bluuebunny/crossref_metadata_2025_split huggingface dataset:
A low-cost and versatile paramagnetic bead DNA extraction method for
Mycobacterium ulcerans
environmental surveillance
Authors: Lee Jean Y. H. , Porter Jessica L. , Hobbs Emma C. , Whiteley Pam , Buultjens Andrew H. , Stinear Timothy P. 
Published: September 2024

ABSTRACT

In Australia, native possums are a major wildlife reservoir for
Mycobacterium ulcerans
, the causative agent of the neglected tropical skin disease Buruli ulcer (BU). Large-scale possum excreta surveys that use PCR to detect
M. ulcerans
in 100–1,000 s of excreta specimens are an important tool that can inform geospatial modeling and predict locations of future human BU risk. However, the significant expense of commercial kits used to extract DNA from specimens is a major barrier to routine implementation. Here, we developed a low-cost method for DNA extraction from possum excreta, possum tissue, and pure mycobacterial cultures, using a guanidinium isothiocyanate lysis solution and paramagnetic beads. In a 96-well plate format for high-throughput processing, the paramagnetic bead DNA extraction method was threefold less sensitive but only 1/6 the cost of a commonly used commercial kit. Applied to tissue swabs, the method was fourfold more sensitive and 1/5 the cost of a commercial kit. When used for preparing DNA from pure mycobacterial cultures, the method yielded purified genomic DNA with quality metrics comparable to more lengthy techniques. Our paramagnetic bead method is an economical means to undertake large-scale
M. ulcerans
environmental surveillance that will directly inform efforts to halt the spread of BU in Victoria, Australia, with potential for applicability in other endemic countries.

IMPORTANCE

Buruli ulcer (BU) is a neglected tropical skin disease, with an incidence that has dramatically increased in temperate southeastern Australia over the last decade. In southeastern Australia, BU is a zoonosis with native possums the major wildlife reservoir of the causative pathogen,
Mycobacterium ulcerans
. Infected possums shed
M. ulcerans
in their excreta, and excreta surveys using PCR to screen for the presence of pathogen DNA are a powerful means to predict future areas of Buruli ulcer risk for humans. However, excreta surveys across large geographic areas require testing of many thousands of samples. The cost of commercial DNA extraction reagents used for preparing samples for PCR testing can thus become prohibitive to effective surveillance. Here, we describe a simple, low-cost method for extracting DNA from possum excreta using paramagnetic beads. The method is versatile and adaptable to a variety of other sample types including swabs collected from possum tissues and pure cultures of mycobacteria.
Eosinophils respond to, but are not essential for control of an acute
Salmonella enterica
serovar Typhimurium infection in mice
Authors: FitzPatrick Rachael D. , Noone Jonathan R. , Cartwright Richard A. , Gatti Dominique M. , Brosschot Tara P. , Lane Jenna M. , Jensen Erik L. , Kroker Kimber Isabella , Reynolds Lisa A. 
Published: September 2024

ABSTRACT

Eosinophils are a highly abundant cell type in the gastrointestinal tract during homeostatic conditions, where they have recently been reported to take on an activated phenotype following colonization by the bacterial microbiota. To date, there have been few studies investigating whether eosinophils respond to infection with enteric bacterial pathogens and/or investigating the requirements for eosinophils for effective bacterial pathogen control. In this study, we investigated the response of eosinophils to an acute enteric infection of mice with the bacterial pathogen
Salmonella enterica
serovar Typhimurium. We also assessed whether eosinophil deficiency impacted
Salmonella
burdens in the intestinal tract or impacted the systemic dissemination of
Salmonella
following an oral infection of littermate wild-type BALB/cJ and eosinophil-deficient ΔdblGATA BALB/cJ mice. We found comparable
Salmonella
burdens in the intestinal tract of wild-type and eosinophil-deficient mice and no significant differences in the levels of
Salmonella
disseminating to systemic organs within 3 days of infection. Despite our evidence suggesting that eosinophils are not an essential cell type for controlling bacterial burdens in this acute infection setting, we found higher levels of eosinophils in gut-draining lymph nodes following infection, indicating that eosinophils do respond to
Salmonella
infection. Our data contribute to the growing evidence that eosinophils are responsive to bacterial stimuli, yet the influence of and requirements for eosinophils during bacterial infection appear to be highly context-dependent.
Genome of
Dietzia cinnamea
55, a desert-isolated microbe with plant growth-promoting properties for grain crops
Authors: Hirsch Ann M. , Khan Noor , Humm Ethan , Rubbi Mila , Del Vecchio Giorgia , Ha Sung Min , Pellegrini Matteo , Gunsalus Robert P. 
Published: September 2024

