bluuebunny/crossref_metadata_2025 huggingface dataset:
An extreme-ultraviolet wave associated with the possible expansion of sheared arcades
Authors: Liu Yihan , Zheng Ruisheng , Zhang Liang , Wei Hengyuan , Zhong Ze , Yang Shuhong , Chen Yao
Published: April 2023

Context. Solar extreme-ultraviolet (EUV) waves are propagating disturbances in the corona, and they are usually accompanied with various solar eruptions, from large-scale coronal mass ejections to small-scale coronal jets.

Aims. Generally, it is believed that EUV waves are driven by the rapid expansion of coronal loops overlying the erupting cores. In this paper, we present an exception of an EUV wave that was not triggered by the expansion of coronal loops overlying the erupting core.

Methods. Combining the multiwavelength observations from multiple instruments, we studied the event in detail.

Results. The eruption was restricted in the active region (AR) and disturbed the nearby sheared arcades (SAs) connecting the source AR to a remote AR. Interestingly, following the disturbance, an EUV wave formed close to the SAs, but far away from the eruption source.

Conclusions. All the results show that the EUV wave had a closer temporal and spatial relationship with the disappearing part of SAs than the confined eruption. Hence, we suggest that the EUV wave was likely triggered by the expansion of some strands of SAs, rather than the expansion of erupting loops. It can be a possible complement for the driving mechanisms of EUV waves.
Europium enrichment and hierarchical formation of the Galactic halo
Authors: Cavallo L. , Cescutti G. , Matteucci F.
Published: April 2023

Context.The origin of the large star-to-star variation of the [Eu/Fe] ratios observed in the extremely metal-poor (at [Fe/H] ≤ −3) stars of the Galactic halo is still a matter of debate.

Aims.In this paper, we explore this problem by putting our stochastic chemical evolution model in the hierarchical clustering framework, with the aim of explaining the observed spread in the halo.

Methods.We compute the chemical enrichment of Eu occurring in the building blocks that have possibly formed the Galactic halo. In this framework, the enrichment from neutron star mergers can be influenced by the dynamics of the binary systems in the gravitational potential of the original host galaxy. In the least massive systems, the neutron stars can merge outside the host galaxy and so only a small fraction of newly produced Eu can be retained by the parent galaxy itself.

Results.In the framework of this new scenario, the accreted merging neutron stars are able to explain the presence of stars with sub-solar [Eu/Fe] ratios at [Fe/H] ≤ −3, but only if we assume a delay time distribution for merging of the neutron stars ∝t−1.5. We confirm the correlation between the dispersion of [Eu/Fe] at a given metallicity and the fraction of massive stars which give origin to neutron star mergers. The mixed scenario, where both neutron star mergers and magneto-rotational supernovae do produce Eu, can explain the observed spread in the Eu abundance also for a delay time distribution for mergers going either as ∝t−1or ∝t−1.5.
A decomposition of book structure through ousiometric fluctuations in cumulative word-time
Authors: Fudolig Mikaela Irene , Alshaabi Thayer , Cramer Kathryn , Danforth Christopher M. , Dodds Peter Sheridan
Published: April 2023

While quantitative methods have been used to examine changes in word usage in books, studies have focused on overall trends, such as the shapes of narratives, which are independent of book length. We instead look at how words change over the course of a book as a function of the number of words, rather than the fraction of the book, completed at any given point; we define this measure as “cumulative word-time”. Using ousiometrics, a reinterpretation of the valence–arousal–dominance framework of meaning obtained from semantic differentials, we convert text into time series of power and danger scores, with time corresponding to cumulative word-time. Each time series is then decomposed using empirical mode decomposition into a sum of constituent oscillatory modes and a non-oscillatory trend. By comparing the decomposition of the original power and danger time series with those derived from shuffled text, we find that shorter books exhibit only a general trend, while longer books have fluctuations in addition to the general trend. These fluctuations typically have a period of a few thousand words regardless of the book length or library classification code but vary depending on the content and structure of the book. Our findings suggest that, in the ousiometric sense, longer books are not expanded versions of shorter books, but rather are more similar in structure to a concatenation of shorter texts. Further, they are consistent with editorial practices that require longer texts to be broken down into sections, such as chapters. Our method also provides a data-driven denoising approach that works for texts of various lengths, in contrast to the more traditional approach of using large window sizes that may inadvertently smooth out relevant information, especially for shorter texts. Altogether, these results open up avenues for future work in computational literary analysis, particularly the possibility of measuring a basic unit of narrative.
Challenges and opportunities to build quantitative self-confidence in biologists
Authors: Cuddington Kim , Abbott Karen C , Adler Frederick R , Aydeniz Mehmet , Dale Rene , Gross Louis J , Hastings Alan , Hobson Elizabeth A , Karatayev Vadim A , Killion Alexander , Madamanchi Aasakiran , Marraffini Michelle L , McCombs Audrey L , Samyono Widodo , Shiu Shin-Han , Watanabe Karen H , White Easton R
Published: April 2023

