bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction accounting for dominance and epistatic genetic effects on litter size traits in Large White pigs
Authors: Chen Jianmei , Dou Tengfei , Wu Ziyi , Bai Liyao , Xu Man , Zhang Yongqian , Yang Songbai , Xu Shiqian , Han Xuelei , Qiao Ruimin , Wang Kejun , Yang Feng , Li Xin-Jian , Wang Xianwei , Li Xiu-Ling 
Published: January 2025

Abstract
Litter size traits of sows are crucial for the economic benefits of the pig industry. Three phenotypic traits of 1,206 Large White (LW) pigs, that is, the total number born (TNB), number born alive (NBA), and number of healthy piglets (NHP), were recorded. We evaluated a series of genomic best linear unbiased prediction (GBLUP) models that sequentially added additive effects (model A), dominance effects (model A+D), and epistatic effects (model A+D+AA, model A+D+AA+AD, and model A+D+AA+AD+DD) using chip data and imputed whole-genome sequencing (WGS) data to estimate genetic parameters and predictive accuracy. The reproductive traits of sows showed low heritability in this study, with narrow heritability of the three traits ranging from 0.030 to 0.064, and broad heritability ranging from 0.125 to 0.145. The inclusion of non-additive effects in the model improved the accuracy of genomic selection. In the chip data, compared with that of the A model, the A+D+AA+AD+DD model showed the greatest increase in accuracy for TNB, NBA, and NHP, with improvements of 1.78, 1.67, and 1.74%, respectively. Additionally, the accuracy of the imputed WGS data was greater compared to the chip data. For the TNB, NBA, and NHP traits, the predictive accuracy of the imputed WGS data improved by 3.26, 7.72, and 3.00%, respectively, compared with that of the chip data. In summary, these results suggest that non-additive effects in genomic selection could improve prediction accuracy and should be considered in pig genomic evaluation procedures.
Identification of a novel Eps 15 homology domain-containing protein 1 (EHD1) and EHD4-binding motif in phostensin
Authors: Huang Kuang-Yung , Yu Hui-Chun , Lu Ming-Chi , Tseng Hsien-Yu Huang , Shen Jyun-Jie , Lin Chia-Ying , Chen Pin-Chen , Shen Ya-Ting , Chung Pei-Rong , Tsai Hsiao-Kuei , Zhou Si-Ru , Wang Chia-Lin , Lai Ning-Sheng , Lin Ta-Hsien , Huang Hsien-Bin 
Published: January 2025

Abstract
Phostensin (PTS) encoded by KIAA1949 binds to protein phosphatase 1, F-actin, Eps 15 homology domain-containing protein 1 (EHD1) and EHD4. Most EHD-binding proteins contain a consensus motif, Asn-Pro-Phe (NPF), which interacts with the C-terminal EH domain of EHD proteins. Nevertheless, the NPF motif is absent in PTS. The binding motif for PTS to interact with EHD1 (or EHD4) remains unknown. Here, we identified that PTS-α binds to EHD1 (or EHD4) through the region of residues 51–80, which contains a consensus motif, 64ILV(X)4(L/V)RL74S. This novel consensus motif is also found in vacuolar protein sorting-35 (vps35). Replacement of 64ILV(X)4(L/V)RL74S with 64AAA(X)4(L/V)RL74S or with 64ILV(X)4AEA74A significantly reduces the binding efficiency of PTS-α to either EHD1 or EHD4 in GST pull-down assay and far western blotting assay. In addition, replacement of 218ILV(X)4VRL228S with 218AAA(X)4AEA228A decreases the binding ability of vps35 to EHD4 in far western blotting assay. Overexpression of the PTS-β in 293 T cells attenuated the endocytic trafficking of transferrin. However, this attenuation of transferrin in endocytic trafficking was disrupted when 293 T cells overexpressed the mutant PTS-β with a defective EHD-binding motif, suggesting that PTS-β can regulate the endocytic recycling via associating with EHD1 or EHD4.
Decreased emergence rates of adult house flies (Musca domestica; Diptera: Muscidae) due to exposure to commercially available insecticidal baits during larval development
Authors: Pitzer Jimmy B , Navarro Jessica D , Phillips Evan S 
Published: January 2025

