bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural equation models to infer relationships between energy-related blood metabolites and milk daily energy output in Holstein cows
Authors: Pegolo Sara , Ramirez Mauricio Marco Aurelio , Mancin Enrico , Giannuzzi Diana , Bisutti Vittoria , Mota Lucio Flavio Macedo , Ajmone Marsan Paolo , Trevisi Erminio , Cecchinato Alessio 
Published: September 2024

Abstract
During lactation, high-yielding cows experience metabolic disturbances due to milk production. Metabolic monitoring offers valuable insights into how cows manage these challenges throughout the lactation period, making it a topic of considerable interest to breeders. In this study, we used Bayesian networks to uncover potential dependencies among various energy-related blood metabolites, i.e., glucose, urea, beta-hydroxybutyrate (BHB), non-esterified fatty acids (NEFA), cholesterol (CHOL), and daily milk energy output (dMEO) in 1,254 Holstein cows. The inferred causal structure was then incorporated into structural equation models (SEM) to estimate heritabilities and additive genetic correlations among these phenotypes using both pedigree and genotypes from a 100k chip. Dependencies among traits were determined using the Hill-Climbing algorithm, implemented with the posterior distribution of the residuals obtained from the standard multiple-trait model. These identified relationships were then used to construct the SEM, considering both direct and indirect relationships. The relevant dependencies and path coefficients obtained, expressed in units of measurement variation of 1σ, were as follows: dMEO → CHOL (0.181), dMEO → BHB (−0.149), dMEO → urea (0.038), glucose → BHB (−0.55), glucose → urea (−0.194), CHOL → urea (0.175), BHB → urea (−0.049), and NEFA → urea (−0.097). Heritabilities for traits of concern obtained with SEM ranged from 0.09 to 0.2. Genetic correlations with a minimum 95% probability (P) of the posterior mean being &gt;0 for positive means or &lt;0 for negative means include those between dMEO and glucose (−0.583, P = 100), dMEO and BHB (0.349, P = 99), glucose and CHOL (0.325, P = 100), glucose and NEFA (−0.388, P = 100), and NEFA and BHB (0.759, P = 100). The results of this analysis revealed the existence of recursive relationships among the energy-related blood metabolites and dMEO. Understanding these connections is paramount for establishing effective genetic selection strategies, enhancing production and animal welfare.
Effects of a veterinary gastrointestinal diet on fecal characteristics, metabolites, and microbiota concentrations of adult cats treated with metronidazole
Authors: Belchik Sara E , Oba Patricia M , Lin Ching-Yen , Swanson Kelly S 
Published: September 2024

Abstract
Antibiotics are used to treat gastrointestinal diseases or infections but are known to negatively affect stool quality and gut microbiota in cats and dogs. Therefore, identifying dietary strategies that may aid in antibiotic recovery is of interest. The objective of this study was to determine how a veterinary gastrointestinal diet affected the fecal characteristics, microbiota, and metabolite and bile acid (BA) concentrations of cats recovering from metronidazole administration. Twenty-four healthy adult cats were used in an 8-wk completely randomized design study. During a 2-wk baseline, all cats consumed a leading grocery brand diet (GBD). Over the next 2 wk, cats consumed GBD and received metronidazole (20 mg/kg body weight twice daily). At week 4, cats were randomly allotted to one of 2 treatments [GBD; BLUE Natural Veterinary Diet GI Gastrointestinal Support (BB)] and fed for 4 wk. Fecal scores were recorded daily and fresh fecal samples were collected at weeks 2, 4, 5, 6, 7, and 8 for measurement of pH, dry matter (DM) %, metabolites, and microbiota. Microbiota was analyzed by 16S rRNA gene sequencing and qPCR, which was used to calculate dysbiosis index. Data were analyzed as repeated measures using the Mixed Models procedure of SAS 9.4, testing for effects of diet, time and diet*time. Metronidazole had dramatic effects on all outcomes, including increased fecal scores (looser stools), reduced fecal pH and DM%, reduced fecal short-chain fatty acid, branched-chain fatty acid, ammonia, phenol, and indole concentrations, and altered fecal BA concentrations (increased primary BA; reduced secondary BA). Metronidazole reduced fecal bacterial alpha diversity, increased dysbiosis index, and altered the relative abundance of 78 bacterial genera. Fecal outcomes partially recovered over the next 4 wk, with some being impacted by diet. Fecal acetate concentrations were higher after metronidazole in cats fed BB. Dysbiosis index and alpha diversity measures slowly recovered over 4 wk, without diet differences. Recovery of 16 bacterial genera was impacted by diet. Fecal BA profiles demonstrated a prolonged impairment of primary to secondary BA conversion, with cholic acid being lower after metronidazole in cats fed BB. In conclusion, our data demonstrate that metronidazole is a powerful antibiotic that has long-lasting effects on the fecal microbiota and metabolites of cats. Outcome variables slowly recovered over time, but a gastrointestinal diet may aid in recovery.
Farmed crickets (Orthoptera: Gryllidae) raised with dermestids (Coleoptera: Dermestidae) suffer from reduced and delayed growth, but not enough to explain reports of dramatic yield loss
Authors: Muzzatti Matthew J , Ritchie Marshall W , Bess Emilie C , Bertram Susan M , MacMillan Heath A 
Published: September 2024