New graduate students in biology programs may lack the quantitative skills necessary for their research and professional careers. The acquisition of these skills may be impeded by teaching and mentoring experiences that decrease rather than increase students’ beliefs in their ability to learn and apply quantitative approaches. In this opinion piece, we argue that revising instructional experiences to ensure that both student confidence and quantitative skills are enhanced may improve both educational outcomes and professional success. A few studies suggest that explicitly addressing productive failure in an instructional setting and ensuring effective mentoring may be the most effective routes to simultaneously increasing both quantitative self-efficacy and quantitative skills. However, there is little work that specifically addresses graduate student needs, and more research is required to reach evidence-backed conclusions.
Leg Ulcer Pathway Acceleration (LUPA) study
Authors: Livingstone Vanessa , Johnson Oscar , Peta Sujith , Mengtsu Azeb , Quintana Belen , Moyna Cory , Hunter Caroline , Thulasidasan Narayanan , Black Stephen A
Published: April 2023

Background

Leg ulcers are common, costly, and significantly impair quality of life, but their management is variable and associated with considerable delays in healing. The aim of this study was to design an accelerated leg ulcer care pathway in a community and hospital setting to improve patient outcomes.

Methods

A new referral pathway was developed using a series of healthcare professional and patient interviews, focus groups, and stakeholder workshops. The referral pathway, investigation and treatment protocols were further informed by clinical guidelines to develop the Leg Ulcer Pathway Acceleration care pathway. The outcomes of a consecutive series of patients enrolled in the Leg Ulcer Pathway Acceleration care pathway were compared with the outcomes of patients from a historical leg ulcer cohort from the same community and hospital setting.

Results

A total of 110 eligible patients were enrolled and followed prospectively through the Leg Ulcer Pathway Acceleration care pathway. Their outcomes were compared with those of 183 patients with venous leg ulcers identified from existing hospital and community ulcer centres, and acting as the historical control group. The 110 patients in the Leg Ulcer Pathway Acceleration group consisted of 73 (66 per cent) men, had a mean(s.d.) age of 55.7(17.2) years, and had a median initial ulcer duration of 14.5 (i.q.r. 6–30) months. The 183 patients in the historical control group consisted of 119 (65 per cent) men, had a mean(s.d.) age of 56.4(17.2) years, and had a median initial ulcer duration of 13.5 (i.q.r. 6–47) months. Venous disease was treated in 67/110 (61 per cent) and deep venous disease was treated in 33/110 (30 per cent) of patients in the Leg Ulcer Pathway Acceleration cohort. In contrast, only 16/183 (8 per cent) of patients in the control group were treated for superficial venous insufficiency and 4/183 (2 per cent) of patients in the control group were treated for deep venous disease. Ulcer healing rates at 12 months were 80 and 20 per cent in the Leg Ulcer Pathway Acceleration group and the control group respectively (P < 0.001). Adjusted for baseline characteristics, the OR for a healed ulcer at 12 months was 21.21 (95 per cent c.i.. 11.32 to 42.46) (P < 0.001).

Conclusion

The introduction of an accelerated leg ulcer care pathway significantly improves ulcer healing when compared with historical controls.
How to critically appraise a systematic review: an aide for the reader and reviewer
Authors: Frewen John , de Brito Marianne , Pathak Anjali , Barlow Richard , Williams Hywel C
Published: April 2023

The number of published systematic reviews has soared rapidly in recent years. Sadly, the quality of most systematic reviews in dermatology is substandard. With the continued increase in exposure to systematic reviews, and their potential to influence clinical practice, we sought to describe a sequence of useful tips for the busy clinician reader to determine study quality and clinical utility. Important factors to consider when assessing systematic reviews include: determining the motivation to performing the study, establishing if the study protocol was prepublished, assessing quality of reporting using the PRISMA checklist, assessing study quality using the AMSTAR 2 critical appraisal checklist, assessing for evidence of spin, and summarizing the main strengths and limitations of the study to determine if it could change clinical practice. Having a set of heuristics to consider when reading systematic reviews serves to save time, enabling assessment of quality in a structured way, and come to a prompt conclusion of the merits of a review article in order to inform the care of dermatology patients.
Topical steroid withdrawal: an emerging clinical problem
Authors: Brookes Tenzin Sung-rab , Barlow Richard , Mohandas Padma , Bewley Anthony
Published: April 2023

Background

Topical steroid withdrawal (TSW) is a newly described disease characterized by erythema and burning following discontinuation of prolonged use of mid- to high-potency topical corticosteroids. No consensus diagnostic criterion exists. TSW is frequently interpreted as flaring of the underlying disorder or contact allergy to topical treatment.

