bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroinvasive Francisella tularensis Infection: Report of 2 Cases and Review of the Literature
Authors: Cash-Goldwasser Shama , Beeson Amy , Marzec Natalie , Ho Dora Y , Hogan Catherine A , Budvytiene Indre , Banaei Niaz , Born Donald E , Gephart Melanie H , Patel Jatinbhai , Dietrich Elizabeth A , Nelson Christina A 
Published: January 2024

Abstract

Background
Neuroinvasive infection with Francisella tularensis, the causative agent of tularemia, is rare. Establishing clinical suspicion is challenging if risk factors or clinical features classically associated with tularemia are absent. Tularemia is treatable with antibiotics; however, there are limited data to inform management of potentially fatal neuroinvasive infection.

Methods
We collected epidemiologic and clinical data on 2 recent US cases of neuroinvasive F. tularensis infection, and performed a literature review of cases of neuroinvasive F. tularensis infection published after 1950.

Results
One patient presented with focal neurologic deficits and brain lesions; broad-range molecular testing on resected brain tissue detected F. tularensis. The other patient presented with meningeal signs; tularemia was suspected based on animal exposure, and F. tularensis grew in cerebrospinal fluid (CSF) culture. Both patients received combination antibiotic therapy and recovered from infection. Among 16 published cases, tularemia was clinically suspected in 4 cases. CSF often displayed lymphocytic pleocytosis. Among cases with available data, CSF culture was positive in 13 of 16 cases, and F. tularensis antibodies were detected in 11 of 11 cases. Treatment typically included an aminoglycoside combined with either a tetracycline or a fluoroquinolone. Outcomes were generally favorable.

Conclusions
Clinicians should consider neuroinvasive F. tularensis infection in patients with meningitis and signs suggestive of tularemia or compatible exposures, lymphocyte-predominant CSF, unrevealing standard microbiologic workup, or lack of response to empiric bacterial meningitis treatment. Molecular testing, culture, and serologic testing can reveal the diagnosis. Favorable outcomes can be achieved with directed antibiotic treatment.
Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin
Authors: Venetz Jessica , Żygadłowska Olga M , Dotsios Nicky , Wallenius Anna J , van Helmond Niels A G M , Lenstra Wytze K , Klomp Robin , Slomp Caroline P , Jetten Mike S M , Veraart Annelies J 
Published: January 2024

Abstract
In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water–air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water–air fluxes remained below 0.6 mmol m−2 d−1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water–air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.
Height increment patterns in Pinus pinaster seedlings emerging in naturally regenerated gaps
Authors: de Frutos Sergio , Manso Rubén , Roig-Gómez Sonia , Ruiz-Peinado Ricardo , del Río Miren , Bravo-Fernández José Alfredo 
Published: January 2024

Abstract
The group selection cutting system provides a promising technique for transforming monospecific even-aged stands into uneven-aged, mixed stands. However, this system has scarcely been used to regenerate Mediterranean shade-intolerant species. In this study, we analyze the height increment patterns of Pinus pinaster seedlings emerging in naturally regenerated gaps. P. pinaster is a shade-intolerant pine species distributed throughout the Mediterranean basin. An experimental trial was established in a 50-year-old P. pinaster (maritime pine) plantation located in the mountains of central Spain. Gaps of two different sizes (diameter equal to 1.5 and 2.5 times the dominant height of the stand, 26 and 44 m, respectively) were opened during winter 2017–18. A total of 531 subplots with a 1-m radius were installed in spring 2018, distributed within the gaps as well as in control plots adjacent to the gaps. Seedlings were tagged individually and variables including height, along with other ecological variables, were collected twice a year (in spring and autumn), providing six time intervals for the development of our models. We applied seemingly unrelated regression to analyze the height growth in this polycyclic species, allowing us to model spring and autumn height increments at the same time. Our results showed that seedling height growth depended on the silvicultural treatment, meteorological conditions during the spring growth season, inter-specific scrub competition, position within the gap, and seedling characteristics, such as the ontogenetic development or the size of the seedling itself. This work, along with germination and survival analysis, aims to provide a holistic perspective on the suitability of the group selection cutting system to regenerate maritime pine stands, taking into account current and future climate change scenarios.
Epigenetic Regulation of Autophagy in Bone Metabolism
Authors: Zhang Yazhou , Wang Qianqian , Xue Hongjia , Guo Yujin , Wei Shanshan , Li Fengfeng , Gong Linqiang , Pan Weiliang , Jiang Pei 
Published: January 2024