ABSTRACT

Here, we report the genome sequence of
Dietzia cinnamea
55, isolated from the Negev Desert, Israel.
D. cinnamea
55 was found to promote the growth of several cereal crops (corn, wheat, and pearl millet) in greenhouse and field studies.
Thirteen draft genome assemblies of
Bacillus
spp. isolated from HLB-impacted citrus trees
Authors: Campos Vieira Flávia , Blacutt Alex , Drozd Christopher , Viravathana Polrit , Ginnan Nichole , Roper M. Caroline 
Published: September 2024

ABSTRACT

We report the draft genome assembly, annotation, and phylogenetic placement of 13
Bacillus
spp. isolates isolated from citrus groves under high (Florida) or low (California) Huanglongbing disease pressure.
Complete genome sequences of 12 lytic phages against multidrug-resistant
Enterococcus faecalis
Authors: Soro Oumarou , Kigen Collins , Nyerere Andrew , Gachoya Moses , Wachira James , Onyonyi Vanessa , Georges Martin , Wataka Allan , Ondolo Stephen , Cherono Karen , Odoyo Erick , Musila Lillian 
Published: September 2024

ABSTRACT

We report the genome sequences of 12
Enterococcus faecalis
phages isolated in Kenya, belonging to the genus
Copernicusvirus
,
Efquatrovirus
,
Saphexavirus
, and
Kochikohdavirus
. They have double-stranded DNA with lengths varying from 17,979 to 147,374 bp and G+C content from 33.14% to 40.05%. The genomes contain 28–250 coding sequences.
The occurrence of
Aerococcus urinaeequi
and non-aureus staphylococci in raw milk negatively correlates with
Escherichia coli
clinical mastitis
Authors: Jung Dongyun , Park Soyoun , Kurban Daryna , Dufour Simon , Ronholm Jennifer 
Published: September 2024

ABSTRACT

Escherichia coli
is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to
E. coli
CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing
E. coli
are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed
E. coli
CM during lactation, including milk from both healthy and diseased quarters (
n
= 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing
E. coli
CM, indicating that
E. coli
displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera,
Staphylococcus
and
Aerococcus
, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera,
Staphylococcus auricularis, Staphylococcus haemolyticus,
and
Aerocussus urinaeequi
, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage
E. coli
colonization without triggering inflammation.

IMPORTANCE

In this study, we show that
E. coli
outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by
S. auricularis, S. haemolyticus, A. urinaeequi,
and
S. marcescens
without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of
E. coli
CM.
A new Re-Os age constraint informs the dynamics of the Great Oxidation Event
Authors: Millikin Alexie E.G. , Uveges Benjamin T. , Izon Gareth , Bauer Ann M. , Summons Roger E. , Evans David A.D. , Rooney Alan D. 
Published: September 2024

Abstract
The early Paleoproterozoic (ca. 2.5–2.2 Ga) represents a critical juncture in Earth history, marking the inception of an oxygenated atmosphere while bearing witness to potentially multiple widespread and severe glaciations. Deciphering the nature of this glacial epoch and its connection with atmospheric oxygenation has, however, proven difficult, hindered by a reliance on disputed stratigraphic correlations given the paucity of direct radiometric age constraints. Nowhere is this more acute than within the South African Transvaal Supergroup: Here, while the loss of oxygen-sensitive mass-independent sulfur isotope fractionation (S-MIF) has been reported from both the Duitschland and Rooihoogte formations, divided opinion surrounding the time-equivalence of these units has prompted authors to argue for vastly different oxygenation trajectories. Addressing this debate, we present a depositional Re-Os age (2443 ± 33 Ma) from diamictite samples preserved in drillcore of the upper Duitschland Formation. The 100-million-year separation between the Duitschland Formation and its previously presumed equivalent reveals at least two isolated disappearances of S-MIF, requiring that the Great Oxidation Event was dynamic and proceeded via discrete oxygenation episodes whose structure remains incompletely understood. Importantly, our revised framework aligns the lower Duitschland diamictite with the low-latitude glacigenic Makganyene Formation, supporting hypotheses of widespread regional, and potentially global, early Paleoproterozoic glaciation.
Training health workers and community influencers to be Vaccine Champions: a mixed-methods RE-AIM evaluation
Authors: Kaufman Jessica , Overmars Isabella , Fong James , Tudravu Jemesa , Devi Rachel , Volavola Litiana , Vodonaivalu Luisa , Jenkins Kylie , Leask Julie , Seale Holly , Mohamed Yasmin , Joshi Kshitij , Datt Halitesh , Sagan Sonya , Dynes Michelle , Hoq Monsurul , Danchin Margie 
Published: September 2024