Objectives

To better characterize TSW symptomatology, detail our experience with management and assess the proportion of patients who pursue nonconventional management.

Methods

A retrospective review of case notes collected from our multidisciplinary service between January 2019 and June 2021 was carried out to identify patients presenting with TSW.

Results

Nineteen cases of TSW were identified, 15 in females and 4 in males. The majority were < 35 years old. Eighteen had atopic dermatitis. The most frequently reported features were redness, skin pain (typically ‘burning’), skin sensitivity, excessive skin flaking, insomnia and severe itching. There was a high burden of anxiety and depression, with three patients expressing suicidal thoughts. Nonconventional treatments were pursued by approximately half the cohort, some of whom sought private consultation with international dermatologists. Improvements were noted in the context of open psychodermatology consultations with an earlier introduction of conventional management options.

Conclusions

Many patients report dismissal by dermatology healthcare professionals, often driving them to seek help from unregulated online sources, heightening the burden of mental, social and physical morbidity. Dermatology healthcare professionals need to be aware of TSW and offer support with shared decision-making when considering treatments.
Atopic dermatitis in skin of colour. Part 2: considerations in clinical presentation and treatment options
Authors: Gan Christian , Mahil Satveer , Pink Andrew , Rodrigues Michelle
Published: April 2023

Recent advances in atopic dermatitis (AD) present the condition as a heterogeneous disease of distinct endotypes across ethnic groups. AD in people with skin of colour may appear psoriasiform, lichenoid, scaly or papular, with a violaceous colour and there is a higher prevalence of post-inflammatory dyspigmentation compared with affected individuals of White ethnicity. These differences in clinical presentation may limit the use of AD assessment tools in people with skin of colour, leading to the potential for misdiagnosis and underestimation of severity, particularly in relation to assessment of erythema. Recent targeted therapies for AD have been studied in multiple ethnic groups; however, ethnicity-based subgroup analysis is often not performed. Further research is required to understand whether treatment responses or safety may differ among ethnic groups.
Kaposi sarcoma of the penis successfully treated with oral propranolol
Authors: Navarro-Bielsa Alba , Gil-Pallares Pedro , Diago-Irache Adrian , Martínez-Arnau Neus , Gracia-Cazaña Tamara , Gilaberte Yolanda
Published: April 2023

Kaposi sarcoma (KS) is a vascular tumour associated with human herpesvirus-8 infection, with a benign course in most cases. Local or minimally invasive treatments have been suggested for localized KS, including cryotherapy, electrosurgery or topical drugs, among others. However, relapse is frequent, and certain therapies might not be convenient in certain locations such as glans penis. Herein, we present a case of primary KS of the glans penis in an immunocompetent man successfully treated with oral propranolol, with total response.
Multimodal evidence for predictive coding in sentence oral reading
Authors: Zhao Bin , Zhang Gaoyan , Wang Longbiao , Dang Jianwu
Published: April 2023

Sentence oral reading requires not only a coordinated effort in the visual, articulatory, and cognitive processes but also supposes a top-down influence from linguistic knowledge onto the visual-motor behavior. Despite a gradual recognition of a predictive coding effect in this process, there is currently a lack of a comprehensive demonstration regarding the time-varying brain dynamics that underlines the oral reading strategy. To address this, our study used a multimodal approach, combining real-time recording of electroencephalography, eye movements, and speech, with a comprehensive examination of regional, inter-regional, sub-network, and whole-brain responses. Our study identified the top-down predictive effect with a phrase-grouping phenomenon in the fixation interval and eye-voice span. This effect was associated with the delta and theta band synchronization in the prefrontal, anterior temporal, and inferior frontal lobes. We also observed early activation of the cognitive control network and its recurrent interactions with the visual-motor networks structurally at the phrase rate. Finally, our study emphasizes the importance of cross-frequency coupling as a promising neural realization of hierarchical sentence structuring and calls for further investigation.
Diapause of the Western cherry fruit fly, Rhagoletis indifferens (Diptera: Tephritidae): metabolic rate and overwintering adaptations
Authors: Neven Lisa G
Published: April 2023

