bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Hypolimnas misippus Genome Supports a Common Origin of the W Chromosome in Lepidoptera
Authors: Orteu Anna , McCarthy Shane A , Hornett Emily A , Gemmell Matthew R , Reynolds Louise A , Warren Ian A , Gordon Ian J , Hurst Gregory D D , Durbin Richard , Martin Simon H , Jiggins Chris D 
Published: October 2024

Abstract
Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early-diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of 2 Hypolimnas species (Hypolimnas misippus and Hypolimnas bolina) and use the H. misippus assembly to explore the evolution of W chromosomes in butterflies and moths. We show that in H. misippus, the W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins.
Chromosomal-Level Genome Assembly of the Antarctic Sea Urchin Sterechinus neumayeri: A Model for Antarctic Invertebrate Biology
Authors: Warner Jacob F , Range Ryan C , Fenner Jennifer , Ka Cheikouna , Waits Damien S , Boddy Kristen , David Kyle T , Mahon Andrew R , Halanych Kenneth M 
Published: October 2024

Abstract
The Antarctic sea urchin Sterechinus neumayeri (Echinoida; Echinidae) is routinely used as a model organism for Antarctic biology. Here, we present a high-quality genome of S. neumayeri. This chromosomal-level assembly was generated using PacBio long-read sequencing and Hi-C chromatin conformation capture sequencing. This 885.3-Mb assembly exhibits high contiguity with a scaffold length N50 of 36.7 Mb assembled into 20 chromosomal length scaffolds. These putative chromosomes exhibit a high degree of synteny compared to other sea urchin models. We used transcript evidence gene modeling combined with sequence homology to identify 21,638 gene models that capture 97.4% of BUSCO orthologs. Among these, we were able to identify and annotate conserved developmental gene regulatory network orthologs, positioning S. neumayeri as a tractable model for comparative studies on evolution and development.
Performance evaluation of evaporator coil of a domestic refrigerator under frosting
Authors: Kumar Manav , Kiran Kumar K , Mondal Sharifuddin , Khan Mohammad Amir , Khan T M Yunus , Almakayeel Naif , Khan Wahaj Ahmad 
Published: October 2024

Abstract
The frost deposition on the outer exterior of the evaporator coil degrades the thermal performance by building up the thermic resistance and the pressure drop across the air side. In this study, numerical performance investigations of domestic refrigerator evaporator coil in frosted condition are presented. For this purpose, evaporator coil having two kinds of fin configurations such as plain and wavy in staggered tube arrangement is considered. The mass, momentum, and energy equations along with empirical correlations are employed for simultaneous transfer of heat and mass during the process. The air-side parameters, such as air flow rate and relative humidity, are varied whilst cooling fluid-side parameters are kept fixed. The cooling fluid is selected as the commonly used haloalkane refrigerant (R-134a) in domestic refrigerators. The numerical analyses are carried out for 2 h working and the effect on growing frost and its density is noted. It is found that total conductivity (UA) decreases 15.6% and 14.2% and air-side pressure drop increases by 99% and 84.3%, respectively, for two considered fin configurations—plain and wavy. The minimum free flow area is reduced by 29.6%.
Detection of Soybean GMO Events Using Two Multiplex Droplet Digital PCR Assays
Authors: Demeke Tigst , Eng Monika 
Published: October 2024

Abstract

Background
Detection methods for GMO events are required because of regulatory compliance requirements. Efficient detection and quantification of GMO events saves time and resources. Multiplex digital PCR (dPCR) allows detection and quantification of more than one GMO event at the same time.

Objective
The study used two tetraplex droplet digital PCR (ddPCR) assays for the detection of 19 soybean GMO events.

Methods
Two multiplex dPCR assays were developed and optimized for the detection of 19 soybean GMO events. The first tetraplex ddPCR assay contained four element-specific targets commonly found in GMO plants (P-35S, T-nos, tE9, and Pat). The second event-specific tetraplex ddPCR assay targeted four soybean GMO events that are not detected with the element-specific tetraplex ddPCR (CV127, DP305423, MON87701, and MON87751).

Results
The element-specific tetraplex ddPCR assay detected all the expected 15 soybean GMO events. The element-specific tetraplex ddPCR assay also detected selected soybean GMO events at the 0.01% level. The event-specific tetraplex ddPCR assay was successfully used to quantify the four soybean GMO events at the 0.1, 1, 2, and 5% levels. The event-specific tetraplex ddPCR assay also detected the four soybean GMO events at the 0.01% level.