Abstract
The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy’s impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.
T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality
Authors: Zhang Shuwen , Yu Zheping , Sun Li , Liang Senmiao , Xu Fei , Li Sujuan , Zheng Xiliang , Yan Lijv , Huang Yinghong , Qi Xingjiang , Ren Haiying 
Published: January 2024

Abstract
Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar ‘Zaojia’ using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.
A successful shift from thoracotomy to video-assisted thoracoscopic lobectomy for non-small cell lung cancer in a low-volume center
Authors: Asbjornsson Viktor , Johannsdottir Gyda , Myer Daniel , Runarsson Thorri Geir , Heitmann Leon Arnar , Oskarsdottir Gudrun N , Silverborn Per Martin , Hansen Henrik Jessen , Gudbjartsson Tomas 
Published: January 2024

Abstract

OBJECTIVES
Although video-assisted thoracoscopic surgery (VATS) lobectomy has become the gold standard for pulmonary resections of non-small-cell lung cancer (NSCLC), lobectomy is still performed via thoracotomy in many European and North American centres. VATS lobectomy was implemented overnight from thoracotomy in our low-volume centre in early 2019, after 1 senior surgeon undertook observership VATS-training overseas, and immediately became the mainstay of surgical treatment for NSCLC in Iceland. We aimed to investigate our short-term outcomes of VATS lobectomy.

METHODS
This was a retrospective study on all pulmonary resections for NSCLC in Iceland 2019–2022, especially focusing on VATS lobectomies, all at cTNM stage I or II. Data were retrieved from hospital charts, including information on perioperative complications, mortality, length of stay and operation time.

RESULTS
Out of 204 pulmonary resections, mostly performed by a single senior cardiothoracic surgeon, 169 were lobectomies (82.9%) with 147 out of 169 (87.0%) being VATS lobectomies. Anterolateral thoracotomy was used in 34 cases (16.7%), including 22 lobectomies (64.7%), and 5 (3.4%) conversions from VATS lobectomy. The median postoperative stay for VATS lobectomy was 4 days and the average operating time decreased from 155 to 124 min between the first and last year of the study (P &lt; 0.001). The rate of major and minor complications was 2.7% and 15.6% respectively. One year survival was 95.6% and all patients survived 30 days postoperatively.

CONCLUSIONS
The implementation of VATS lobectomy has been successful in our small geographically isolated centre, serving a population of 390 000. Although technically challenging, VATS lobectomy was implemented fast for most NSCLC cases, with short-term outcomes that are comparable to larger high-volume centres.
Protozoan predation enhances stress resistance and antibiotic tolerance in Burkholderia cenocepacia by triggering the SOS response
Authors: Morón Álvaro , Tarhouchi Alaa E , Belinchón Iván , Valenzuela Juan M , de Francisco Patricia , Martín-González Ana , Amaro Francisco 
Published: January 2024

Abstract
Bacterivorous protists are thought to serve as training grounds for bacterial pathogens by subjecting them to the same hostile conditions that they will encounter in the human host. Bacteria that survive intracellular digestion exhibit enhanced virulence and stress resistance after successful passage through protozoa but the underlying mechanisms are unknown. Here we show that the opportunistic pathogen Burkholderia cenocepacia survives phagocytosis by ciliates found in domestic and hospital sink drains, and viable bacteria are expelled packaged in respirable membrane vesicles with enhanced resistance to oxidative stress, desiccation, and antibiotics, thereby contributing to pathogen dissemination in the environment. Reactive oxygen species generated within the protozoan phagosome promote the formation of persisters tolerant to ciprofloxacin by activating the bacterial SOS response. In addition, we show that genes encoding antioxidant enzymes are upregulated during passage through ciliates increasing bacterial resistance to oxidative radicals. We prove that suppression of the SOS response impairs bacterial intracellular survival and persister formation within protists. This study highlights the significance of protozoan food vacuoles as niches that foster bacterial adaptation in natural and built environments and suggests that persister switch within phagosomes may be a widespread phenomenon in bacteria surviving intracellular digestion.
A national survey of digital health company experiences with electronic health record application programming interfaces
Authors: Barker Wesley , Maisel Natalya , Strawley Catherine E , Israelit Grace K , Adler-Milstein Julia , Rosner Benjamin 
Published: January 2024

Abstract

Objectives
This study sought to capture current digital health company experiences integrating with electronic health records (EHRs), given new federally regulated standards-based application programming interface (API) policies.