IntroductionIncreasing trust and confidence in vaccines is a global priority, as countries have grappled with delivering COVID-19 vaccines, maintaining routine childhood vaccination rates and introducing new vaccines. Community-based vaccine promotion interventions are commonly implemented, but effectiveness evidence is limited. In 2022, supported by the Australian Government and in partnership with Fiji’s Ministry of Health and UNICEF, we codesigned, delivered and comprehensively evaluated a vaccine education and communication training programme for health workers and community influencers to promote COVID-19 and routine immunisation.MethodsThe Vaccine Champions programme included three phases: (1) codesign with Fiji stakeholders; (2) vaccine education and communication training for Vaccine Champions and (3) support for Champions to deliver community vaccine discussion sessions over 6 months.The RE-AIM framework evaluation measured programme reach, effectiveness, adoption, implementation and maintenance. Mixed-methods data were collected through interviews, surveys and field notes, integrating qualitative and quantitative data to triangulate findings. Primary outcomes included Champions’ knowledge, communication self-efficacy, trust in COVID-19 vaccines, programme satisfaction and community members’ intention to vaccinate.ResultsWe trained 35 Champions (27/35 female), including health workers, faith and community influencers. Half had a health background (17/35). Champions conducted 54 discussion sessions, reaching 1717 community members. Most Champions (22/35) conducted at least 1 session, with 16 running 3 or more. Champions who did not run sessions reported barriers like lack of confidence and competing duties. Training increased Champions’ communication self-efficacy and trust in COVID-19 vaccines. Community member intention to vaccinate increased from 41% (394/960) to 83% (822/991) before and after a session. The programme was well received with interest in continued engagement.ConclusionTraining health workers and community Vaccine Champions can promote vaccine confidence. Programmes require government support and engagement for sustainability. Robust evaluation frameworks are needed to build the evidence base.
Zongertinib (BI 1810631), an Irreversible HER2 TKI, Spares EGFR Signaling and Improves Therapeutic Response in Preclinical Models and Patients with HER2-Driven Cancers
Authors: Wilding Birgit , Woelflingseder Lydia , Baum Anke , Chylinski Krzysztof , Vainorius Gintautas , Gibson Neil , Waizenegger Irene C. , Gerlach Daniel , Augsten Martin , Spreitzer Fiona , Shirai Yukina , Ikegami Masachika , Tilandyová Sylvia , Scharn Dirk , Pearson Mark A. , Popow Johannes , Obenauf Anna C. , Yamamoto Noboru , Kondo Shunsuke , Opdam Frans L. , Bruining Annemarie , Kohsaka Shinji , Kraut Norbert , Heymach John V. , Solca Flavio , Neumüller Ralph A. 
Published: September 2024

Abstract
Mutations in ERBB2 (encoding HER2) occur in 2% to 4% of non–small cell lung cancer (NSCLC) and confer poor prognosis. ERBB-targeting tyrosine kinase inhibitors, approved for treating other HER2-dependent cancers, are ineffective in HER2-mutant NSCLC due to dose-limiting toxicities or suboptimal potency. We report the discovery of zongertinib (BI 1810631), a covalent HER2 inhibitor. Zongertinib potently and selectively blocks HER2, while sparing EGFR, and inhibits the growth of cells dependent on HER2 oncogenic driver events, including HER2-dependent human cancer cells resistant to trastuzumab deruxtecan. Zongertinib displays potent antitumor activity in HER2-dependent human NSCLC xenograft models and enhances the activities of antibody–drug conjugates and KRASG12C inhibitors without causing obvious toxicities. The preclinical efficacy of zongertinib translates in objective responses in patients with HER2-dependent tumors, including cholangiocarcinoma (SDC4–NRG1 fusion) and breast cancer (V777L HER2 mutation), thus supporting the ongoing clinical development of zongertinib.
Significance: HER2-mutant NSCLC poses a challenge in the clinic due to limited options for targeted therapies. Pan-ERBB blockers are limited by wild-type EGFR–mediated toxicity. Zongertinib is a highly potent and wild-type EGFR–sparing HER2 inhibitor that is active in HER2-driven tumors in the preclinical and clinical settings.
The Political Economy of China’s Presence in Africa
Authors: Bitew Birhanu 
Published: September 2024

