar spectra with uniformly distributed properties ($\lambda _{\rm {Mg\, {\small II},2796}}$, $\rm {EW}_{\rm {Mg\, {\small II},2796}}^{\rm {rest}} = 0.05\!-\!5.15$ Å, $\rm {SNR} = 3\!-\!50$), the algorithm has a robust classification accuracy of 98.6 per cent and a mean wavelength accuracy of 6.9 Å. For high signal-to-noise (SNR) spectra ($\rm {SNR \gt 20}$), the algorithm robustly detects and localizes Mg ii absorbers down to equivalent widths of $\rm {EW}_{\rm {Mg\, {\small II},2796}}^{\rm {rest}} = 0.05$ Å. For the lowest SNR spectra ($\rm {SNR=3}$), the CNN reliably recovers and localizes EW$_{\rm {Mg\, {\small II},2796}}^{\rm {rest}}$ ≥0.75 Å absorbers. This is more than sufficient for subsequent Voigt profile fitting to characterize the detected Mg ii absorbers. We make the code publicly available through GitHub. Our work provides a proof-of-concept for future analyses of quasar spectra data sets numbering in the millions, soon to be delivered by the next generation of surveys.
An investigation of the ‘10 keV feature’ in the spectra of accretion powered X-ray pulsars with NuSTAR
Authors: Manikantan Hemanth , Paul Biswajit , Rana Vikram
Published: September 2023

Some of the accreting X-ray pulsars are reported to exhibit a peculiar spectral feature at ∼10 keV, known as the ‘10 keV feature’. The feature has been characterized as either an emission line or an absorption line, and its origin is unknown. It has been found in multiple observations of the same source by different observatories, but not all the observations of any particular source consistently showed the presence of it. In this work, we have carried out a systematic investigation for the presence of the ‘10 keV feature’ using data from NuSTAR, a low background spectroscopic observatory having uninterrupted wide band coverage on either side of 10 keV. We performed a systematic spectral analysis on 58 archival NuSTAR observations of 30 bright X-ray pulsars. The 3–79 keV spectral continua of these selected sources were fitted with a model chosen on the basis of its fitting quality in 3–15 keV and model simplicity, and then inspected for the presence of the ‘10 keV feature’. Our analysis indicates the presence of such a feature in 16 out of 58 the NuSTAR observations of 11 different sources and is fitted with a Gaussian absorption model centred around 10 keV. Our analysis also suggests that such a feature could be wrongly detected if flare data is not analysed separately from persistent emission.
A differentiable model of the evolution of dark matter halo concentration
Authors: Stevanovich Dash , Hearin Andrew P , Nagai Daisuke
Published: September 2023

We introduce a new model of the evolution of the concentration of dark matter haloes, c(t). For individual haloes, our model approximates c(t) as a power law with a time-dependent index, such that at early times, concentration has a nearly constant value of c ≈ 3–4, and as cosmic time progresses, c(t) smoothly increases. Using large samples of halo merger trees taken from the Bolshoi–Planck and MultiDark Planck 2 cosmological simulations, we demonstrate that our three-parameter model can approximate the evolution of the concentration of individual haloes with a typical accuracy of 0.1 dex for $t\gtrsim 2\, {\rm Gyr}$ for all Bolshoi–Planck and MultiDark Planck 2 haloes of present-day peak mass $M_{0}\gtrsim 10^{11.5}\, {\rm M}_{\odot }$. We additionally present a new model of the evolution of the concentration of halo populations, which we show faithfully reproduces both average concentration growth and the diversity of smooth trajectories of c(t), including capturing correlations with halo mass and halo assembly history. Our publicly available source code, diffprof, can be used to generate Monte Carlo realizations of the concentration histories of cosmologically representative halo populations. diffprof is differentiable due to its implementation in the jax autodiff library, which facilitates the incorporation of our model into existing analytical halo model frameworks.
Search for a possible quasi-periodic structure based on data of the SDSS DR12 LOWZ
Authors: Ryabinkov A I , Kaminker A D
Published: September 2023

We carry out a statistical analysis of the spatial distribution of galaxies at cosmological redshifts 0.16 ≤ z ≤ 0.47 based on the SDSS DR12 LOWZ catalogue. Our aim is to search and study possible large-scale quasi-regular structures embedded in the cosmic web. We calculate projections of the Cartesian galaxy coordinates on different axes (directions), densely covering certain regions in the sky to look for special directions along which 1D distributions of the projections contain significant quasi-periodic components. These components appear as peaks in the power spectra and lie in a narrow range of wave numbers 0.05 < k < 0.07. Particular attention is paid to the evaluation of the significance of the peaks. It is found that the significance of the dominant peaks for some selected directions exceeds (4–5)σ. In order to reduce possible selection effects, we create a mock homogeneous catalogue of spatial distribution of galaxies by adding a random set of artificial objects (points) to the real galaxies under study. The power spectrum of this cumulative model data also demonstrates significant peak corresponding to approximately the same scale. As a result we assume the existence of an anisotropic cosmological quasi-periodic structure with characteristic scale (116 ± 10) h−1 Mpc.
Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages
Authors: Chen Heidi I , Turakhia Yatish , Bejerano Gill , Kingsley David M
Published: September 2023

Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
Inference of Coalescence Times and Variant Ages Using Convolutional Neural Networks
Authors: Nait Saada Juba , Tsangalidou Zoi , Stricker Miriam , Palamara Pier Francesco
Published: September 2023

Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs of individuals and of the age of genomic variants is key in several population genetic analyses. We developed a likelihood-free approach, called CoalNN, which uses a convolutional neural network to predict pairwise TMRCAs and allele ages from sequencing or SNP array data. CoalNN is trained through simulation and can be adapted to varying parameters, such as demographic history, using transfer learning. Across several simulated scenarios, CoalNN matched or outperformed the accuracy of model-based approaches for pairwise TMRCA and allele age prediction. We applied CoalNN to settings for which model-based approaches are under-developed and performed analyses to gain insights into the set of features it uses to perform TMRCA prediction. We next used CoalNN to analyze 2,504 samples from 26 populations in the 1,000 Genome Project data set, inferring the age of ∼80 million variants. We observed substantial variation across populations and for variants predicted to be pathogenic, reflecting heterogeneous demographic histories and the action of negative selection. We used CoalNN’s predicted allele ages to construct genome-wide annotations capturing the signature of past negative selection. We performed LD-score regression analysis of heritability using summary association statistics from 63 independent complex traits and diseases (average N=314k), observing increased annotation-specific effects on heritability compared to a previous allele age annotation. These results highlight the effectiveness of using likelihood-free, simulation-trained models to infer properties of gene genealogies in large genomic data sets.