Abstract
The mass production of insects for food and feed is an expanding North American industry. Facilities that mass rear insects are at risk of pest infestations because the optimal environmental conditions for rearing beneficial species may also support the development of pest species. Here, we present the first recorded results detailing the interactions between dermestids and farmed crickets. Cricket farms have reported extremely low harvest yield during heavy dermestid infestations, but the exact reasons for this low yield are unknown. Many dermestid larvae are covered in dense, detachable, barbed setae called hastisetae, which are used by the larvae as an active trapping system against arthropod predators. We designed a series of experiments to test the hypotheses that a dermestid pest of cricket farms, black larder beetle (Dermestes ater DeGeer (Coleoptera: Dermestidae)), may be directly impacting Gryllodes sigillatus Walker (Orthoptera: Gryllidae) yield through the physical effects of hastisetae ingestion and/or indirectly impacting cricket yield through competition for fishmeal, a primary source of protein in conventional cricket feed. Our predictions that G. sigillatus life history and survival would be negatively affected by dermestids were largely refuted. Females fed infested diets grew less mass, but not smaller body size, compared to females fed uninfested diets. We also found that while G. sigillatus experienced delayed growth early in life after living with dermestids, they were able to tolerate living with, and consuming, dermestid larvae. We discuss how these findings have led to new hypotheses concerning how dermestid infestations drive reductions in cricket farm yield.
Dynamics of tumor evolution after Gamma Knife radiosurgery for sporadic vestibular schwannoma: Defining volumetric patterns characterizing individual trajectory
Authors: Balossier Anne , Olteanu Madalina , Delsanti Christine , Troude Lucas , Thomassin Jean-Marc , Roche Pierre-Hugues , Chavent Marie , Régis Jean 
Published: September 2024

Abstract

Background
The definition of tumor control and treatment failure after Gamma Knife radiosurgery (GKRS) for vestibular schwannoma (VS) is still debated. The lack of knowledge on the dynamics of tumor evolution can lead to misinterpretation and subsequent inappropriate second treatment. The aim of this study was to evaluate the post-GKRS dynamics of the evolution of tumor volume and characterize volumetric patterns.

Methods
We included patients with sporadic VS treated by GKRS with an MRI follow-up of a minimum of 3 years. A clustering was performed in 2 steps: Definition of the patterns of evolution based on a subset of patients with the most comprehensive follow-up, and then the assignment of the remaining patients on a best-fit basis. The minimum length of follow-up was assessed by measuring the consistency of the clusters over time (adjusted rand index and normalized mutual information). An analysis of the discriminant variables was finally performed.

Results
A total of 1607 patients were included (median follow-up: 67 months). Five patterns were defined with 1 pattern gathering almost all cases of treatment failure. The clustering at 5 years afforded the highest consistency with long-term follow-up. Discriminant variables for clusters were as follows: sex, initial symptoms, delay of diagnosis, Koos grading, fundus invasion, and number of isocenters.