Conclusions
The two tetraplex ddPCR assays can be used for the detection of 19 soybean GMO events.

Highlights
An element-specific tetraplex ddPCR assay was used to detect 15 soybean GMO events, and an event-specific tetraplex ddPCR assay was used to detect and quantify four soybean GMO events that are not detected by the element-specific ddPCR assay.
Late gestation maternal infection with bovine viral diarrhea virus impacts offspring feedlot performance, digestion, blood parameters, and hot carcass weights
Authors: Engle Terry E , Guimaraes Octavio , Loh Huey Yi , Thorndyke Meghan P , Van Campen Hana , Kincade Jessica N , Eder Jordan M , Hansen Thomas R 
Published: October 2024

Abstract
Fetal infection with bovine viral diarrhea virus (BVDV) after 150 d results in transient fetal infections (TI). Twenty-five unvaccinated, yearling Hereford heifers, seronegative for antibodies to BVDV1 and BVDV2, were bred by artificial insemination with X chromosome-bearing sperm from 1 Angus sire to examine the impact of TI on postnatal growth, estimated dry matter digestibility, blood parameters, and carcass characteristics. On day 175 of pregnancy, dams were intranasally inoculated with either sham control or 4.0 log median tissue culture infectious dose noncytopathic type2 BVDV to generate control or TI offspring, respectively. All control dams remained seronegative and all BVDV-inoculated dams seroconverted by day 14 post-inoculation. All control offspring were seronegative and all TI offspring were seropositive for antibodies to type 2 BVDV at birth. All offspring were raised on pasture until weaning. At weaning, all calves were transported to our research feedlot facility, housed in 3 pens, and transitioned to a high-energy concentrate-based diet. Heifer body weights (BW) and jugular blood samples were collected every 28 d. On day 84 of the feeding period, titanium dioxide was added to the diet of 12, age-paired, individually fed, heifers (6 control and 6 TI heifers; approximately 1 yr of age) for 28 d and used to estimate dry matter digestibility. On days 105 and 240 ruminal fluid (approximately 900 mL) was collected from every animal using a stomach pump and analyzed for short-chain fatty acids (SCFA). After approximately 287 d on feed, heifers were transported to a USDA-inspected abattoir and harvested. TI heifers had lighter final BW (P &lt; 0.04) when compared to control heifers. Average daily gain was greater (P &lt; 0.01) in control compared to TI heifers. TI heifers had a 2.2% lesser (P &lt; 0.05) apparent dry matter digestibility, lighter (P &lt; 0.01) hot carcass weights, but similar ruminal SCFA compared to controls. Blood glucose concentrations were similar (P &gt; 0.8) between control and TI heifers. Ceruloplasmin activity (P &lt; 0.03) and the oxidized form of glutathione (GSSG; P &lt; 0.01), indicators of chronic inflammation, were increased in plasma from TI heifers compared to controls. Other indicators of oxidative stress were not impacted (P &gt; 0.10) by TI status. These data suggest that fetal BVDV transient infection negatively impacts growth throughout the feeding period, possibly by impacting gastrointestinal tract function and increasing systemic inflammation.
Topical steroid use for suppression of hypergranulation in burns: Trends across the Atlantic
Authors: Shoham Yoram , Comish Paul , Tsur Rotem , Silberstein Eldad , Krieger Yuval , Eliav Tal , Cleary Michelle , Kornhaber Rachel , Goverman Jeremy 
Published: October 2024

