bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating DNA cross-contamination risk using different tissue sampling procedures on board fishing and research vessels
Authors: Anderson Giulia , Macdonald Jed I , Potts Joanne , Feutry Pierre , Grewe Peter M , Boutigny Marion , Davies Campbell R , Muir Jeff A , Roupsard Francois , Sanchez Caroline , Nicol Simon J 
Published: February 2023

Abstract
Sample cross-contamination remains a pervasive issue in genetics and genomics. With growing reliance on molecular methods for managing marine resources, the need to ensure the integrity of tissue samples that underpin these methods has never been more pressing. We conducted an experiment on wild-caught bigeye tuna (Thunnus obesus) to assess cross-contamination risk under seven at-sea and laboratory-based tissue sampling treatments. The six at-sea treatments (T1–T6) differ in sampling equipment, cleaning, and storage procedures. Combining observed heterozygosity (Ho) and relatedness coefficients (r) to flag cross-contamination, treatments T2–T6 proved effective at mitigating contamination risk. Each exhibited significantly smaller mean Ho and less Ho variability compared with intentionally contaminated samples in the T1 treatment. In T2-T6, no samples flagged as contaminated based on Ho outlier thresholds and elevated r were traced to the point of sampling at sea. Laboratory-based subsampling of T1 tissue (T7) also led to significantly smaller, less variable Ho values compared to T1, suggesting that recovery of samples contaminated onboard, or those of unknown provenance, is possible. We show that simple adjustments to current tissue sampling protocols dramatically reduce cross-contamination risk for downstream genetic analyses on tunas and potentially on other species and fisheries.
Effects of maternal methionine supplementation on the response of Japanese quail (Coturnix coturnix japonica) chicks to heat stress
Authors: Santana Thaís Pacheco , Gasparino Eliane , de Souza Khatlab Angélica , Pereira Angela Maria Favaro Elias , Barbosa Leandro Teixeira , Fernandes Roberta Pereira Miranda , Lamont Susan J , Del Vesco Ana Paula 
Published: February 2023

AbstractThis study investigated the hypothesis that methionine supplementation of Japanese quail (Coturnix coturnix japonica) hens can reduce the effects of oxidative stress and improve the performance of the offspring exposed to heat stress during growth. For that, the quail hens were fed with three diets related to the methionine supplementation: methionine-deficient diet (Md); diet supplemented with the recommended methionine level (Met1); and diet supplemented with methionine above the recommended level (Met2). Their chicks were identified, weighed, and housed according to the maternal diet group from 1 to 14 d of age. On 15 d of age, chicks were weighed and divided into two groups: thermoneutral ambient (constant temperature of 23 °C) and intermittent heat stress ambient (daily exposure to 34 °C for 6 h). Methionine-supplemented (Met1 and Met2) hens had higher egg production, better feed conversion ratio, higher hatchability of total and fertile eggs, and offspring with higher body weight. Supplemented (Met1 and Met2) hens showed greater expression of glutathione synthase (GSS) and methionine sulfoxide reductase A (MSRA) genes, greater total antioxidant capacity, and lower lipid peroxidation in the liver. The offspring of hens fed the Met2 diet had lower death rate (1 to 14 d), higher weight on 15 d of age, weight gain, and better feed conversion ratio from 1 to 14 d of age. Among chicks reared under heat stress, the progeny of methionine-supplemented hens had higher weight on 35 d, weight gain, expression of GSS, MSRA, and thermal shock protein 70 (HSP70) genes, and total antioxidant capacity in the liver, as well as lower heterophil/lymphocyte ratio. Positive correlations between expression of glutathione peroxidase 7 (GPX7) and MSRA genes in hens and offspring were observed. Our results show that maternal methionine supplementation contributes to offspring development and performance in early stages and that, under conditions of heat stress during growth, chicks from methionine-supplemented hens respond better to hot environmental conditions than chicks from nonsupplemented hens. Supplementation of quail hens diets with methionine promoted activation of different metabolic pathways in offspring subjected to stress conditions.
Inferring causal structures of gut microbiota diversity and feed efficiency traits in poultry using Bayesian learning and genomic structural equation models
Authors: Haas Valentin , Rodehutscord Markus , Camarinha-Silva Amélia , Bennewitz Jörn 
Published: February 2023