Abstract
This paper seeks to examine the political economy of China in Africa to unpack whether this foreign presence represents a miracle or a mirage for the continent. Data was gleaned from books, articles, official documents and the 2021 Afrobarometer Dispatch 489 survey (AD489). The paper argues that China is a rational actor that engages with Africa to advance its national interests. The Chinese presence in Africa has elicited divergent reactions from Africans of different social groups. The non-interference principle of the Beijing Consensus has led African power elites to embrace China as a reliable partner. Yet, the reactions of local Africans are mixed. While some applaud China’s contributions to infrastructure development, others criticise it for employing debt-trap diplomacy to assert hegemonic dominance on the continent, exploit African labour and extract resources. The criticism from Africans has led China to attempt to formulate corporate social responsibility policies, establish environmentally sustainable industries and ensure favourable working conditions.
Deep Circulation Variability through the Eastern Subpolar North Atlantic
Authors: Li Feili , Fu Yao , Lozier M. Susan , Le Bras Isabela A. , de Jong M. Femke , Wang Yuan , Sanchez-Franks Alejandra 
Published: September 2024

Abstract
The export of the North Atlantic Deep Water (NADW) from the subpolar North Atlantic is known to affect the variability in the lower limb of the Atlantic meridional overturning circulation (AMOC). However, the respective impact from the transport in the upper NADW (UNADW) and lower NADW (LNADW) layers, and from the various transport branches through the boundary and interior flows, on the subpolar overturning variability remains elusive. To address this, the spatiotemporal characteristics of the circulation of NADW throughout the eastern subpolar basins are examined, mainly based on the 2014–20 observations from the transatlantic Overturning in the Subpolar North Atlantic Program (OSNAP) array. It reveals that the time-mean transport within the overturning’s lower limb across the eastern subpolar gyre [−13.0 ± 0.5 Sv (1 Sv ≡ 106 m3 s−1)] mostly occurs in the LNADW layer (−9.4 Sv or 72% of the mean), while the lower limb variability is mainly concentrated in the UNADW layer (57% of the total variance). This analysis further demonstrates a dominant role in the lower limb variability by coherent intraseasonal changes across the region that result from a basinwide barotropic response to changing wind fields. By comparison, there is just a weak seasonal cycle in the flows along the western boundary of the basins, in response to the surface buoyancy-induced water mass transformation.
Mid-term outcomes of different treatments of internal iliac artery in endovascular aneurysm repair
Authors: Ji Jie , Bi Jiaxue , Chen Yonghui , Zhang Xiaoxing , Zhao Bin , Liang Hao , Fan Jibo , Dai Xiangchen 
Published: September 2024