Abstract
Hypergranulated wounds from thermal injury remain a complex and debilitating problem for burn patients. Currently, there is no standard therapy to prevent or treat hypergranulation following burn injury. Many centers use topical corticosteroids; however, their use seems to be geographically dependent and controversial. The primary aim of this study was to quantify the current use of topical corticosteroids for post-burn hypergranulation in North America (NA) and Europe, while secondarily assessing for perceptions of safety and efficacy. We designed a survey that was distributed to the members of the European and American Burn Associations. Data was extracted and analyzed using SPSS software. A total of 165 respondents completed the survey (90 and 75 for the European and NA members, respectively). Seventy-one of the 90 (78.9%) European respondents reported they routinely use topical steroids for suppression of hypergranulation tissue in burns, versus 25 of the 75 (33.3%) NA respondents (p&lt;0.001). European respondents, compared to NA respondents, were significantly more likely to consider topical steroid use safe (100% vs. 74.4%, p &lt;0.001) and effective (98.6% vs. 66.7%, p &lt; 0.001) for treatment of hypergranulated burn wounds. There was no significant difference in reported systemic effects seen after topical steroid use when comparing NA respondents and European respondents (6.5% vs. 6.9%, p &gt; 0.10). The results of this study suggest that the use of steroids for hypergranulation tissue in burn care is more prevalent in Europe than NA, which may be due to discordant views on safety and efficacy despite minimal reported adverse effects.
Use digital rock physics to characterize velocity and attenuation signatures of deep cavity-fracture carbonate reservoirs
Authors: Liu Weihua , Zhao Luanxiao , Qiu Xuangan , Wang Yirong , Wang Yang , Zhu Wei 
Published: October 2024

Abstract
Conventional rock physics experiments and well logging analyses face challenges in deep carbonate formation containing meter-scale cavity-fracture system, since it is unfeasible to extract representative samples from targeted formation. In this study, differing from the conventional digital rock models at the core scale, we construct a digital rock model from realistic outcrop images with meter-scale heterogeneity of cavities and fractures. Using a dynamic stress–strain simulation, we investigate how reservoir type, fracture density and spacing, cavity porosity and size, fluid saturation, and connectivity influence wave dispersion and attenuation. By selecting the simulation frequency of 0.3 MHz approximately corresponding to the field seismic measuring frequency of 30 Hz, the simulation results can reflect the realistic seismic velocity and attenuation characteristics of deep carbonate reservoir rocks. We find that the P-wave velocity decreases linearly with increasing fracture and cavity porosity. The P-wave attenuation is sensitive to variations in fracture density but shows limited sensitivity to changes in cavity porosity and size. Fractures with narrower spacing result in higher attenuation when fracture density remains constant. Deep carbonate rocks with cavity-fracture systems saturated with two immiscible fluids display enhanced attenuation compared to fully saturated conditions. The velocity demonstrates an almost linear increase with water saturation, while attenuation initially increases before decreasing at a peak water saturation of 70%–80%. The connectivity between fractures and cavities significantly influences the attenuation behavior. Our simulation results provide valuable guidance for seismic data processing and interpretation of deep carbonate reservoir rocks with cavity-fracture systems.
Low-grade postoperative spine infection with a history of oral cavity infections: think of Peptoniphilus asaccharolyticus
Authors: Zygogiannis Konstantinos , Pappa Eleni , Antonopoulos Spiridon , Chatzikomninos Ioannis , Kalampokis Anastasios 
Published: October 2024

Abstract
Peptoniphilus asaccharolyticus is a typical gram-positive commercial microorganism of the skin that depending on the occasion can also be detected in the gut and in the genitourinary system. There is a paucity in the literature regarding the role of P. asaccharolyticus in spine infections and the potential impact in postoperative implications. A case report of a patient suffering from infection of spinal instrumentation of the uncommon pathogen above is presented.
Sensitization of melanoma cells to standard chemotherapy: G-quadruplex binders as synergistic agents
Authors: Persico Carolina , Iaccarino Nunzia , Romano Francesca , Giustiniano Mariateresa , Russo Camilla , Laneri Sonia , Di Lorenzo Ritamaria , Aiello Immacolata , Abate Sara , Izzo Luana , Merlino Francesco , Brancaccio Diego , Pagano Bruno , Amato Jussara , Marzano Simona , D’Aria Federica , De Tito Stefano , Di Porzio Anna , Randazzo Antonio 
Published: October 2024