The Western cherry fruit fly, Rhagoletis indifferens (Curran), is a Tephritid fly in the Pacific Northwest and is known to infest native bitter cherry, Prunus emarginata (Douglas ex Hooker), which is distributed throughout the Cascade Mountain range. This species occupies temperate to alpine climates and exhibits overwintering adaptations of diapause and supercooling. Isothermal and differential scanning calorimetry were used to determine the effects of diapause chilling duration and post-chilling warm rearing on the metabolic rate and supercooling point of R. indifferens. Previous studies have included the effects of chilling duration on post-diapause development and emergence as well as on the levels of metabolic reserves. Metabolic rate of R. indifferens, was used to calculate the ability of this species to remain in diapause for more than 1 yr as well as predicting the potential effects of climate change on the future abundance and distribution. It was determined that R. indifferens could diapause for more than 1 yr based on the levels of metabolic reserves and metabolic rate.
EJE Prize 2023: genes on steroids—genomic control of hepatic metabolism by the glucocorticoid receptor
Authors: Quagliarini Fabiana , Makris Konstantinos , Friano Marika E , Uhlenhaut Nina Henriette
Published: April 2023

Glucocorticoids are essential hormones produced by the adrenal cortex with prominent circadian rhythmicity and in times of stress. Glucocorticoids maintain liver homeostasis through coordinated activities that control the major pathways of energy metabolism. Glucocorticoids activate the glucocorticoid receptor (GR), a nuclear hormone receptor that regulates the transcription of hundreds of genes in response to ligand. This review aims to provide a comprehensive overview of glucocorticoid receptor signaling impact on glucose, amino acid, and lipid metabolism in the liver. We integrate fundamental and current findings elucidating key GR-regulated pathways from a physiologic, biochemical, and molecular point-of-view. Here, we focus on the transcriptional regulation of well-characterized hepatic GR target genes, and on those GR co-factors that coordinate nutritional and hormonal signals.
Intra-household risk perceptions and climate change adaptation in sub-Saharan Africa
Authors: Ginbo Tsegaye , Hansson Helena
Published: April 2023

We examine the effects of spouses’ climate risk perceptions (CRPs), defined by their beliefs about unfavourable climatic events and associated damages, on climate change adaptation (CCA) and the observed gender gap in adaptation. Our analysis uses the intra-household data collected by independent interviews with 1,274 female and male spouses in Kenya, Uganda and Senegal. By addressing the CRP endogeneity issue using the exogenous weather shocks during data collection months as instruments, we find that a higher CRP of both female and male spouses increases their probability of adopting CCA strategies. We also find that a higher CRP of female spouses reduces the adaptation gap by increasing their relative adoption of soil and water conservation practices. Our results highlight the importance of understanding gender-differentiated behavioural and economic factors to design effective climate policy interventions.
Changes in self-rated physical and mental health and life satisfaction associated with opioid and potentially inappropriate opioid prescribing in primary care older adults
Authors: Pitrou Isabelle , D’Aiuto Carina , Lunghi Carlotta , Guénette Line , Berbiche Djamal , Bertrand Karine , Vasiliadis Helen-Maria
Published: April 2023

Objective

To examine changes in life satisfaction and physical and mental health associated with opioid and potentially inappropriate opioid prescribing (PIOP) among older adults.

Methods

Secondary data analysis from the Étude sur la Santé des Aînés (ESA)-Services study. The sample consisted of 945 older adults recruited in primary care with available health survey information linked to administrative medical record data. The exposure of interest was categorized as no prescription, opioid prescription, and PIOP, defined using the Beers criteria. Outcomes were self-rated physical health, mental health, and life satisfaction measured at baseline and at a 3-year follow-up. Generalized estimating equations were used to examine 3-year changes in outcomes as a function of opioid prescribing. Analyses were adjusted for covariates relating to health, psychosocial, and sociodemographic factors as well as duration/frequency of opioid prescribing. Analyses were conducted in the overall sample and in non-cancer patients.

Results

The sample had an average age of 73.1 years; the majority was Canadian-born (96.3%) while females made up over half (55.4%) the sample. Compared to not receiving an opioid prescription, PIOP was associated with a deterioration in physical health (ORadjusted = 0.65; 95%CI = 0.49, 0.86), but not mental health and life satisfaction. In non-cancer patients, PIOP was associated with poorer physical health (ORadjusted = 0.59; 95%CI = 0.40, 0.87) and opioid prescribing was marginally associated with improved life satisfaction (ORadjusted = 1.58; 95%CI = 0.96, 2.60).