Abstract
House flies, Musca domestica L. (Diptera: Muscidae), are commonplace pests in both urban and agricultural settings. The potential for house flies as vectors of many disease-causing organisms to humans and animals, coupled with their incessant nuisance behaviors toward these hosts has resulted in a desire to manage their populations. Although many house fly management tools are available, insecticide use continues to predominate as the preferred choice. One such option, insecticidal baits, is commercially available in a variety of active ingredients that encompass several modes of action. Though they can be effective, resistance to many of the active ingredients used in bait formulations has been documented. The primary pathway for resistance evolution to bait products likely has been selection at the targeted adult stage. However, exposure at the larval stage may occur when these products are scattered on substrates, contaminating sub-surface developmental areas and ultimately, playing a selective role as well. A study was conducted to assess the potential mortality effects of insecticidal bait products on house fly larval development when applied according to the manufacturer’s recommended label rate. Adult house fly emergence was reduced by nearly 40% due to treatment, supporting the implication that bait-driven mortality during larval development may represent a previously unrecognized selection pathway contributing to resistance evolution against these products.
Macroeconomic Drivers of Inflation Expectations and Inflation Risk Premia
Authors: Boeckx Jef , Iania Leonardo , Wauters Joris 
Published: January 2025

Abstract
We propose a new affine term structure model to decompose inflation-linked swap (ILS) rates into genuine inflation expectations and inflation risk premia. The model accounts for both short-term macroeconomic factors and long-term economic trends, namely trend inflation and the equilibrium real interest rate. We estimate the model for the US and euro area and find that the inflation risk premium significantly drives ILS rates, with macroeconomic shocks playing different roles across maturities and regions. International factors, particularly oil prices, impact market-based inflation expectations during key global events like the COVID-19 pandemic and the Russian invasion of Ukraine.
Encapsulation, vacuolation and phagocytosis of the opportunistic fungal pathogen Cryptococcus in the liver of an immunocompetent host
Authors: Yoon Chul Jong , Chi Je Geun , Kim Ki Woo 
Published: January 2025

Abstract
The cellular characteristics of the opportunistic fungal pathogen Cryptococcus species were investigated in the infected liver of an immunocompetent host using transmission electron microscopy (TEM). With no records of immunodeficiency, the 3-year-old female patient displayed a high-grade fever, lethargy and increasing jaundice. TEM analysis revealed the presence of round yeast cells in the patient’s liver. These fungal yeast cells exhibited an array of cellular events in the host’s liver: (i) the formation of polysaccharide capsules outside the cell wall, (ii) vacuolation in the cytoplasm and (iii) phagocytosis by Kupffer cells. The yeast cells were surrounded by electron-transparent polysaccharide capsules (approximately 5 μm thick). A series of yeast vacuolations were observed at different stages of cell development. As vacuoles occupied the cytoplasm of yeast cells, the polysaccharide capsules were thinner and more electron-dense than those of intact yeast cells. Certain yeast cells were phagocytosed by Kupffer cells through the budding scars or discontinued regions in the cell walls. These observations suggested that the patient was suffering from liver cryptococcosis. This study provides insights into the behavior of opportunistic fungal pathogens in the livers of immunocompetent patients.
Cross-sector collaboration in cities: learning journey or blame game?
Authors: Pulido-Gómez Santiago , de Jong Jorrit , Rivkin Jan W 
Published: January 2025

Abstract
The success of cross-sector collaborations (CSCs) in cities is mixed, and important questions remain about what distinguishes effective from ineffective collaborations. This comparative case study examined nine CSCs in three US cities, focusing on three public policy areas: education, economic development, and public safety. Nine group interviews, 110 individual interviews, and analysis of archival documents revealed common patterns that allow us to build grounded theory about the roots of CSC success. We propose that how a collaboration responds to setbacks plays a crucial role. Success arises in collaborations that respond to setbacks with a process of mutual learning, in which participants anticipate each other’s actions, devise new ways of apportioning labor, and approach problems collectively. In contrast, failure follows when setbacks lead collaborations into a process of mutual blaming. No single mode of network governance is especially associated with success, but more successful collaborations tend to be characterized by adaptability concerning governance mode. Mutual learning appears to be facilitated by a few key actions: building on prior relationships, relying on trusted key participants, engaging with the community, using data to advantage, and investing in joint problem-solving. Our findings suggest that collaborative leaders in public, private, and nonprofit organizations should emphasize these key actions to enable collaboration and facilitate mutual learning.
Interactions of the Pneumococcus with the Central Nervous System: Postnatal Meningitis Versus Fetal Neurodevelopment
Authors: Davis Amy , Tuomanen Elaine 
Published: January 2025

Abstract
In young children, pneumococcal meningitis epitomizes the paradigm of a destructive innate inflammatory response in the central nervous system: a five-alarm fire. In contrast, cell-free bacterial components reaching the fetal brain from an infected mother signal a quiet, noninflammatory immune response that drives abnormal neurodevelopment, changing brain architecture through neuroproliferation. This review addresses the difference between prenatal and postnatal bacterial–host signaling within the brain.
Enterovirus and Parechovirus Neurologic Infections in Children: Clinical Presentations and Neuropathogenesis
Authors: Freeman Megan Culler , Messacar Kevin 
Published: January 2025