AbstractFeed and phosphorus (P) efficiency are of increasing importance in poultry breeding. It has been shown recently that these efficiency traits are influenced by the gut microbiota composition of the birds. The efficiency traits and the gut microbiota composition are partly under control of the host genome. Thus, the gut microbiota composition can be seen as a mediator trait between the host genome and the efficiency traits. The present study used data from 749 individuals of a Japanese quail F2 cross. The birds were genotyped for 4k single-nucleotide polymorphism (SNP) and trait recorded for P utilization (PU) and P retention (PR), body weight gain (BWG), and feed per gain ratio (F:G). The gut microbiota composition was characterized by targeted amplicon sequencing. The alpha diversity was calculated as the Pielou’s evenness index (Jʹ). A stable Bayesian network was established using a Hill-Climbing learning algorithm. Pielou’s evenness index was placed as the most upstream trait and BWG as the most downstream trait, with direct and indirect links via PR, PU, and F:G. The direct and indirect effects between Jʹ, PU, and PR were quantified with structural equation models (SEM), which revealed a causal link from Jʹ to PU and from PU to PR. Quantitative trait loci (QTL) linkage mapping revealed three genome-wide significant QTL regions for these traits with in total 49 trait-associated SNP within the QTL regions. SEM association mapping separated the total SNP effect for a trait into a direct effect and indirect effects mediated by upstream traits. Although the indirect effects were in general small, they contributed to the total SNP effect in some cases. This enabled us to detect some shared genetic effects. The method applied allows for the detection of shared genetic architecture of quantitative traits and microbiota compositions.
A comparison of the baryonic Tully–Fisher relation in MaNGA and IllustrisTNG
Authors: Goddy Julian S , Stark David V , Masters Karen L , Bundy Kevin , Drory Niv , Law David R 
Published: February 2023

ABSTRACT
We compare an observed baryonic Tully–Fisher relation (BTFR) from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) and HI-MaNGA surveys to a simulated BTFR from the cosmological magnetohydrodynamical simulation, IllustrisTNG. To do so, we calibrate the BTFR of the local universe using 377 galaxies from the MaNGA and HI-MaNGA surveys, and perform mock 21 cm observations of matching galaxies from IllustrisTNG. The mock observations are used to ensure that the comparison with the observed galaxies is fair since it has identical measurement algorithms, observational limitations, biases, and uncertainties. For comparison, we also calculate the BTFR for the simulation without mock observations and demonstrate how mock observations are necessary to fairly and consistently compare between observational and theoretical data. We report a MaNGA BTFR of log$_{10} (M_{ \rm Bary}/M_\odot)= (2.97 \pm 0.18)$ log$_{10} V_{ \rm Rot} + (4.04 \pm 0.41)\, \log _{10}{M_{\odot }}$ and an IllustrisTNG BTFR of log$_{10} (M_{ \rm Bary}/M_\odot) = (2.94 \pm 0.23$) log$_{10} V_{ \rm Rot} + (4.15 \pm 0.44)\, \log _{10}{M_{\odot }}$. Thus, MaNGA and IllustrisTNG produce BTFRs that agree within uncertainties, demonstrating that IllustrisTNG has created a galaxy population that obeys the observed relationship between mass and rotation velocity in the observed universe.
Testis-specific actin-like 7A (ACTL7A) is an indispensable protein for subacrosomal-associated F-actin formation, acrosomal anchoring, and male fertility
Authors: Ferrer P , Upadhyay S , Ikawa M , Clement T M 
Published: February 2023

AbstractFormation of the acrosome during spermiogenesis is an essential process for creating fertilization-competent sperm. Of the numerous aspects required for acrosome biogenesis, adherence of the acrosomal outer membrane to the nuclear surface is mediated by the subacrosomal perinuclear theca. However, the cellular dynamics and congruent functions pertaining to these acrosomal anchoring factors are not well understood despite many of them being implicated as potential causes for human male infertility. Actin-like 7A (ACTL7A) is one such factor for which deleterious polymorphisms have recently been shown to cause human male infertility. It is thought that acrosomal attachment is coordinated by cytoskeletal associations between the acrosome and nucleus via the acroplaxome. To further illuminate the mechanistic underpinnings of ACTL7A for essential acrosome associations, in this study, we investigated its dynamic localization in the developing germline, molecular associations with other cytoskeletal components, and the cellular consequences of ablation. Our intracellular localization data show ACTL7A to be dynamically present within the nucleus and subacrosomal space and later associated with postacrosomal regions of developing spermatids. Through the generation of an Actl7a knock-out mouse model, we consistently observed disruption of acrosomal biogenesis with abnormal migration of the acrosomal granule and peeling acrosomes during spermatid elongation. Significantly, we found a complete loss of subacrosomal filamentous actin (F-actin) structures in knock-out spermatids suggesting a regulatory role for subacrosomal F-actin. Considering our reported data together with existing literature, we propose a mechanistic model explaining the essential role of ACTL7A for acroplaxome-associated F-actin, acrosomal attachment integrity, and male fertility.
MALDI mass spectrometry imaging shows a gradual change in the proteome landscape during mouse ovarian folliculogenesis
Authors: Fiorentino Giulia , Smith Andrew , Nicora Giovanna , Bellazzi Riccardo , Magni Fulvio , Garagna Silvia , Zuccotti Maurizio 
Published: February 2023