Conclusion

PIOP was associated with a deterioration in physical health. Patient-centred chronic pain management and the effect on health and well-being require further study in older adults.
Updating forest road networks using single photon LiDAR in northern Forest environments
Authors: Morley Ilythia D , Coops Nicholas C , Roussel Jean-Romain , Achim Alexis , Dech Jeff , Meecham Dawson , McCartney Grant , Reid Douglas E B , McPherson Scott , Quist Lauren , McDonell Chris
Published: April 2023

Knowledge about the condition and location of forest roads is important for forest management. Coupling accurate forest road information with planning and conservation strategies supports forest resource management. In Canada, spatial data of forestry road networks are available provincially; however, they lack spatial accuracy, and up-to-date information on key attributes such as road width is missing. In this study, we apply a novel approach to update forest road networks and characterize road conditions in Ontario’s Boreal and Great Lakes—St. Lawrence (GLSL) Forest regions. We use airborne laser scanning (ALS), to facilitate the identification of forest roads across densely forested landscapes. We categorized roads into four classes based on driveable width, edge vegetation, as well as surface and edge degradation as derived from high-density Single Photon LiDAR (SPL) data. Using a novel road extraction method, we produced a road probability raster and map road centerlines. We validated road location and attribute information using Global Navigation Satellite System (GNSS) ground truth data in two Ontario forest management units, in the boreal forest and the GLSL. Road segments in some regions have been altered to account for land cover changes, such as flooding or fallen trees. In other situations, the road path may deviate from the planned layout of the road, which is not always followed in the field. Our results highlight inaccuracies in the existing road networks, with 30 per cent of ‘Full access’ roads and 29 per cent of ‘Partial access’ roads being undriveable by standard vehicles and 45 per cent of ‘Status unknown’ roads, which make up 48 per cent of the pre-existing network, being driveable by standard vehicles. Results show that the average positional accuracy of updated road centerlines is 0.4 m, and the average road width error is 2 m. The production of spatially accurate forest road networks and road attribute information is important for characterizing large road networks for which often minimal information is available.
A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae
Authors: Ngo Katrina , Gittens Tristen H , Gonzalez David I , Hatmaker E Anne , Plotkin Simcha , Engle Mason , Friedman Geofrey A , Goldin Melissa , Hoerr Remington E , Eichman Brandt F , Rokas Antonis , Benton Mary Lauren , Friedman Katherine L
Published: April 2023

Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition (dnTA) on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker's yeast, Saccharomyces cerevisiae, that act as hotspots of dnTA [termed Sites of Repair-associated Telomere Addition (SiRTAs)], but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.
Tissue-specific chromatin-binding patterns of Caenorhabditis elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression
Authors: de la Cruz-Ruiz Patricia , Rodríguez-Palero María Jesús , Askjaer Peter , Artal-Sanz Marta
Published: April 2023

Heterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs in Caenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them with heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with the methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements conversely with HPL-1, which exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a corepressive role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.
Cell state-dependent chromatin targeting in NUT carcinoma
Authors: Alekseyenko Artyom A , Zee Barry M , Dhoondia Zuzer , Kang Hyuckjoon , Makofske Jessica L , Kuroda Mitzi I
Published: April 2023

Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of 2 normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC, and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
Tsunami initial profile and maximum runup through earthquake source parameters
Authors: Sharghivand Naeimeh , Kânoğlu Utku
Published: April 2023

The 1992 September 1 Nicaragua tsunami manifested itself with an initial shoreline recession, resulting in a fundamental change in approach to define the initial waveform of tsunamis from a solitary wave to an N-wave. Here, we first fit N-wave profile to seafloor deformation for a large set of earthquake scenarios, assuming that the seafloor deformation resulting from an earthquake instantaneously transfers to the sea surface. Then, relating the N-wave parameters to the earthquake source parameters, we express the initial tsunami profile in terms of the earthquake source parameters. Further, we calculate the maximum tsunami runup through earthquake source parameters and test our results against field runup measurements for several events, observing good agreement.
ART and the forgotten siblings: a call for research
Authors: Somigliana Edgardo , Parazzini Fabio , Goisis Alice , Esposito Giovanna , Li Piani Letizia , Filippi Francesca , Vigano’ Paola
Published: April 2023

A broader definition of infertility is the incapacity to have the intended number of children. However, most literature on ART exclusively focuses on live birth as an outcome, rather than on the capacity to fully realize the reproductive wishes of the couples. This issue has probably received scant attention because the total fertility rate is below replacement levels in affluent countries, and one may simplistically assume that only a minority of couples may be interested in more than one child. This assumption, however, is unproven and presumably erroneous. Unfortunately, evidence on the rate of return in couples who conceived their first child with ART is scant and information on the intended number of children in infertile couples is lacking. In general, we plea for more research on this subject. The documentation of an intended number of children above two and a high return rate in infertile couples may lead to changes in clinical practice, such as the storage of oocytes or embryos prior to initiating embryo transfers. This could improve the chance of conceiving the second child when the couple comes back some years later. In addition, the identification of the determinants for non-return as well as those explaining the gap between the intended and the realized number of children may reveal specific barriers and possibly how to tackle them. However, at present, available evidence is insufficient to advocate any intervention. Thorough research is warranted.
Human organoid systems in modeling reproductive tissue development, function, and disease
Authors: Haider Sandra , Beristain Alexander G
Published: April 2023