Materials and methods
We developed and fielded a survey among companies that develop solutions enabling human interaction with an EHR API. The survey was developed by the University of California San Francisco in collaboration with the Office of the National Coordinator for Health Information Technology, the California Health Care Foundation, and ScaleHealth. The instrument contained questions pertaining to experiences with API integrations, barriers faced during API integrations, and API-relevant policy efforts.

Results
About 73% of companies reported current or previous use of a standards-based EHR API in production. About 57% of respondents indicated using both standards-based and proprietary APIs to integrate with an EHR, and 24% worked about equally with both APIs. Most companies reported use of the Fast Healthcare Interoperability Resources standard. Companies reported that standards-based APIs required on average less burden than proprietary APIs to establish and maintain. However, companies face barriers to adopting standards-based APIs, including high fees, lack of realistic clinical testing data, and lack of data elements of interest or value.

Discussion
The industry is moving toward the use of standardized APIs to streamline data exchange, with a majority of digital health companies using standards-based APIs to integrate with EHRs. However, barriers persist.

Conclusion
A large portion of digital health companies use standards-based APIs to interoperate with EHRs. Continuing to improve the resources for digital health companies to find, test, connect, and use these APIs “without special effort” will be crucial to ensure future technology robustness and durability.
Loss of 24-hydroxylated catabolism increases calcitriol and fibroblast growth factor 23 and alters calcium and phosphate metabolism in fetal mice
Authors: Bennin David , Hartery Sarah A , Kirby Beth J , Maekawa Alexandre S , St-Arnaud René , Kovacs Christopher S 
Published: January 2024

Abstract
Calcitriol circulates at low levels in normal human and rodent fetuses, in part due to increased 24-hydroxylation of calcitriol and 25-hydroxyvitamin D by 24-hydroxylase (CYP24A1). Inactivating mutations of CYP24A1 cause high postnatal levels of calcitriol and the human condition of infantile hypercalcemia type 1, but whether the fetus is disturbed by the loss of CYP24A1 is unknown. We hypothesized that loss of Cyp24a1 in fetal mice will cause high calcitriol, hypercalcemia, and increased placental calcium transport. The Cyp24a1+/− mice were mated to create pregnancies with wildtype, Cyp24a1+/−, and Cyp24a1 null fetuses. The null fetuses were hypercalcemic, modestly hypophosphatemic (compared to Cyp24a1+/− fetuses only), with 3.5-fold increased calcitriol, 4-fold increased fibroblast growth factor 23 (FGF23), and unchanged parathyroid hormone. The quantitative RT-PCR confirmed the absence of Cyp24a1 and 2-fold increases in S100g, sodium–calcium exchanger type 1, and calcium-sensing receptor in null placentas but not in fetal kidneys; these changes predicted an increase in placental calcium transport. However, placental 45Ca and 32P transport were unchanged in null fetuses. Fetal ash weight and mineral content, placental weight, crown-rump length, and skeletal morphology did not differ among the genotypes. Serum procollagen 1 intact N-terminal propeptide and bone expression of sclerostin and Blgap were reduced while calcitonin receptor was increased in nulls. In conclusion, loss of Cyp24a1 in fetal mice causes hypercalcemia, modest hypophosphatemia, and increased FGF23, but no alteration in skeletal development. Reduced incorporation of calcium into bone may contribute to the hypercalcemia without causing a detectable decrease in the skeletal mineral content. The results predict that human fetuses bearing homozygous or compound heterozygous inactivating mutations of CYP24A1 will also be hypercalcemic in utero but with normal skeletal development.
Mapping of geological structures and sediment thickness from analysis of aeromagnetic data over the Obudu Basement Complex of Nigeria
Authors: Ekwok Stephen E , Eldosuoky Ahmed M , Thompson Edward A , Ojong Romeo A , George Anthony M , Alarifi Saad S , Kharbish Sherif , Andráš Peter , Akpan Anthony E 
Published: January 2024

