bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high copy suppressor screen identifies factors enhancing the allotopic production of subunit II of cytochrome c oxidase
Authors: Nieto-Panqueva Felipe , Vázquez-Acevedo Miriam , Barrera-Gómez David F , Gavilanes-Ruiz Marina , Hamel Patrice P , González-Halphen Diego 
Published: December 2024

Abstract
Allotopic expression refers to the artificial relocation of an organellar gene to the nucleus. Subunit 2 (Cox2) of cytochrome c oxidase, a subunit with 2 transmembrane domains (TMS1 and TMS2) residing in the inner mitochondrial membrane with a Nout-Cout topology, is typically encoded in the mitochondrial cox2 gene. In the yeast Saccharomyces cerevisiae, the cox2 gene can be allotopically expressed in the nucleus, yielding a functional protein that restores respiratory growth to a Δcox2 null mutant. In addition to a mitochondrial targeting sequence followed by its natural 15-residue leader peptide, the cytosol synthesized Cox2 precursor must carry one or several amino acid substitutions that decrease the mean hydrophobicity of TMS1 and facilitate its import into the matrix by the TIM23 translocase. Here, using a yeast strain that contains a COX2W56R gene construct inserted in a nuclear chromosome, we searched for genes whose overexpression could facilitate import into mitochondria of the Cox2W56R precursor and increase respiratory growth of the corresponding mutant strain. A COX2W56R expressing strain was transformed with a multicopy plasmid genomic library, and transformants exhibiting enhanced respiratory growth on nonfermentable carbon sources were selected. We identified 3 genes whose overexpression facilitates the internalization of the Cox2W56R subunit into mitochondria, namely: TYE7, RAS2, and COX12. TYE7 encodes a transcriptional factor, RAS2, a GTP-binding protein, and COX12, a non-core subunit of cytochrome c oxidase. We discuss potential mechanisms by which the TYE7, RAS2, and COX12 gene products could facilitate the import and assembly of the Cox2W56R subunit produced allotopically.
High-resolution GPU-based simulations of quasi-static poroelasticity: seismic attenuation and modulus dispersion in three-dimensional stochastic fracture networks
Authors: Alkhimenkov Yury 
Published: December 2024

SUMMARY
Fractures significantly impact the elastic and hydraulic properties of geological structures, influencing fields like geothermal energy, hydrocarbon exploration, nuclear waste disposal and $\mathrm{ \mathrm{CO}}_2$ storage. Characterizing these formations is challenging due to the scale disparity between seismic wavelengths and fracture sizes. This study leverages decades of analytical and numerical advancements to evaluate the effective mechanical properties of fractured solids at the mesoscopic scale. A novel numerical method for modelling quasi-static Biot’s poroelastic equations using graphics processing units (GPUs) is introduced for simulating hydromechanically coupled systems. Capable of handling up to 133 million voxel elements on a single GPU, this method offers unprecedented spatial resolution to model complex fracture networks. The GPU-accelerated solver, FastBiot_QS, delivers exceptional performance, achieving a computational speedup of approximately 520 times compared to central processing unit-based methods. The solver’s accuracy is rigorously validated in 1-D and 3-D setups. Simulations reveal that fracture clustering and spatial distribution significantly affect seismic attenuation and modulus dispersion. Clusters of interconnected fractures lead to higher attenuation at higher frequencies, while sparsely distributed fractures result in higher attenuation at lower frequencies. Simulations with log-normal and uniform distributions present intermediate behaviours between densely clustered and sparsely distributed fractures. The study can improve interpretations of seismic data and hydraulic properties in fractured media.
Gender and Sex Differences in Abdominal Pain, Fatigue, And Psychological Symptoms Among Adults with Inflammatory Bowel Disease: A Network Analysis
Authors: Kamp Kendra , Yang Pei-Lin , Tsai Chi-Shan , Zhang Xiaoyu , Yoo Linda , Altman Molly R , Heitkemper Margaret , Conley Samantha , Kane Sunanda , Winders Samantha 
Published: December 2024

Abstract

Background and Aims
Individuals with inflammatory bowel disease (IBD) experience a high symptom burden, including abdominal pain, fatigue, anxiety, depression, and sleep disturbances; yet, little is known regarding the relationship between sex and gender on symptoms. We sought to report symptom severity for cisgender men, cisgender women, and transgender and gender-diverse (TGD) individuals. In addition, we used network analysis to identify core symptoms and explore if symptoms and their relationships differ between cisgender men and cisgender women.