Conclusions
The definition of these robust distinct patterns is likely to help the physicians tremendously to distinguish tumor control from potential failure. We advocate for no retreatment decision before 5 years post-GKRS. Further investigations are required to decide if the dynamics of evolution can be predicted at GKRS on an individual basis.
Large-volume fully automated cell reconstruction generates a cell atlas of plant tissues
Authors: Hu Zijian , Liu Jiazheng , Shen Shiya , Wu Weiqian , Yuan Jingbin , Shen Weiwei , Ma Lingyu , Wang Guangchao , Yang Shunyao , Xu Xiuping , Cui Yaning , Li Zhenchen , Shen Lijun , Li Linlin , Bian Jiahui , Zhang Xi , Han Hua , Lin Jinxing 
Published: September 2024

Abstract
The geometric shape and arrangement of individual cells play a role in shaping organ functions. However, analyzing multicellular features and exploring their connectomes in centimeter-scale plant organs remain challenging. Here, we established a set of frameworks named large-volume fully automated cell reconstruction (LVACR), enabling the exploration of 3D cytological features and cellular connectivity in plant tissues. Through benchmark testing, our framework demonstrated superior efficiency in cell segmentation and aggregation, successfully addressing the inherent challenges posed by light sheet fluorescence microscopy imaging. Using LVACR, we successfully established a cell atlas of different plant tissues. Cellular morphology analysis revealed differences of cell clusters and shapes in between different poplar (Populus simonii Carr. and Populus canadensis Moench.) seeds, whereas topological analysis revealed that they maintained conserved cellular connectivity. Furthermore, LVACR spatiotemporally demonstrated an initial burst of cell proliferation, accompanied by morphological transformations at an early stage in developing the shoot apical meristem of Pinus tabuliformis Carr. seedlings. During subsequent development, cell differentiation produced anisotropic features, thereby resulting in various cell shapes. Overall, our findings provided valuable insights into the precise spatial arrangement and cellular behavior of multicellular organisms, thus enhancing our understanding of the complex processes underlying plant growth and differentiation.
Phylogenomics of Bivalvia Using Ultraconserved Elements Reveal New Topologies for Pteriomorphia and Imparidentia
Authors: Li Yi-Xuan , Ip Jack Chi-Ho , Chen Chong , Xu Ting , Zhang Qian , Sun Yanan , Ma Pei-Zhen , Qiu Jian-Wen 
Published: September 2024

Abstract
Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus, especially within Pteriomorphia and Imparidentia. Here, we inferred the relationships of key lineages within Bivalvia using matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources and 85 newly sequenced specimens from 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average of 849 UCEs with 1085 bp in mean length from in vitro experiments. Our results introduced novel schemes from 6 major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata, and Imparidentia), though some inner nodes were poorly resolved, such as paraphyletic Heterodonta in some topologies potentially due to insufficient taxon sampling. The resolution increased when analyzing specific matrices for Pteriomorphia and Imparidentia. We recovered 3 Pteriomorphia topologies different from previously published trees, with the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida + (Limida + Pectinida))). Limida were nested within Pectinida, warranting further studies. For Imparidentia, our results strongly supported the new hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible non-monophyly of Lucinida was inferred but poorly supported. Overall, our results provide important insights into the phylogeny of Bivalvia and show that target enrichment sequencing of UCEs can be broadly applied to study both deep and shallow phylogenetic relationships.
A reappraisal of mitochondrial DNA introgression in the Mus musculus musculus/Mus musculus domesticus hybrid zone suggests ancient North-European associations between mice and humans
Authors: Macholán Miloš , Baird Stuart J E , Fornůsková Alena , Ďureje Ľudovít , Burgstaller Jörg P , Goüy de Bellocq Joëlle , Heitlinger Emanuel , Klusáčková Pavla , Koshev Yordan , Piálek Jaroslav 
Published: September 2024

ABSTRACT
The house mouse is the best-studied mammal species after humans, yet our understanding of its evolutionary history remains incomplete. Here, we focused on the colonisation of Europe by two subspecies and formation of a hybrid zone between them. We carried out a large-scale study of ~7000 mice sampled across an area embracing an ~900 km long portion of the zone, supplemented with cytochrome b and D-loop sequencing of ~1200 individuals collected worldwide. We demonstrate that the course of the mtDNA contact front is intricate and highly discordant with the consensus front for autosomal and X-linked markers, suggesting that local snapshots of mtDNA introgression may be misleading when treated in isolation. While multiple unrelated M. m. domesticus haplotypes occur in the zone area, the diversity of M. m. musculus haplotypes is limited. Moreover, we uncovered a vast region of domesticus introgression into musculus territory in northern areas and showed this introgression is unlikely to be driven by positive selection. We consider two previously published hypotheses explaining this phenomenon and put forth an alternative scenario assuming associations between mice and humans in northern Europe during the Nordic Bronze Age and subsequent zone movement associated with the expansion of Balto-Slavic peoples.
Assessment of Racial, Ethnic, and Sex-Based Disparities in Time-to-Antibiotics and Sepsis Outcomes in a Large Multihospital Cohort*
Authors: Pak Theodore R. , Sánchez Sarimer M. , McKenna Caroline S. , Rhee Chanu , Klompas Michael 
Published: September 2024

OBJECTIVES:
To characterize associations between race/ethnicity/sex, time-to-antibiotics, and mortality in patients with suspected sepsis or septic shock.