Research focused on human reproductive biology has primarily relied upon clinical samples affording mainly descriptive studies with limited implementation of functional or mechanistic understanding. More importantly, restricted access to human embryonic material has necessitated the use of animals, primarily rats and mice, and short-term primary cell cultures derived from human patient material. While reproductive developmental processes are generally conserved across mammals, specific features unique to human reproduction have resulted in the development of human-based in vitro systems designed to retain or recapitulate key molecular and cellular processes important in humans. Of note, major advances in 3D epithelial stem cell-based systems modeling human reproductive organ development have been made. These cultures, broadly referred to as organoids, enable research aimed at understanding cellular hierarchies and processes controlling cellular differentiation and function. Moreover, organoids allow the pre-clinical testing of pharmacological substances, both from safety and efficacy standpoints, and hold large potential in driving aspects of personalized medicine that were previously not possible with traditional models. In this mini-review, we focus on summarizing the current state of regenerative organoid culture systems of the female and male reproductive tracts that model organ development, maintenance, and function. Specifically, we will introduce stem cell-based organoid models of the ovary/fallopian tube, endometrium, cervix, prostate gland, and testes. We will also describe organoid systems of the pre-implanting blastocyst and trophoblast, as the blastocyst and its extraembryonic trophectoderm are central to fetal, maternal, and overall pregnancy health. We describe the foundational studies leading to their development and outline the utility as well as specific limitations that are unique and common to many of these in vitro platforms.
Biogeographic provinces and genomically delineated stocks are congruent in snapper (Chrysophrys auratus) from southeastern Australia
Authors: Bertram A , Bell J , Brauer C J , Fowler A , Hamer P , Sandoval-Castillo J , Stewart J , Wellenreuther M , Beheregaray L B
Published: April 2023

Marine species often exhibit genetic discontinuities concordant with biogeographic boundaries, frequently occurring due to changes in ocean circulation, bathymetry, coastline topography, and temperature. Here, we used 10 916 single nucleotide polymorphisms (SNPs) to assess the concordance between population genomic differentiation and coastal biogeography in the fishery-important snapper (Chrysophrys auratus) across southeastern Australia. Additionally, we investigated whether spatial scales of assessment and management of snapper align with evidence from population genomics. We detected genomic structure concordant with the region's three biogeographic provinces across snapper from 11 localities (n = 488) between the west coast of South Australia and the south coast of New South Wales. We also detected fine-scale genetic structuring relating to spatial variation in spawning and recruitment dynamics, as well as temporal stability in the genomic signal associated with two important spawning areas. The current management boundaries in the region coincided with either the genetic breaks at bioregional boundaries or with local-scale variation. Our study highlights the value of population genomic surveys in species with high dispersal potential for uncovering stock boundaries and demographic variation related to spawning and recruitment. It also illustrates the importance of marine biogeography in shaping population structure in commercial species with high dispersal potential.
Effect of SCD probiotics supplemented with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota composition
Authors: Ceylani Taha
Published: April 2023

Aims

In this study, the effects of SCD Probiotics with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota (GM) composition were investigated.

Methods and results

Twenty-four-month-old Sprague–Dawley rats were given 300 mg/kg of TUDCA along with 3 mL (1 × 108 CFU) of SCD probiotics for 7 days. The bacterial profile was determined by the metagenome applied to the cecum content. TUDCA, SCD probiotics, and TUDCA with SCD probiotics designed GM differently. TUDCA and SCD probiotics have the most different dominant species profiles.

Conclusions

SCD probiotics and TUDCA have their own unique effects on the species found in GM, and when they are evaluated together, the species found in GM are restructured differently.
Multiphasic mixed growth models for turkeys
Authors: van der Klein Sasha A S , Willems Owen W , Zuidhof Martin J
Published: April 2023