Methods
This was a cross-sectional study. We recruited adults with IBD online through ResearchMatch. Individuals responded to Patient-Reported Outcomes Measurement Information symptom questionnaires, as well as demographic and clinical questionnaires. Network analysis was used to identify the core symptoms driving the symptom structure.

Results
One-hundred and fifty-seven (63.3%) participants identified as cisgender women, 84 (33.9%) as cisgender men, and 7 (2.8%) as TGD. Cisgender men (M = 61.8) and TGD (M = 61.3) groups reported higher abdominal pain levels compared with cisgender women (M = 57.8; P = .02). Transgender and gender-diverse individuals reported higher depression levels (M = 64.8) compared with cisgender men (M = 56.7) and cisgender women (M = 54.4; P = .01). Using a network analysis approach, anxiety and fatigue emerged as core symptoms for the entire sample (clinically active and inactive disease), and among only those with active clinical disease. Fatigue was a top core symptom for cisgender women; anxiety emerged as a top core symptom for cisgender men.

Conclusions
This study highlights that fatigue and anxiety are core symptoms among individuals with IBD and demonstrates a potential sex and/or gender difference in core symptoms. Replication of this study is needed with further consideration of inclusion of TGD patients.
Estimating Standard-Dose and High-Dose Fluzone Vaccine Efficacies for Influenza A Based on Hemagglutination Inhibition Titers
Authors: Hammerton Savannah M , Billings W Zane , Hemme Hayley , Ross Ted M , Shen Ye , Handel Andreas 
Published: December 2024

Abstract

Background
The high-dose (HD) Fluzone influenza vaccine is recommended for individuals aged ≥65 years due to its improved antibody responses and vaccine efficacy (VE) over the standard-dose (SD) formulation. Since influenza vaccines are frequently reformulated, monitoring VE changes is crucial. Traditional efficacy trials are costly and time-consuming, but immunogenicity studies using hemagglutination inhibition (HAI) titers—a reliable correlate of protection—can be used to estimate VE more efficiently.

Methods
We analyzed data from a human vaccine cohort who received either the SD or HD Fluzone split-inactivated influenza vaccine during influenza seasons 2013–2014 to 2021–2022. We used a previously developed statistical model to map pre- and postvaccination HAI titers to protection probabilities, and computed differences in VE of the HD vaccine in older (≥65 years) populations compared to SD vaccines in the same age group and in younger (&lt;65 years) adults.

Results
We found that the HD vaccine generally improved the estimated VE in older adults. We also found that HD recipients often had a lower estimated VE than younger SD recipients.

Conclusions
While HD vaccines lead to a small increase in estimated VE compared to SD in older adults, further increases in dose or other developments to improve VE should be considered.
Protracted Tuberculosis Outbreak in a Pasifika Diaspora in Western Sydney, Australia: The Importance of Community Engagement
Authors: Koirala Archana , Smith Katherine , Britton Philip N , Howard-Jones Annaleise R , Sintchenko Vitali , Donnan Ellen J , Ulbricht Evan , Martinez Elena , Toma Reta , Marais Ben J 
Published: December 2024

Abstract
A prolonged tuberculosis outbreak, linked by whole-genome sequencing, occurred in a Pasifika extended family over 10 years (2013–2022) in Sydney, Australia. Despite Australia's low tuberculosis incidence, social and cultural complexities, and coronavirus disease 2019 (COVID-19) disruptions exacerbated transmission. Control required culturally sensitive, family-centered care and robust health system engagement.
Multi-Devotionalism and Mono-Devotionalism: Beyond the Problems of Polytheism and Monotheism
Authors: Hedges Paul 
Published: December 2024