AbstractIn this study, geologic structures, as well as attendant orientations and sediment thickness, in the Nigerian Obudu Complex were delineated using the Centre for Exploration Targeting (CET), and depth determination methods such as source parameter imaging (SPI) and standard Euler deconvolution (SED). The CET, SPI, and SED procedures were applied on the total magnetic intensity data. Also, the enhanced TMI data using analytic signal, first-vertical derivative, total-horizontal derivative, and tilt-angle derivative filters were further subjected to CET operation, with the aim of mapping both subtle and prominent lineaments. In general, mapped geologic structures trends in the NE–SW, NNE–SSW, E–W, and N–S directions. Overall, the dominant geologic structural orientations of NE–SW and NNE–SSW reflect the regional strike orientation. The regional striking of the lineation, which is caused by the Pan-African orogeny and subsequent post-orogenic processes, has an impact on these orientations. The N–S and E–W structural deviations from the main NE–SW and NNE–SSW trends are initiated by the YGS of the post-orogenic events. Overall, these complex geologic structures are probable sites for metallogenic minerals.
Simulating the population impact of interventions to reduce racial gaps in breast cancer treatment
Authors: Yanguela Juan , Jackson Bradford E , Reeder-Hayes Katherine E , Roberson Mya L , Rocque Gabrielle B , Kuo Tzy-Mey , LeBlanc Matthew R , Baggett Christopher D , Green Laura , Laurie-Zehr Erin , Wheeler Stephanie B 
Published: January 2024

Abstract

Background
Inequities in guideline-concordant treatment receipt contribute to worse survival in Black patients with breast cancer. Inequity-reduction interventions (eg, navigation, bias training, tracking dashboards) can close such treatment gaps. We simulated the population-level impact of statewide implementation of inequity-reduction interventions on racial breast cancer inequities in North Carolina.

Methods
Using registry-linked multipayer claims data, we calculated inequities between Black and White patients receiving endocrine therapy (n = 12 033) and chemotherapy (n = 1819). We then built cohort-stratified (endocrine therapy and chemotherapy) and race-stratified Markov models to simulate the potential increase in the proportion of patients receiving endocrine therapy or chemotherapy and subsequent improvements in breast cancer outcomes if inequity-reducing intervention were implemented statewide. We report uncertainty bounds representing 95% of simulation results.

Results
In total, 75.6% and 72.1% of Black patients received endocrine therapy and chemotherapy, respectively, over the 2006-2015 and 2004-2015 periods (vs 79.3% and 78.9% of White patients, respectively). Inequity-reduction interventions could increase endocrine therapy and chemotherapy receipt among Black patients to 89.9% (85.3%, 94.6%) and 85.7% (80.7%, 90.9%). Such interventions could also decrease 5-year and 10-year breast cancer mortality gaps from 3.4 to 3.2 (3.0, 3.3) and from 6.7 to 6.1 (5.9, 6.4) percentage points in the endocrine therapy cohorts and from 8.6 to 8.1 (7.7, 8.4) and from 8.2 to 7.8 (7.3, 8.1) percentage points in the chemotherapy cohorts.

Conclusions
Inequity-focused interventions could improve cancer outcomes for Black patients, but they would not fully close the racial breast cancer mortality gap. Addressing other inequities along the cancer continuum (eg, screening, pre- and postdiagnosis risk factors) is required to achieve full equity in breast cancer outcomes.
A new method of solving plane-strain boundary value problems for the double slip and rotation model
Authors: Alexandrov Sergei , Lyamina Elena , Jeng Yeau-Rean 
Published: January 2024

Abstract
A method of solving plane-strain boundary value problems for a reduced version of the double slip and rotation model is developed. It is assumed that the intrinsic spin vanishes. Elastic strains are neglected. The Mohr–Coulomb yield criterion is adopted. An analogy between the solutions for this model and classical rigid plastic solutions of pressure-independent plasticity is revealed. The method is based on introducing auxiliary variables that satisfy the equation of telegraphy in regions where both families of characteristics are curved. Therefore, Riemann's method can conveniently be applied to solving boundary value problems. The method is employed for analyzing the processes of plane-strain drawing and extrusion through a wedge-shaped die. Friction is neglected. The solution is given in terms of ordinary integrals. The effect of the angle of internal friction on processes’ parameters is revealed. The solution reduces to available solutions of pressure-independent plasticity if the angle of internal friction vanishes.