DESIGN:
Retrospective cohort study, with race/ethnicity/sex as the exposure, and time-to-antibiotics (relative to emergency department arrival) and in-hospital mortality as the outcome.

SETTING:
Five Massachusetts hospitals.

PATIENTS:
Forty-nine thousand six hundred nine adults admitted 2015–2022 with suspected sepsis or septic shock (blood cultures drawn and IV antibiotics administered within 24 hr of arrival, plus evidence of organ dysfunction for sepsis, and hypotension or lactate ≥ 4.0 mmol/L for septic shock).

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Among included patients, 22,598 (46%) were women, 36,626 (75%) were White, and 4,483 (9.2%) were Black. Women had longer median time-to-antibiotics than men when presenting with either suspected sepsis (203 vs. 190 min) or septic shock (160 vs. 142 min). Differences in time-to-antibiotics for women vs. men persisted after adjusting for age, race, comorbidities, source of infection, and severity of illness (adjusted odds ratio [aOR] for 3–6 vs. < 3 hr; 1.16 [95% CI, 1.07–1.25] for sepsis and aOR, 1.09 [95% CI, 1.01–1.18] for septic shock). Median time-to-antibiotics was also longer for Black vs. White patients for both sepsis (215 vs. 194 min; aOR for 3–6 vs. < 3 hr; 1.24 [95% CI, 1.06–1.45]) and septic shock (median 159 vs. 148 min; aOR, 1.32 [95% CI, 1.12–1.55]). There was no association between race/ethnicity/sex and in-hospital mortality for sepsis without shock; however, women with septic shock had higher mortality (aOR, 1.16; 95% CI, 1.04–1.29) vs. men. Higher mortality for women with septic shock persisted when also adjusting for time-to-antibiotics (aOR, 1.16; 95% CI, 1.03–1.32).

CONCLUSIONS:
In a large cohort of patients with sepsis, time-to-antibiotics was longer for both women and Black patients even after detailed risk-adjustment. Women with septic shock had higher adjusted in-hospital mortality than men, but this association was not moderated by time-to-antibiotics.
The Burden and Clinical Features of Neovascular Glaucoma in a Major Tertiary Care Center in China
Authors: Lin Huishan , Gao Xinbo , Xu Zixing , Zhang Yuxuan , Liao Yunru , Ren Jiawei , Qin Xi , Liu Yao , Huang Wei , Zuo Chengguo , Lin Mingkai 
Published: September 2024

Précis:
This research presents the burden and clinical characteristics of NVG in Zhongshan Ophthalmic Center, employing the most extensive sample size and the longest uninterrupted temporal duration so far, which may provide a theoretical reference for the effective prevention and diagnosis of NVG.

Purpose:
To summarize the burden and clinical characteristics of neovascular glaucoma (NVG) in a major tertiary care center in China.

Methods:
The clinical data of NVG patients in Zhongshan Ophthalmic Center (ZOC) between 2012 and 2021 were collected retrospectively, including their age, sex, the affected eye, best-corrected visual acuity (BCVA), intraocular pressure (IOP), clinical stage and etiology.

Results:
In this study, we included 1877 eyes of 1749 patients who developed NVG, with a 2.01:1 ratio of male to female. Their mean age was 53.14±16.69 years and those aged 41–70 years (65.2%) were most affected. Monocular patients were more predominant in most of them (92.7%), while 7.3% were binocular and 1667 eyes (88.8%) were at the angle closure stage. The BCVA and IOP were 2.42±0.70 logMAR and 38.6±12.2 mm Hg, respectively. Over the decade, the number of NVG patients and the proportion of NVG patients among glaucoma patients showed an increasing trend, with annual percentage changes (APCs) of 9.1% (95% CI: 5.0%–13.3%, P=0.001) and 4.8% (95% CI: 2.2%–7.4%, P=0.003), respectively. The top 3 primary conditions were diabetic retinopathy (DR), retinal vein occlusion (RVO), and retinal detachment (RD). Moreover, the APCs for the constituent ratio of DR and RVO were 4.4% (95% CI: 0.5%–8.4%, P=0.031) and −4.6% (95% CI: −8.4% to −0.7%, P=0.028), respectively. However, the first and second causes of NVG in minors (below 18 years old) were Coat’s disease and ocular tumors, followed by RD and RVO in third place. The top cause of NVG in patients aged 65 years and older was RVO.