ABSTRACT
It is argued that the terms polytheism and monotheism are both problematically rhetorical and analytically weak, while they are typically applied in essentializing ways. Noting the history of these terms, especially in relation to such terms as idolatry, this article makes the argument that more analytical language is needed. The terms mono-devotionalism and multi-devotionalism are introduced, not as replacements, but as a reconceptualization. Pointing to trends and tendencies within traditions, it is argued that this pair of terms provides a preferable way to talk about how singular or multiple ends, modes of devotion, and practices may occur both within and across traditions. Particular attention is paid to Christianity and Hinduism as traditions intimately bound up with the history of how the terms monotheism and polytheism have been deployed.
Safety, tolerability and pharmacokinetics of subcutaneous cefazolin as an alternative to intravenous administration
Authors: Murray Fionnuala , Yoo Okhee , Brophy-Williams Samuel , Rawlins Matthew , Wallis Steven C , Roberts Jason A , Raby Edward , Salman Sam , Manning Laurens 
Published: December 2024

Abstract

Background
Subcutaneous (SC) administration of antibiotics is a practical alternative to IV administration. Cefazolin is widely used for skin and soft tissue infections and other complex infections by IV administration.

Methods
In this prospective, cross-over self-controlled study, a single dose of SC cefazolin was administered to 15 stable inpatients established on IV cefazolin as part of their management plan. The equivalent dose of cefazolin was diluted in 50 mL of normal saline via gravity feed over 30 min. Venous blood samples were collected at baseline and 0.5, 1, 2, 4 and 8 h following both the SC and IV doses. Antibiotic concentrations were measured using UPLC-MS/MS. Pharmacokinetic data were analysed using a non-linear mixed-effects modelling approach. Pain scores and infusion site reactions (oedema/erythema) were evaluated.

Results
SC cefazolin was well tolerated. The bioavailability of SC administration was 74.8% (95% CI 66.7%–81.7%). Slower absorption from SC tissue was associated with a BMI of ≥30. Lower peak, and higher trough concentrations were observed with SC administration. Although lower bioavailability was observed with SC administration, the PTA for unbound drug concentrations greater than the MIC for more than 90% of the time between doses was higher for SC compared with IV administration at MICs between 0.25 and 4 mg/L. Simulated SC doses of 3 g twice daily had similar PTA to standard IV dosing of 2 g three times daily. A simulated 6 g continuous 24 h infusion of SC cefazolin had a favourable pharmacokinetic profile.

Conclusion
SC cefazolin appears to be well tolerated, with an improved pharmacokinetic profile compared with IV administration. Either 3 g twice daily, or 6 g as a 24 h SC infusion could be considered for future evaluation.
Patterns of genotype-specific interactions in an obligate host-specific insect pathogenic fungus
Authors: Edwards Sam , Naundrup Andreas , Becher Paul G , De Fine Licht Henrik H 
Published: December 2024

Abstract
Host–pathogen infections and possible effects on co-evolutionary patterns depend on the genotypes of both host and pathogen. Obligate fungal pathogens of plants are often characterized by host–pathogen genotype-by-genotype (GxG) interactions, but whether these patterns exist in obligate insect fungal pathogens is unclear. We take advantage of the obligate insect pathogenic fungus Entomophthora muscae, where individual isolates are specific to different dipteran host species in nature but can cross-infect multiple fly species in the laboratory. We collected three new isolates of E. muscae from Drosophila species. Phylogenetic analysis showed that Drosophila-isolated E. muscae represents a distinct geographically widespread Drosophila lineage compared to the house fly (Musca domestica) or Delia species-isolated E. muscae. We used the three new E. muscae isolates from Drosophila spp. together with a genetically distinct E. muscae isolate from house flies and assessed their virulence in a cross-infection experiment using one house fly, three Drosophila suzukii, and two D. melanogaster genotypes as hosts. All fungal isolates successfully infected hosts, induced behavioural manipulation, sporulated in all fly hosts, and differed in virulence between host genotypes, revealing GxG interactions. While house flies were most susceptible to fungal infection with 99% mortality, we found a lower virulence of 49% and 25% mortality in D. melanogaster and D. suzukii genotypes, respectively. Furthermore, all isolates harboured a specific mycovirus (family Iflaviridae), but co-phylogenetic branching patterns did not support fungus–virus co-speciation. We show that the genetic makeup of both fungal pathogen and fly host influence E. muscae infectivity, confirming GxG interactions in obligate fly fungal pathogens.
Cold storage of Ganaspis kimorum (Hymenoptera: Figitidae) immature stages for optimized classical biological control of Drosophila suzukii (Diptera: Drosophilidae)
Authors: Lisi Fabrizio , Biondi Antonio , Hogg Brian N , Rossi Stacconi Marco Valerio , Wang Xingeng , Daane Kent M 
Published: December 2024