AbstractOur knowledge regarding the role proteins play in the mutual relationship among oocytes, surrounding follicle cells, stroma, and the vascular network inside the ovary is still poor and obtaining insights into this context would significantly aid our understanding of folliculogenesis. Here, we describe a spatial proteomics approach to characterize the proteome of individual follicles at different growth stages in a whole prepubertal 25-day-old mouse ovary. A total of 401 proteins were identified by nano-scale liquid chromatography–electrospray ionization–tandem mass spectrometry (nLC-ESI-MS/MS), 69 with a known function in ovary biology, as demonstrated by earlier proteomics studies. Enrichment analysis highlighted significant KEGG and Reactome pathways, with apoptosis, developmental biology, PI3K-Akt, epigenetic regulation of gene expression, and extracellular matrix organization being well represented. Then, correlating these data with the spatial information provided by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) on 276 follicles enabled the protein profiles of single follicle types to be mapped within their native context, highlighting 94 proteins that were detected throughout the secondary to the pre-ovulatory transition. Statistical analyses identified a group of 37 proteins that showed a gradual quantitative change during follicle differentiation, comprising 10 with a known role in follicle growth (NUMA1, TPM2), oocyte germinal vesicle-to-metaphase II transition (SFPQ, ACTBL, MARCS, NUCL), ovulation (GELS, CO1A2), and preimplantation development (TIF1B, KHDC3). The proteome landscape identified includes molecules of known function in the ovary, but also those whose specific role is emerging. Altogether, this work demonstrates the utility of performing spatial proteomics in the context of the ovary and offers sound bases for more in-depth investigations that aim to further unravel its spatial proteome.
Materiality of Sonic Imagery: On Analysis of Contemporary Chinese Compositions
Authors: Rao Nancy Yunhwa 
Published: February 2023

AbstractThis essay explores concepts related to the materiality of sound and considers the aesthetics of contemporary Chinese music (and of other Asian heritages) through this lens. In compositions such as Guo Wenjing’s chamber work She Huo, musical expression is prominently shaped by sonic ideas rooted in socio-historical and cultural contexts, and associated with materials of substance and matter. Analysis of such works requires reconceptualizing the modes of analysis and listening practice. Through a focus on materiality, I argue, we gain insight about the music in ways unattainable from established, ingrained modes of musical analysis. Examples explored include the significance of onomatopoeic words for the notation of percussion music in Peking opera; the concept of sawari in Japanese instrumental music, as discussed by Tōru Takemitsu; and Isang Yun’s notion of Hauptton. Music’s materiality comprises many dimensions, the consideration of which is of great importance as we seek to broaden the canon.
Identification of circulating microRNA patterns in patients in psoriasis and psoriatic arthritis
Authors: Haschka Judith , Simon David , Bayat Sara , Messner Zora , Kampylafka Eleni , Fagni Filippo , Skalicky Susanna , Hackl Matthias , Resch Heinrich , Zwerina Jochen , Kleyer Arnd , Cavallaro Alexander , Sticherling Michael , Schett Goerg , Kocijan Roland , Rech Juergen 
Published: February 2023

Abstract

Objective
miRNAs are small non-coding RNAs that control gene expression. Specific intra- and extracellular miRNA signatures have been identified in various diseases. Whether certain miRNA signatures are associated with psoriasis (PsO) and PsA is currently unknown. We aimed to search for circulating miRNA signatures associated with PsO and PsA patients.