Growth models are important for optimization of feed formulation and breeding programs in turkeys. The objectives of this study were 1) to compare sex and line differences in turkeys in parameter estimates of mono- and di-phasic Gompertz growth models, and 2) to evaluate mono and diphasic mixed Gompertz growth models to determine the variation in parameter estimates in a group of female line turkey toms. A total of 1,056 manually recorded weekly average body weight (BW) observations from male and female turkeys of a male and female line from weeks 1 to 20 were used for objective 1. Daily median values of automatically collected individual BW of female line turkey toms were used for objective 2 and random components associated with individual subject animals related to mature weight and/or timing of maximum gain during each phase were introduced in the Gompertz model. Growth curve shapes were different between male line toms, male line hens, female line toms, and female line hens (P < 0.001). However, inflection points were similar between male and female line toms and between male and female line hens (14.06 vs. 13.72 wk and 11.22 and 10.71 wk, respectively), while mature BW differed between lines by 6.49 and 3.81 kg for toms and hens, respectively. The normalized growth rate constant (growth rate constant corrected for mature weight) was around the same magnitude between male and female line toms (0.0031 vs. 0.0038, respectively), but slightly lower in male line hens compared to female line hens (0.0072 vs. 0.0091, respectively). Diphasic Gompertz models described growth better in all line × sex combinations compared to the monophasic models (P < 0.001) and mixed diphasic Gompertz models showed improved fit over mixed monophasic Gompertz models. The correlation structure of the random components identified that individuals with a higher mature weight had a later inflection point and lower growth rate coefficients. These results provide tools for improved breeding practices and a structure to evaluate the effects of dietary or environmental factors on growth trajectories.
Standardized ileal digestibility of amino acids in cottonseed meal fed to pregnant and non-pregnant sows
Authors: Zhuo Yong , Zou Xiangyang , Wang Ya , Jiang Xuemei , Sun Mengmeng , Xu Shengyu , Lin Yan , Hua Lun , Li Jian , Feng Bin , Fang Zhengfeng , Che Lianqiang , Wu De
Published: April 2023

This study determined the apparent ileal digestibility (AID) and standard ileal digestibility (SID) of crude protein (CP) and amino acids (AA) of six cottonseed meal (CSM) samples in pregnant and non-pregnant sows. Two CSM samples were processed by expelling with a CP level of 40.67% (ECSM41) and 44.64% (ECSM45), and four samples were processed by solvent-extracted which contained graded CP levels of 45% (SECSM45), 51.16% (SECSM51), 56.44% (SECSM56), and 59.63% (SECSM60). Landrace ×Yorkshire third parity sows, 7 at gestation and 14 non-pregnant, were fitted with T-cannula in the distal ileum. Pregnant sows were allotted to a 7 × 6 Latin square design with a cornstarch-based nitrogen-free (NF) diet and the six CSM diets, and non-pregnant sows were allotted to a replicated 7 × 3 Latin square design with seven diets and three periods, respectively, resulting in a total of six replicates per treatment. All experimental sows were fed 3.0 kg/d of the experimental diets. The AID of CP in ECSM41 (75.58%) was lower than in SECSM51 (80.42%), SECSM56 (80.50%), and SECSM60 (82.44%) diets for pregnant sows (P < 0.05). The AID of CP in ECSM41 (77.88%) was significantly lower than in SECSM60 (81.87%) diets for non-pregnant sows (P < 0.05). The physiological phase did not affect the AID of CP (P > 0.05). The SID of CP was affected by diets for both pregnant (P < 0.01) and non-pregnant sows (P = 0.06). The physiological phase also affected the SID of CP (P < 0.01). The AID of histidine, leucine, methionine, threonine, and tryptophan significantly differed between different CSM samples in both pregnant (P < 0.05) and non-pregnant sows (P < 0.05). The AID of dispensable AA aspartic acid, cysteine, glutamic acid, serine, and tyrosine differed between different CSM samples of both pregnant (P < 0.05) and non-pregnant sows (P < 0.05). For pregnant sows, the indispensable AA cysteine, glycine, proline, and tyrosine had significantly different SID between different groups (P < 0.05). For non-pregnant sows, the SID of arginine, lysine, methionine, threonine, aspartic acid, cysteine, and serine had different values among different diets (P < 0.05). In conclusion, the current study presented that the ileal AA digestibility of CSM fed to pregnant and non-pregnant sows increased with the decreased of fiber content, and the current findings can contribute to a precise formulation of diets for sows using CSM.
Nutritional value of high protein ingredients fed to growing pigs in comparison to commonly used protein sources in swine diets
Authors: Garavito-Duarte Yesid R , Levesque Crystal L , Herrick Kevin , Perez-Palencia Jorge Y
Published: April 2023