Abstract
Programs to mass rear and release Ganaspis kimorum Buffington (Hymenoptera: Figitidae) are ongoing in many countries to manage its host Drosophila suzukii (Matsumura) (Diptera: Drosophilidae). To optimize parasitoid production and synchronize field releases with pest outbreaks, we investigated a cold storage protocol by exposing different immature G. kimorum stages to 2 storage temperatures (10 or 15°C) for 2, 4, 6, or 8 wk. We further studied those temperature/exposure time combinations that allowed survival but prevented parasitoid emergence before the end of each cold exposure, or the cold storage suitability (CSS). The impact of cold storage on G. kimorum emergence time, total development time, and emergence rate was then evaluated for temperature/exposure time combinations with CSS &gt; 60%. We also assessed fitness costs in terms of longevity and parasitism rates of emerging parasitoids. Results showed that only G. kimorum larvae and pupae were suitable for cold storage under this methodology. Cold exposure significantly delayed the emergence time and total development time of larvae and pupae, whereas the emergence rate was significantly reduced only for larvae at 10°C for 6 wk. The longevity of emerging male and female parasitoids was significantly reduced when stored cold as larvae, while no effects were reported for the parasitism rate by emerged females. These findings provide new insights into G. kimorum cold sensitivity and offer valuable options to better schedule mass rearing and wasp releases for biological control of D. suzukii.
Prospects for PARG inhibitors in cancer therapy
Authors: Hu Yangchan , Meng Yuxin , Zhuang Zirui , Li Yuancong , Nan Junjun , Xu Ning , Ye Zu , Jing Ji 
Published: December 2024

Abstract
Poly(ADP-ribose) glycosylhydrolase (PARG) is an enzyme involved in hydrolyzing the ribose–ribose bonds present in poly(ADP-ribose) (PAR), which are primarily found in the nucleus. Along with poly(ADP-ribose) polymerase (PARP), PARG regulates the level of PAR in cells, playing a crucial role in DNA maintenance and repair processes. Recent studies have revealed elevated levels of PARG in various cancers, such as breast, liver, prostate, and esophageal cancers, indicating a link to unfavorable cancer outcomes. PARG is a significant molecular target for treating PAR-related cancers. This review provides a comprehensive overview of the physiological role of PARG and the development of its inhibitors, highlighting its potential as an innovative target for cancer treatment.
Competence by default: do listeners assume that speakers are knowledgeable when computing conversational inferences?
Authors: Bale Alan , Noguchi Hisako , Rolland Marguerite , Barner David 
Published: December 2024

Abstract
When engaged in conversation, do listeners make default assumptions about the epistemic states of speakers? According to some accounts, when listeners hear a sentence like “Sarah solved some of the math problems,” they infer by default that speakers believe that the stronger statement involving “all” is false (i.e. that Sarah did not solve all of the problems). However, drawing on tests of reading time, eye tracking, and manipulations of cognitive load, multiple studies have argued that this form of inference (i.e. strong scalar implicature) is not computed by default. In this study, while acknowledging this claim, we explore whether important subprocesses of implicature might nevertheless involve default inferences. In particular, we tested whether listeners assume by default that speakers are knowledgeable about alternative utterances that are left unsaid—a critical precondition for computing strong scalar implicatures. To do this, we tested 60 English-speaking participants who heard utterances made by either knowledgeable speakers or ignorant speakers. In addition, half of these participants were placed under cognitive load using a dot-array memory task. We found that participants placed under load over-computed implicatures when speakers were ignorant, as though assuming that they were knowledgeable by default.
Comprehensive surgical management of a severe 270-degree circumferential penetrating neck injury from an industrial accident: a case report
Authors: Jaber Jana , Al Jebawi Kholoud , Nasrallah Jamil , Al Shoufy Mira , Mehta Shubh , Hashim Hashim Talib , AL-Mukhtar Mahmoud Mussleh 
Published: December 2024