Methods
Expression of miRNAs was analysed by reverse transcription quantitative real-time PCR (RT-qPCR) in the serum of PsA, PsO patients and healthy controls. Demographic and disease-specific characteristics and imaging data from hand MRI were recorded. In the discovery phase, 192 miRNA assays were analysed in 48 samples (PsA, PsO, controls: each N = 16). For validation, 17 selected miRNAs were measured in the total population.

Results
A total of 141 patients and controls were analysed (51 PsA, 40 PsO, 50 controls). In the discovery phase 51 miRNAs in PsO and 64 miRNAs in PsA were down- or upregulated compared with controls, with 33 miRNAs being changed in both (adj. P &lt; 0.05). The 17 top candidates from discovery were assessed in the validation phase, 9 of them discriminated PsA and PsO from controls [area under the curve (AUC) ≥0.70, all P &lt; 0.05]. Four miRNAs (miR-19b-3p, miR-21-5p, miR-92a-3p and let-7b-5p) were significantly differently regulated between PsO and PsA. A combination of these miRNAs increased the AUC to 0.92 in multivariate regression model to discriminate PsO and PsA.

Conclusion
miRNA signatures in PsA and PsO patients differ from controls. Nine miRNAs were differentially regulated in PsA and PsO patients, five of them previously reported to be involved in bone and cartilage metabolism, indicating an intimate association of psoriatic inflammation and bone/cartilage changes.
Diagnostic Delays in Sepsis: Lessons Learned From a Retrospective Study of Canadian Medico-Legal Claims
Authors: Neilson Heather K. , Fortier Jacqueline H. , Finestone PJ. , Ogilby Catherine M. , Liu Richard , Bridges Eileen J. , Garber Gary E. 
Published: February 2023

IMPORTANCE:
Although rapid treatment improves outcomes for patients presenting with sepsis, early detection can be difficult, especially in otherwise healthy adults.

OBJECTIVES:
Using medico-legal data, we aimed to identify areas of focus to assist with early recognition of sepsis.

DESIGN, SETTING, AND PARTICIPANTS:
Retrospective descriptive design. We analyzed closed medico-legal cases involving physicians from a national database repository at the Canadian Medical Protective Association. The study included cases closed between 2011 and 2020 that had documented peer expert criticism of a diagnostic issue related to sepsis or relevant infections.

MAIN OUTCOMES AND MEASURES:
We used univariate statistics to describe patients and physicians and applied published frameworks to classify contributing factors (provider, team, system) and diagnostic pitfalls based on peer expert criticisms.

RESULTS:
Of 162 involved patients, the median age was 53 years (interquartile range [IQR], 34–66 yr) and mortality was 49%. Of 218 implicated physicians, 169 (78%) were from family medicine, emergency medicine, or surgical specialties. Eighty patients (49%) made multiple visits to outpatient care leading up to sepsis recognition/hospitalization (median = two visits; IQR, 2–4). Almost 40% of patients were admitted to the ICU. Deficient assessments, such as failing to consider sepsis or not reassessing the patient prior to discharge, contributed to the majority of cases (81%).

CONCLUSIONS AND RELEVANCE:
Sepsis continues to be a challenging diagnosis for clinicians. Multiple visits to outpatient care may be an early warning sign requiring vigilance in the patient assessment.
Impact of Extended Adjuvant Temozolamide Beyond 6 Months in the Management of Glioblastoma Patients
Authors: Elsaka Rasha , Kitagwa Joan Minyika , Refaat Tamer , Mahmoud Amr A. , Shaikh Hamza , Meheissen Mohamed A.M. , Elsaid Amr Abdelaziz 
Published: February 2023

Objectives:
Our study aimed to assess the benefit of prolonging adjuvant temozolomide (TMZ) therapy beyond 6 cycles in glioblastoma multiform patients.

Materials and Methods:
The medical records of 329 patients in 2 cancer centers in Egypt were reviewed from January 2008 to December 2018 who were diagnosed with diffuse gliomas. Data were collected on patient demographics, presenting complaints, tumor size, treatment modalities (extent of surgery, radiotherapy dose and technique, concomitant TMZ, and the number of adjuvant TMZ cycles), and reported adverse events.