Two experiments were conducted to test the hypothesis that two high protein dried distillers with solubles and yeast mass added (GDDY) products fed to growing pigs had comparable amino acid (AA) digestibility and metabolizable energy (ME) to feeds commonly used in swine diets. In experiment 1, seven barrows with an initial body weight (BW) of 25 ± 0.8 kg were fitted with a simple T-cannula at the distal ileum to allow for digesta collection. Experimental diets were N-free diets and six cornstarch-based diets containing six ingredients as the sole source of AA: spray dried GDDY, ring dried GDDY, corn distillers dried grains with solubles (DDGS), soybean meal (SBM), enzymatically treated soybean meal (ESBM), and fish meal (FM) provided at 4% of BW. The experiment was conducted as a 7 × 7 Latin square design with seven collection periods of 7 d (5 d adaptation and 2 d ileal digesta collection). In experiment 2, a total of 28 barrows (28.8 ± 1.4 kg BW) were used in a two-period switch-back design with seven diets and four replicate pigs in each period (n = 8 reps per diet). Experimental diets were a corn-based basal diet and six corn-based diets containing spray dried GDDY, ring dried GDDY, DDGS, SBM, ESBM, and FM. Fecal and urine samples were collected using the marker-to-marker approach for 5 d after 7 d of adaptation to determine ME concentration. Overall, standardized ileal digestibility (SID) values were within the mean ± SD of NRC (2012) values for all ingredients evaluated. The SID of AA was greater (P < 0.05) in ESBM than the other protein feedstuffs (90.09% vs. 78.71%–81.51%). There were no significant differences in SID of AA (P > 0.05) in SBM, FM, spray dried GDDY, and ring dried GDDY (81.49%, 78.71%, 81.52%, and 79.20%). With respect to the most common first limiting AA for swine, the SID of Lys was greater (P < 0.05) in spray dried GDDY than ring dried GDDY and DDGS (83.56% vs. 77.33% and 68.53%, respectively). There were no significant differences (P > 0.05) for ME in corn (3,313 kcal/kg), ESBM (3,323 kcal/kg), and FM (3,454 kcal/kg) when compared with spray dried GDDY and ring dried GDDY (3,995 and 3,442 kcal/kg respectively). However, spray dried GDDY had greater DE and ME when compared to SBM. Collectively, this study demonstrates that GDDY products have an AA profile and digestibility comparable to SBM; ME in GDDY products is not different from corn. Therefore, GDDY has the potential as a feed ingredient for pigs, which could provide an alternative source of protein and energy in swine diets.
Reflections on a career as graduate mentor—from baby steps at Wisconsin to today
Authors: Hansen Peter J
Published: April 2023

Graduate education is an important aspect of the life of most academic scientists and a serious responsibility because it comes with the obligation to help students achieve their career and life goals. It can also be very fulfilling for the graduate mentor in terms of personal satisfaction and advancement of the research program. Learning to be a good major professor is an active process that depends on developing a formal framework of education and modifying that framework for each student based on past experiences and experimentation, advice from colleagues, and the individual personality of the student. Perhaps most important is for the graduate mentor to buy into the success and well-being of the student. Among the characteristics that a major professor could seek to instill in his or her students are critical and independent thinking, self-confidence, a thick skin, teamwork, laboratory skills and understanding, and the ability for hard work. Work to make science joyful by celebrating accomplishments, creating a fun environment in the lab, and stressing the societal value of science as compared to personal rewards or ambition.
Impacts of ZnO and multi-walled carbon nanotubes (MWCNTs) on biological parameters of the Oriental river prawn Macrobrachium nipponense De Haan, 1849 (Decapoda: Caridea: Palaemonidae)
Authors: Rezaei Tavabe Kamran , Samadi Kuchaksaraei Bahareh , Javanmardi Sina
Published: April 2023

Nanomaterials (NMs) mainly settle on bottom sediments and accumulate in the benthos of aquatic communities. Decapod crustaceans, being deposit-omnivorous feeders, are appropriate biological models to assay the biological effects of NMs. The present study evaluated the effects of ZnO and multi-walled carbon nanotubes (MWCNTs) NMs separately and in combination on the activities of antioxidant enzymes on crustacean hyperglycemic hormone (CHH), hematology, reproductive performance, and hepatopancreas lesions the Oriental river prawn, Macrobrachium nipponense De Haan, 1849 [De Haan, 1833–1850]. We essayed concentrations of ZnO (0, 1, 10, 30, 50 mg l–1) and MWCNTs (0, 5, 10, 15, 20 mg l–1) and two higher concentrations of the NMs were compared in combined treatments. Both NMs showed dose-dependent effects on reproductive parameters of M. nipponense, especially the fertilization rate of eggs. Inter-molt and inter-spawn periods were postponed and reproduction stopped in 50 ppm ZnO and 15 and 20 ppm MWCNTs treatments. Our findings showed that the release of crustacean hyperglycemic hormone (CHH) and superoxide dismutase (SOD) enzyme activity are directly related to the NMs levels independently as well as in combination. NMs did not show any effect on the activities of alanine transaminase (ALT) and aspartate transaminase (AST) enzymes in muscle tissue independently, but the combined effects of the activities of these enzymes were significant. NMs caused hepatocyte enlargement, melanization, apoptosis, and necrosis damages in the hepatopancreas of prawns. The findings showed that ZnO and MWCNTs NMs have strong adverse biological effects on M. nipponense, and that this species is an appropriate bio-indicator and bio-monitor organism for NMs contaminations in the freshwater aquatic environments.