Abstract
Penetrating neck injury (PNI), involving disruption of the platysma muscle, accounts for 10% of trauma cases and poses significant morbidity and mortality risks. This case report details the management of a 45-year-old male who sustained a 270-degree circumferential neck incision from an industrial accident. The patient presented with a deep neck laceration, severe blood loss, and hypovolemic shock. Pre-hospital care included intubation, oxygen supplementation, and fluid resuscitation. At the hospital, under general anesthesia, surgical interventions involved ligation of posterior neck vessels, hemostasis, muscle repair with Vicryl 1–0, drainage tube placement, and skin closure. Postoperative care included intensive monitoring, neurological assessments, and pain management. Effective management of severe PNI requires a multidisciplinary approach, combining prompt pre-hospital care, meticulous surgical techniques, and comprehensive postoperative management. Future research should focus on standardizing PNI management protocols and advancing surgical and diagnostic techniques to improve outcomes in similar critical cases.
Alleviation of Helicobacter pylori- or aspirin-induced gastritis and neuroinflammation in mice by Lactococcus lactis and Bifidobacterium longum
Authors: Shin Jung-Woo , Shin Yoon-Jung , Lee Dong-Yun , Kim Dong-Hyun 
Published: December 2024

Abstract
Helicobacter pylori (HP) causes gastritis and peptic ulcer. Therefore, we examined whether probiotics Lactococcus lactis P135 and Bifidobacterium longum P142, which inhibited HP growth by 37.9% and 35.3%, respectively, and HP-induced IL-8 expression in KATO III cells by 68.6% and 63.1%, respectively, compared to those of normal controls, could mitigate HP-induced gastritis and psychiatric disorder in mice. Oral administration of P135 and/or P142 alleviated HP- or aspirin-induced gastritis, colitis, neuroinflammation, and depression/cognitive impairment-like behavior. They also suppressed HP infection, neutrophil infiltration, and NF-κB activation in the stomach and TNF-α expression and NF-κB activation in the colon and hippocampus. of P135 and/or P142 alleviated HP- or aspirin-induced gut dysbiosis: they decreased Lachnospiracease, Helicobacteriaceae, and Akkermansiaceae populations and increased Bacteroidaceae and Muribaculaceae populations. These findings suggest that HP growth/inflammation-inhibitory P135 and/or P142 may alleviate gut inflammation (gastritis and colitis) and neuroinflammation through the suppression of neutrophil infiltration, NF-κB activation, and HP growth, thereby leading to the attenuation of systemic inflammation and psychiatric disorder.
Bioremediation of polyaromatic hydrocarbon polluted sewage sludge soil employing a bacterial consortium and phytotoxicity evaluation
Authors: Khan Gulfishan , Tiwari Anshul , Patel Devendra K , Anbumani Sadasivam , Manickam Natesan 
Published: December 2024

Abstract
A consortium of five distinct bacterial strains was evaluated for their ability to biodegrade multiple polyaromatic hydrocarbons (PAHs) in sewage sludge under microcosm studies. The presence of PAHs was determined from the sludge samples collected during pre- and post-monsoon seasons from three different wastewater treatment plants (WWTPs). Among the 16 PAHs found, the lowest concentration detected was 1.75 ng g−1 of benz(k)fluoranthene, and the highest concentration of 5.41 mg g−1 indeno(1,2,3-cd) pyrene was found in both dry and wet samples, perhaps owing to its multiple origin of contamination. A bacterial consortium comprising of well characterized bacteria Stenotrophomonas maltophilia IITR87, Ochrobactrum anthropi IITR07, Microbacterium esteraromaticum IITR47, Pseudomonas aeruginosa IITR48, and Pseudomonas mendocina IITR46 employed for PAHs bioremediation in a microcosm study. In 20 days, 65%–70% of PAHs were remediated, and low molecular weight PAHs such as naphthalene, phenanthrene, and pyrene showed enhanced degradation. Bioremediated samples showed a significant reduction in phytotoxicity using plant germination of wheat (Triticum aestivum), black chickpea (Cicer arietinum), and mustard (Brassica juncea), whereas the contaminated soil showed severe inhibition of plant growth. The results comprehensively suggest a possible remediation option for PAHs occurring in complex sewage sludge, preventing further contamination into other environmental compartments.