Abstract
Enteroviruses (EVs) and parechoviruses (PeVs) are common pathogens of childhood. Enteroviral infections cause a range of clinical syndromes from mild illness to neurologic manifestations of meningitis, encephalitis, and acute flaccid myelitis. Disease manifestations are driven by a combination of viral replication and host immune response. Despite ubiquitousness and clinical importance, there are no approved targeted therapies for these viruses and most are without an available vaccine. Studies of EV neuropathogenesis began with poliovirus and are ongoing for other nonpolio EVs and PeVs. Many unanswered questions remain with regard to cellular tropism, mechanisms of dissemination, receptor usage, immunologic control, and cellular death. This review describes what is known about epidemiology, clinical presentations, and neuropathogenesis of these important pathogens.
The new Dutch default community of acquests regime: key innovations from a comparative perspective
Authors: Thijs Hannelore 
Published: January 2025

Abstract
Prior to 2018, the default matrimonial property regime in the Netherlands was a universal community property regime. As a consequence of a substantial reform that took effect on 1 January 2018, the Dutch default regulation now limits the content of the community property to the assets acquired non-gratuitously during the marriage. This contribution presents an overview of the key innovations of the new Dutch default community of acquests regime, with a particular focus on the content of the community property and the rights of creditors. In order to gain insights from a comparative perspective, the Dutch regulation is compared with the default community of acquests regimes from Belgium and France. This article demonstrates that the principal characteristics of the new Dutch regime are comparable to those of the Belgian and French regimes. Most fundamentally, the Dutch regime now excludes premarital assets and debts, as well as assets and debts related to inheritances and gifts, from the community property. However, the new Dutch regime also exhibits more unique characteristics. These include, most notably, the inclusion of assets that jointly belong to the spouses prior to the marriage in the community property and the limitation of the recoverable basis for creditors of separate debts. These characteristics may serve as a source of inspiration for community property regimes in other jurisdictions.
Impact of Dobbs v. Jackson Women’s Health Organization on Female Sterilization Rates at a Texas Military Medical Center, a Retrospective Cohort Study
Authors: Gottula Jessica L , Downey Abigail G , Shah Shenika P , Munisteri-Duff Meghan K , Keyser Erin A 
Published: January 2025

ABSTRACT

Objective
Female sterilization is a common form of contraception in the United States. On June 24, 2022, the United States Supreme Court eliminated the federal standard protecting a woman’s right to abortion via Dobbs v. Jackson Women’s Health Organization. Since that time, there have been anecdotal increases in sterilization requests across the country, although there are no publications demonstrating this change. This study hypothesized that there would be increased female sterilization rates at a Texas military hospital post-Dobbs decision due to state restrictions as compared with a Washington military hospital.

Methods
This study retrospectively reviewed female sterilization rates from March 2022 to April 2023. The average rate of sterilization procedures performed pre-Dobbs decision was compared to the average rate following the Dobbs decision in a Texas and Washington military facility due to different state restrictions. The rates of sterilization were also stratified among demographic groups at the Texas military facility.

Results
Female sterilizations encompassed 24/230 (10.4%) of the gynecologic surgeries performed pre-Dobbs compared to 110/629 (17.5%) cases performed post-Dobbs (P = .01) in Texas. However, sterilization rates in Washington state remained the same, with 15/80 (18.7%) benign gynecologic surgeries pre-Dobbs and 28/185 (15.1%) post-Dobbs (P = .59). The average age of sterilization pre-Dobbs was 35 years compared to 33 years post-Dobbs (P = .04). Post-Dobbs group was less likely to use a barrier method prior to sterilization (P = 0.01).

Conclusion
The reproductive health of military medical beneficiaries at one military hospital was significantly impacted by the Dobbs v. Jackson Women’s Health Organization decision. Rates of female sterilization increased significantly. In addition, patients choosing permanent sterilization were younger and were less likely to use alternative, reversible contraceptive methods prior to surgery. This study demonstrates a significant change in contraceptive choices toward methods that incur greater surgical risks and potential for regret, as well as greater financial costs to the military health system.
Re-analysis of the anthropogenic effect of the COVID-19 global lockdown on nighttime lunar surface temperatures
Authors: Schonberg W , Haque S 
Published: January 2025

Abstract
A study by Durga Prasad and Ambily (2024) observed an anomalous decrease in the lunar surface temperatures during the period April-May 2020, which they then attributed to the anthropogenic effects of the COVID-19 global lockdown effect. We have re-examined their data and while the anomalous decrease in the lunar surface temperature during April- May 2020 appears in our analysis as well, so does another significant dip in early 2018. Furthermore, the decline to the minimum observed during April-May 2020 is seen to begin in 2019, that is, quite some time before the COVID-19 event that led to the global lockdown and the suggested anthropogenic effect of reduced pollution. We, therefore, conclude that one cannot attribute the effects of the observed changes in the lunar surface temperature during April-May 2020 directly and unambiguously to reduced human activity during the COVD-19 lockdown as claimed by Durga Prasad and Ambily (2024).
Structural and bioinformatics analyses identify deoxydinucleotide-specific nucleases and their association with genomic islands in gram-positive bacteria
Authors: Mortensen Sofia , Kuncová Stanislava , Lormand Justin D , Myers Tanner M , Kim Soo-Kyoung , Lee Vincent T , Winkler Wade C , Sondermann Holger 
Published: January 2025