Abstract
The use of chemotherapeutics has achieved considerable success in cancer therapy; however, their toxicity can severely impact patients’ health. In this study, aiming to reduce the doses and potential side effects of traditional chemotherapeutics, we systematically treated A375MM human melanoma cells with seven clinically approved antineoplastic drugs, in combination with three well-characterized G-quadruplex (G4) ligands, using either simultaneous or sequential dosing schedules. Interestingly, the G4 binders synergized with most of the investigated anticancer drugs, with the degree of synergism being strictly dependent on both the treatment schedule and the drug sequence employed. Notably, some of the synergistic combinations showed selective toxicity toward melanoma cells over nontumorigenic human keratinocytes. Furthermore, immunofluorescence experiments highlighted the potential implication of G4 structures in the molecular mechanisms driving the synergistic interaction between some chemotherapeutics and G4 binders. Overall, our systematic study supports the combination of G4-interacting molecules with standard antineoplastic drugs as a promising antitumor strategy.
CAF to the Rescue! Potential and Challenges of Combination Antifungal Therapy for Reducing Morbidity and Mortality in Hospitalized Patients With Serious Fungal Infections
Authors: Jacobs Samantha E , Chaturvedi Vishnu 
Published: October 2024

Abstract
The global burden of invasive fungal disease is substantial and escalating. Combination antifungal therapy (CAF) may improve patient outcomes by reducing development of resistance, improving drug penetration and rate of fungal clearance, and allowing for lower and less toxic antifungal drug doses; yet, increased cost, antagonism, drug-drug interactions, and toxicity are concerns. Clinical practice guidelines recommend antifungal monotherapy, rather than CAF, for most invasive fungal diseases due to a lack of comparative randomized clinical trials. An examination of the existing body of CAF research should frame new hypotheses and determine priorities for future CAF clinical trials. We performed a systematic review of CAF clinical studies for invasive candidiasis, cryptococcosis, invasive aspergillosis, and mucormycosis. Additionally, we summarized findings from animal models of CAF and assessed laboratory methods available to evaluate CAF efficacy. Future CAF trials should be prioritized according to animal models showing improved survival and observational clinical data supporting efficacy and safety.
Real-world effectiveness of palbociclib plus endocrine therapy in HR+/HER2− advanced breast cancer: final results from the POLARIS trial
Authors: Tripathy Debu , Blum Joanne L , Karuturi Meghan S , McCune Steven , Kurian Sobha , Moezi Mehdi , Anderson Daniel , Gauthier Eric , Zhang Zhe , Montelongo Monica Z , Wang Yao , Rocque Gabrielle B 
Published: October 2024

Abstract

Background
Strict eligibility criteria for participation in randomized clinical trials (RCTs) often limit the generalizability of data when applied to a more heterogeneous real-world population. Thus, evidence generated directly from real-world populations, including subgroups underrepresented in RCTs, can help inform routine clinical practice. POLARIS (NCT03280303), a prospective, observational, multicenter, cohort study, evaluated patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2−) advanced breast cancer (ABC) receiving palbociclib + endocrine therapy (ET) in routine care.

Methods
Demographics, baseline characteristics, and treatment patterns were summarized descriptively. Real-world response and clinical benefit rates, real-world progression-free survival (rwPFS), and overall survival (OS) were summarized descriptively by line of therapy and endocrine partner in the overall cohort and various subgroups.

Results
Between January 2017 and October 2019, 1250 patients (median age of 64.0 years) initiated treatment with palbociclib-based therapy, including 901 in the first-line (1L) setting and 349 in the second-line or later (≥2L) settings. Real-world response and clinical benefit rates with palbociclib + ET were 34.0% and 69.4%, respectively, in 1L, and 21.8% and 57.9% in ≥2L. Median rwPFS was 20.9 (95% CI, 18.7-24.7) and 13.5 (10.6-17.1) months, and median OS was 48.5 (42.0-not estimable) and 37.2 (31.2-40.8) months, with 1L and ≥2L palbociclib + ET, respectively.

Conclusions
Outcomes in this large, heterogeneous, real-world population are generally consistent with previously reported results from clinical trials and other real-world studies, further supporting the use of palbociclib + ET in patients with HR+/HER2− ABC.