Results:
In the studied cohort, 105 patients were treated with adjuvant TMZ, 33 patients received <6 cycles (TMZL), 41 patients received the standard 6 cycles (TMZS), and 31 patients received >6 cycles (TMZE). Our results showed the median overall survival in the TMZL arm was 8.47 months compared with 15.83 months in the TMZS arm and 27.33 months in the TMZE arm (P < 0.001). Furthermore, a median progression-free survival of 6.35 months was reported in the TMZL group versus, 12.7 and 22.90 months in (TMZS) and (TMZE) groups, respectively(P < 0.001). In the multivariate analysis, the extended adjuvant TMZ with a hazard ratio of 3.106 (95% CI: 2.43-14.46; P < 0.001) was statistically significantly associated with a better outcome.

Conclusions:
Extended adjuvant TMZ therapy beyond 6 cycles may significantly improve the progression-free survival and overall survival in patients with glioblastoma multiform.
Validation of the Chinese Versions of the Carolina Human Papillomavirus (HPV) Immunization Attitudes and Beliefs Scale and HPV and Vaccination Knowledge Scales
Authors: Lo Suzanne Hoi Shan , Chau Janita Pak Chun , Butt Laveeza , Choi Kai Chow 
Published: February 2023

Background:
It is vital to address parents’ human papillomavirus (HPV) knowledge, attitudes, and beliefs to reduce vaccine hesitancy and increase adolescent HPV vaccination rates.

Objective:
To validate the Chinese versions of the Carolina HPV Immunization Attitudes and Beliefs Scale (CHIAS), HPV Knowledge scale (GK23), and Vaccination Knowledge Scale (VK9) and to investigate parents’ current perspectives on HPV vaccination.

Methods:
Convenience sampling was used to recruit 195 Chinese parents. The CHIAS, GK23, and VK9 were translated into Chinese and content validity was established. The structural validity of the CHIAS was assessed by confirmatory factor analysis, and internal consistency of the scales was assessed by Cronbach’s alpha (α) for the CHIAS-C and by Kuder-Richardson 20 for the GK23 and VK9.

Results:
Internal consistency of all 3 scales was acceptable, with Cronbach’s α for the 4 domains of the CHIAS-C ranging from 0.68 to 0.85, and Kuder-Richardson 20 score of 0.88 and 0.75 for the GK23 and VK9, respectively. The 4-factor structure of the CHIAS-C was found to be a good fit to the data and its structural validity was established.

Conclusions:
The Chinese versions of the CHIAS, GK23, and VK9 are valid and reliable instruments to evaluate attitudes, beliefs, and knowledge of HPV and HPV vaccination among Chinese-speaking parents.

Implications for Practice:
These instruments may facilitate investigation of parents’ views toward HPV vaccination and inform the design of targeted interventions to address vaccine hesitancy.

What Is Foundational:
Parents’ knowledge and attitudes are determining factors in vaccination decision-making and should be considered in HPV vaccine promotion efforts.
Phenol–Croton Oil Chemical Peeling Induces Durable Improvement of Constitutional Periorbital Dark Circles
Authors: Soon Seaver L. , Wambier Carlos G. , Rullan Peter R. , Sterling J. Bart , Brody Harold J. , Lee Kachiu C. , Kreyden Oliver P. , Landau Marina 
Published: February 2023

BACKGROUND
Constitutional periorbital dark circles (PDC) are common in skin of color and represent a therapeutic challenge.

OBJECTIVE
To summarize the experience of the International Peeling Society on the safety and effectiveness of deep chemical peeling in the treatment of constitutional PDC.

MATERIALS AND METHODS
Multi-institutional, retrospective case series (1990–2020) of constitutional PDC treated by deep chemical peeling. Descriptive analysis by age, sex, Fitzpatrick phototype, phenol–croton formula, degree and durability of improvement, and complications.

RESULTS
Fifty-five phenol–croton oil peels were performed in 52 patients: 3 patients received a second peel for periorbital rhytids 72 to 84 months after the first peel. 92% (48/52) of patients were women; the median age was 46 years (range, 23–68 years). 89% (46/52) of patients were Fitzpatrick III-IV. Most common formula included phenol 60% to 65% and croton oil 0.6% to 0.7%. 89% (49/55) of peels demonstrated >50% clinical improvement. The median duration of improvement was 24 months (range, 1.5–168 months), and 69% (36/52) of patients demonstrated ongoing improvement at the last follow-up. 4% (2/55) of peels exhibited complications of persistent erythema that resolved without scarring.

CONCLUSION
Based on its safety and effectiveness, deep chemical peels are a treatment of choice for constitutional PDC.