Abstract
Dinucleases of the DEDD superfamily, such as oligoribonuclease, Rexo2 and nanoRNase C, catalyze the essential final step of RNA degradation, the conversion of di- to mononucleotides. The active sites of these enzymes are optimized for substrates that are two nucleotides long, and do not discriminate between RNA and DNA. Here, we identified a novel DEDD subfamily, members of which function as dedicated deoxydinucleases (diDNases) that specifically hydrolyze single-stranded DNA dinucleotides in a sequence-independent manner. Crystal structures of enzyme-substrate complexes reveal that specificity for DNA stems from a combination of conserved structural elements that exclude diribonucleotides as substrates. Consistently, diDNases fail to complement the loss of enzymes that act on diribonucleotides, indicating that these two groups of enzymes support distinct cellular functions. The genes encoding diDNases are found predominantly in genomic islands of Actinomycetes and Clostridia, which, together with their association with phage-defense systems, suggest potential roles in bacterial immunity.
One-pot ligation of multiple mRNA fragments on dsDNA splint advancing regional modification and translation
Authors: Xu Yunfan , Qi Shuopeng , Zhang Gongrui , Liu Dan , Xu Dejin , Qin Tong , Cheng Qin , Kang Han , Hu Bei , Huang Zhen 
Published: January 2025

Abstract
Region-specific RNA modifications are crucial for advancing RNA research and therapeutics, including messenger RNA (mRNA)-based vaccines and immunotherapy. However, the predominant method, synthesizing regionally modified mRNAs with short single-stranded DNA (ssDNA) splints, encounters challenges in ligating long mRNA fragments due to the formation of RNA self-folded complex structures. To address this issue, we developed an efficient strategy using an easily obtained long double-stranded DNA (dsDNA) as a ligation splint after in situ denaturing, while parts of this dsDNA are the templates for transcribing mRNA fragments. We observed that the denatured dsDNA formed a long hybrid duplex with these mRNA fragments, overcoming their structures. Further, our novel strategy remarkably facilitated the ligation of long mRNA fragments (especially structured ones), offering ligation efficiency up to 106-fold higher than the ssDNA method. Using this one-pot strategy, we conveniently synthesized the mRNAs with N1-methylpseudouridine (m1ψ) and 5-methylcytidine (m5C) modifications in specific regions. We have found that compared with the fully modified mRNAs, the 3′UTR m1ψ modifications alone increased the translation efficiency, and the combined modifications of the m1ψ-3′UTR and m5C-5′UTR/CDS exhibited higher translation efficiency and lower immunogenicity in general. Our study presents a broadly applicable strategy for producing regionally modified mRNAs, advancing the potential of mRNA therapeutics.
Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases
Authors: Jordano-Raya Marina , Schrader Carol E , Ariza Rafael R , Roldán-Arjona Teresa , Córdoba-Cañero Dolores 
Published: January 2025

Abstract
Apurinic/apyrimidinic (AP) endonucleases are key enzymes responsible for the repair of base-less nucleotides generated by spontaneous hydrolysis or as DNA repair intermediates. APE1, the major human AP endonuclease, is a druggable target in cancer and its biological function has been extensively studied. However, the molecular features responsible for its substrate specificity are poorly understood. We show here that, in contrast to APE1, its Arabidopsis ortholog ARP (apurinic endonuclease-redox protein) exhibits orphan base-dependent activity on double-stranded DNA and very poor AP cleavage capacity on single-stranded DNA (ssDNA). We found that these differences are largely a consequence of the variation at two DNA intercalating amino acids that have undergone divergent changes in the metazoan and plant lineages. Swapping the identity of the residue invading the minor groove is sufficient to switch the orphan base specificities of APE1 and ARP. The affinity for ssDNA is largely determined by the major groove invading residue, and swapping its identity switches the ability of APE1 and ARP to cleave AP sites in ssDNA. Importantly, we show that the critical residue for ssDNA cleavage is crucial for mammalian APE1 function in antibody class switch recombination, suggesting an evolutionary advantage for ssDNA activity. These findings provide new molecular insights into the evolution of AP endonucleases.
A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients
Authors: Park Sarah Y , Goldman Jason D , Levine Deborah J , Haidar Ghady 
Published: January 2025

Abstract

Background
Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.

Methods
We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012–11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.

Results
Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11–1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%–88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.

Conclusions
We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research.