Conclusions:
The burden of NVG is increasing, emphasizing the need to improve preventive strategies focusing on primary diseases such as DR, RVO, and RD, particularly the increasing proportion of DR cases and the previously underemphasized RD patients, while also highlighting the differences in primary diseases across different age groups.
Two Patients With Ipsilateral Cerebellar Hemorrhage After Superficial Temporal Artery–Middle Cerebral Artery Bypass Grafting
Authors: Yan Fengjuan , Pang Chunxiao 
Published: September 2024

Objective:
To summarize the clinical experience of ipsilateral cerebellar hemorrhage after superficial temporal artery–middle cerebral artery bypass surgery.

Methods:
The clinical data of 2 patients with cerebellar hemorrhage after superficial temporal artery–middle cerebral artery bypass grafting were retrospectively collected, including 1 case with left cerebellar hemorrhage after left cerebral artery bypass grafting and 1 case with right cerebellar hemorrhage after right cerebral artery bypass grafting. The perioperative blood pressure, laboratory, and imaging data were analyzed.

Results:
All patients had a history of hypertension, and their perioperative blood pressure was stable. Low-density lipoprotein cholesterol and high-density lipoprotein cholesterol were normal before the operation. Cerebral magnetic resonance imaging showed cerebral atherosclerosis and multiple ischemic cerebral infarcts. At 24 hours after surgery, the patients’ continuous epidural low drainage was 260 mL and 160 mL, respectively. The amount of cerebellar bleeding was small, and no new sequelae were left after conservative treatment with drugs.

Conclusion:
Cerebellar hemorrhage after superficial temporal artery–middle cerebral artery bypass grafting is related to perioperative blood pressure fluctuation, hemodynamic changes, hemorrhagic transformation of ischemic lesions, and excessive cerebrospinal fluid drainage. Maintaining stable blood pressure during the perioperative period and avoiding excessive and rapid loss of cerebrospinal fluid after operation can reduce the occurrence of this complication.
Constructing a diagnostic prediction model to estimate the severe respiratory syncytial virus pneumonia in children based on machine learning
Authors: Liu Yuanwei , Wu Qiong , Zhou Lifang , Tang Yingyuan , Li Fen , Li Shuangjie 
Published: September 2024

Abstract

Background
Severe respiratory syncytial virus (RSV) pneumonia is a leading cause of hospitalization and morbidity in infants and young children. Early identification of severe RSV pneumonia is crucial for timely and effective treatment by pediatricians. Currently, no prediction model exists for identifying severe RSV pneumonia in children.

Methods
This study aimed to construct a diagnostic prediction model for severe RSV pneumonia in children using a machine learning algorithm. We analyzed data from the Gene Expression Omnibus (GEO) Series, including training dataset GSE246622 and testing dataset GSE105450, to identify differential genes between severe and mild-to-moderate RSV pneumonia in children. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on the differential genes, followed by the construction of a protein-protein interaction (PPI) network. An artificial neural network (ANN) algorithm was then used to develop and validate a diagnostic prediction model for severe RSV pneumonia in children.

Results
We identified 34 differentially expressed genes between the severe and mild-to-moderate RSV pneumonia groups. Enrichment analysis revealed that these genes were primarily related to pathogenic infection and immune response. From the PPI network, we identified 10 hub genes and, using the random forest algorithm, screened out 20 specific genes. The ANN-based diagnostic prediction model achieved an area under the curve (AUC) value of 0.970 in the training group and 0.833 in the testing group, demonstrating the model's accuracy.

Conclusions
This study identified specific biomarkers and developed a diagnostic model for severe RSV pneumonia in children. These findings provide a robust foundation for early identification and treatment of severe RSV pneumonia, offering new insights into its pathogenesis and improving pediatric care.