Objective To evaluate the mid-term outcomes of different treatment strategies for the internal iliac artery (IIA) during EVAR. Methods This was a retrospective study. All patients undergoing EVAR, who required treatment of at least one side of IIA from January 2013 to July 2022 in a single center, were included. According to the different treatment strategies for IIA, the patients were divided into UP (unilateral preservation), BP (bilateral preservation) and BE (bilateral embolization) groups. The primary outcomes included buttock claudication, bowel ischemia and iliac-related reintervention. Then patients who underwent IIA reconstruction were divided into IPG (iliac parallel stent graft) and IBG (iliac branch stent graft) groups according to the reconstruction technique. The primary outcomes included endoleak, iliac branch occlusion and iliac-related reintervention. Results A total of 237 patients were included, including 167 in the UP group, 9 in the BP group and 61 in the BE group. The mean follow-up time was 39.0 ± 27.7, 50.0 ± 22.1 and 25.8 ± 18.9 months in UP, BP and BE groups, respectively. Thirty cases (12.7%) of buttock claudication occurred, and it was significantly higher in the BE group than the UP group (26.2% vs. 7.8%, p < 0.001). There were no significant differences in the other follow-up outcomes among three groups. The K–M analysis indicated that the patients in the BE group had a lower survival rate than those in the other two groups (p = 0.024). 24 patients underwent IIA reconstruction, including 8 in the IPG group and 16 in the IBG group. The endoleak in the IBG group was significantly lower than that in the IPG group (0% vs. 25.0%, p = 0.041). The iliac-related reintervention, iliac occlusion and mortality were similar between the two groups. Conclusion Overall it is beneficial for patients to preserve at least one side of IIA during EVAR as much as possible. Compared with IPG, IBG might be more applicable for IIA reconstruction.
Student and Faculty Perceptions of Generative Artificial Intelligence in Student Writing
Authors: Hostetter Autumn B. , Call Natalie , Frazier Grace , James Tristan , Linnertz Cassandra , Nestle Elizabeth , Tucci Miaflora 
Published: September 2024

Background Psychology instructors frequently assign writing-to-learn exercises that include personal reflection. Generative Artificial Intelligence (GenAI) can write text that passes for humans in other domains. Objective Do students and faculty rate a reflection written by GenAI differently than reflections written by students? Do students and faculty agree about the appropriateness of using GenAI for college-level writing? Method Eighty-three students and 82 faculty read four reflections (three written by undergraduate students and one by GenAI). After rating the quality of each, they chose which one they thought was AI-generated. Participants then rated the ethicality of nine potential ways to use GenAI in college-level writing and the potential of each to compromise learning. Results Participants rated the AI-generated reflection similarly to the student-generated reflections and failed to reliably detect AI-generated writing. Faculty and students agreed that using GenAI to produce the final text for a student likely compromises learning more than using it to generate ideas. Conclusion AI-generated reflections blend in with student-written reflections, and students and faculty agree about the potential detriments to learning. Teaching Implications GenAI can be hard to detect in the psychology classroom. Rather than implementing one-size-fits-all policies, instructors might focus classroom conversations on how GenAI could compromise learning.
Do Racial and Ethnic Disparities Exist in Intensity of Intracranial Pressure–Directed Therapies and Outcomes Following Pediatric Severe Traumatic Brain Injury?
Authors: Schopman Lauren E. , Land Megan E. , Rakkar Jaskaran , Appavu Brian L. , Buttram Sandra D.W. 
Published: September 2024

Introduction Studies suggest disparities in outcomes in minoritized children after severe traumatic brain injury. We aimed to evaluate for disparities in intracranial pressure–directed therapies and outcomes after pediatric severe traumatic brain injury. Methods We conducted a secondary analysis of the Approaches and Decisions for Acute Pediatric TBI (ADAPT) Trial, which enrolled pediatric severe traumatic brain injury patients (Glasgow Coma Scale score  ≤8) with an intracranial pressure monitor from 2014 to 2018. Patients admitted outside of the United States were excluded. Patients were categorized by race and ethnicity (Hispanic, non-Hispanic Black, non-Hispanic White, and “Other”). We evaluated outcomes by assessing mortality and 3-month Glasgow Outcome Score–Extended for Pediatrics. Our analysis involved parametric and nonparametric testing. Main Results A total of 671 children were analyzed. Significant associations included older age in non-Hispanic White patients ( P < .001), more surgical evacuations in “Other” ( P < .001), and differences in discharge location ( P = .040). The “other” cohort received hyperventilation less frequently ( P = .046), although clinical status during Paco2 measurement was not known. There were no other significant differences in intracranial pressure–directed therapies. Hispanic ethnicity was associated with lower mortality ( P = .004) but did not differ in unfavorable outcome ( P = .810). Glasgow Outcome Score–Extended for Pediatrics was less likely to be collected for non-Hispanic Black patients (69%; P = .011). Conclusions Our analysis suggests a general lack of disparities in intracranial pressure–directed therapies and outcomes in children after severe traumatic brain injury. Lower mortality in Hispanic patients without a concurrent decrease in unfavorable outcomes, and lower availability of Glasgow Outcome Score–Extended for Pediatrics score for non-Hispanic Black patients merit further investigation.