Trial registration
NCT03280303 (ClinicalTrials.gov).
Using native and synthetic genes to disrupt inositol pyrophosphates and phosphate accumulation in plants
Authors: Freed Catherine , Craige Branch , Donahue Janet , Cridland Caitlin , Williams Sarah Phoebe , Pereira Chris , Kim Jiwoo , Blice Hannah , Owen James , Gillaspy Glenda 
Published: October 2024

Abstract
Inositol pyrophosphates are eukaryotic signaling molecules that have been recently identified as key regulators of plant phosphate sensing and homeostasis. Given the importance of phosphate to current and future agronomic practices, we sought to design plants, which could be used to sequester phosphate, as a step in a phytoremediation strategy. To achieve this, we expressed diadenosine and diphosphoinositol polyphosphate phosphohydrolase (DDP1), a yeast (Saccharomyces cerevisiae) enzyme demonstrated to hydrolyze inositol pyrophosphates, in Arabidopsis thaliana and pennycress (Thlaspi arvense), a spring annual cover crop with emerging importance as a biofuel crop. DDP1 expression in Arabidopsis decreased inositol pyrophosphates, activated phosphate starvation response marker genes, and increased phosphate accumulation. These changes corresponded with alterations in plant growth and sensitivity to exogenously applied phosphate. Pennycress plants expressing DDP1 displayed increases in phosphate accumulation, suggesting that these plants could potentially serve to reclaim phosphate from phosphate-polluted soils. We also identified a native Arabidopsis gene, Nucleoside diphosphate-linked moiety X 13 (NUDIX13), which we show encodes an enzyme homologous to DDP1 with similar substrate specificity. Arabidopsis transgenics overexpressing NUDIX13 had lower inositol pyrophosphate levels and displayed phenotypes similar to DDP1-overexpressing transgenics, while nudix13-1 mutants had increased levels of inositol pyrophosphates. Taken together, our data demonstrate that DDP1 and NUDIX13 can be used in strategies to regulate plant inositol pyrophosphates and could serve as potential targets for engineering plants to reclaim phosphate from polluted environments.
The structure of a Tau fragment bound to tubulin prompts new hypotheses on Tau mechanism and oligomerization
Authors: Ammar Khodja Liza , Campanacci Valérie , Lippens Guy , Gigant Benoît 
Published: October 2024

Abstract
Tau is a protein involved in the regulation of axonal microtubules in neurons. In pathological conditions, it forms filamentous aggregates which are molecular markers of neurodegenerative diseases known as tauopathies. Structures of Tau in fibrils or bound to the microtubule have been reported. We present here a structure of a Tau construct comprising the PHF6 motif, an oligopeptide involved in Tau aggregation, as a complex with tubulin. This Tau fragment binds as a dimer to a new site which, when transposed to the microtubule, would correspond to a pore between protofilaments. These results raise new hypotheses on Tau-induced microtubule assembly and stabilization and on Tau oligomerization.
Extremal Rotating BTZ Black Holes Cannot Be Dressed in (anti-)Self-Dual Maxwell Field
Authors: Maeda Hideki , Podolský Jiří 
Published: October 2024

Abstract
Under the (anti-)self-dual condition for orthonormal components of the Faraday tensor, the 3D Einstein–Maxwell system with a negative cosmological constant $\Lambda$ admits a solution obtained by Kamata and Koikawa and later by Cataldo and Salgado in the most general form. Actually, Clément first obtained this solution and interpreted it as a regular particle-like solution without horizon. Nevertheless, it has been erroneously stated in some literature that this Clément–Cataldo–Salgado (CCS) solution, locally characterized by a single parameter, describes a black hole even in the charged case as it reduces to the extremal rotating Bañados–Teitelboim–Zanelli (BTZ) solution in the vacuum limit and its curvature invariants are constant. In this paper, we supplement Clément’s interpretation by showing that there appears a parallelly propagated curvature singularity corresponding to an infinite affine parameter along spacelike geodesics at the location of the Killing horizon in the extremal rotating BTZ solution when the (anti-)self-dual Maxwell field is added. If the spatial coordinate $\theta$ is periodic, closed timelike curves exist near the singularity. It is also shown that the CCS solution is of Cotton type N (in contrast to charged rotating BTZ black holes which are of type I away from the horizon), and the energy-momentum tensor of the Maxwell field is of Hawking–Ellis type II. The metric solves the Einstein-$\Lambda$ equations also with a massless scalar field or a null dust fluid. We explicitly demonstrate that it belongs to the Kundt shear-free, nontwisting, and nonexpanding class of geometries, whereas extremal rotating BTZ black holes have expanding principal null directions. It means that the CCS metric represents the specific null (i.e. “radiative”) Maxwell field generated by a singular source, rather than an extremal rotating BTZ black hole dressed in an (anti-)self-dual Maxwell field.