bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reliability of Manual Measurements Versus Semiautomated Software for Glenoid Bone Loss Quantification in Patients With Anterior Shoulder Instability
Authors: Karpinski Katrin , Akguen Doruk , Gebauer Henry , Paksoy Alp , Lupetti Mattia , Markova Viktoria , Zettinig Oliver , Moroder Philipp 
Published: February 2024

Background: The presence of glenoid bone defects is indicative in the choice of treatment for patients with anterior shoulder instability. In contrast to traditional linear- and area-based measurements, techniques such as the consideration of glenoid concavity have been proposed and validated. Purpose: To compare the reliability of linear (1-dimensional [1D]), area (2-dimensional [2D]), and concavity (3-dimensional [3D]) measurements to quantify glenoid bone loss performed manually and to analyze how automated measurements affect reliability. Study Design: Cohort study (diagnosis); Level of evidence, 3. Methods: Computed tomography images of 100 patients treated for anterior shoulder instability with differently sized glenoid defects were evaluated independently by 2 orthopaedic surgeons manually using conventional software (OsiriX; Pixmeo) as well as automatically with a dedicated prototype software program (ImFusion Suite; ImFusion). Parameters obtained included 1D (defect diameter, best-fit circle diameter), 2D (defect area, best-fit circle area), and 3D (bony shoulder stability ratio) measurements. Mean values and reliability as expressed by the intraclass correlation coefficient [ICC]) were compared between the manual and automated measurements. Results: When manually obtained, the measurements showed almost perfect agreement for 1D parameters (ICC = 0.83), substantial agreement for 2D parameters (ICC = 0.79), and moderate agreement for the 3D parameter (ICC = 0.48). When measurements were aided by automated software, the agreement between raters was almost perfect for all parameters (ICC = 0.90 for 1D, 2D, and 3D). There was a significant difference in mean values between manually versus automatically obtained measurements for 1D, 2D, and 3D parameters ( P < .001 for all). Conclusion: While more advanced measurement techniques that take glenoid concavity into account are more accurate in determining the biomechanical relevance of glenoid bone loss, our study showed that the reliability of manually performed, more complex measurements was moderate.
Heterogeneity in maternal mRNAs within clutches of eggs in response to thermal stress during the embryonic stage
Authors: Sato Atsuko , Mihirogi Yukie , Wood Christine , Suzuki Yutaka , Truebano Manuela , Bishop John 
Published: February 2024

Abstract
Background
The origin of variation is of central interest in evolutionary biology. Maternal mRNAs govern early embryogenesis in many animal species, and we investigated the possibility that heterogeneity in maternal mRNA provisioning of eggs can be modulated by environmental stimuli.

Results
We employed two sibling species of the ascidian Ciona, called here types A and B, that are adapted to different temperature regimes and can be hybridized. Previous study showed that hybrids using type B eggs had higher susceptibility to thermal stress than hybrids using type A eggs. We conducted transcriptome analyses of multiple single eggs from crosses using eggs of the different species to compare the effects of maternal thermal stress on heterogeneity in egg provisioning, and followed the effects across generations. We found overall decreases of heterogeneity of egg maternal mRNAs associated with maternal thermal stress. When the eggs produced by the F1 AB generation were crossed with type B sperm and the progeny (‘ABB’ generation) reared unstressed until maturation, the overall heterogeneity of the eggs produced was greater in a clutch from an individual with a heat-stressed mother compared to one from a non-heat-stressed mother. By examining individual genes, we found no consistent overall effect of thermal stress on heterogeneity of expression in genes involved in developmental buffering. In contrast, heterogeneity of expression in signaling molecules was directly affected by thermal stress.

Conclusions
Due to the absence of batch replicates and variation in the number of reads obtained, our conclusions are very limited. However, contrary to the predictions of bet-hedging, the results suggest that maternal thermal stress at the embryo stage is associated with reduced heterogeneity of maternal mRNA provision in the eggs subsequently produced by the stressed individual, but there is then a large increase in heterogeneity in eggs of the next generation, although itself unstressed. Despite its limitations, our study presents a proof of concept, identifying a model system, experimental approach and analytical techniques capable of providing a significant advance in understanding the impact of maternal environment on developmental heterogeneity.
ST218 Klebsiella pneumoniae became a high-risk clone for multidrug resistance and hypervirulence
Authors: Yang Ping , Liu Chao , Du Pengcheng , Yi Juan , Wu Zhenchao , Zheng Jiajia , Shen Ning , Cui Liyan , Lu Ming 
Published: February 2024

Abstract
Background
The occurrence of multidrug-resistant and hypervirulent Klebsiella pneumoniae (MDR-hvKp) worldwide poses a great challenge for public health. Few studies have focused on ST218 MDR-hvKp.

Methods
Retrospective genomic surveillance was conducted at the Peking University Third Hospital from 2017 and clinical information was obtained. To understand genomic and microbiological characteristics, antimicrobial susceptibility testing, plasmid conjugation and stability, biofilm formation, serum killing, growth curves and whole-genome sequencing were performed. We also assessed the clinical and microbiological characteristics of ST218 compared with ST23.

Results
A total of eleven ST218 Kp isolates were included. The most common infection type was lower respiratory tract infection (72.7%, 8/11) in our hospital, whereas ST23 hvKp (72.7%, 8/11) was closely associated with bloodstream infection. Notably, nosocomial infections caused by ST218 (54.5%, 6/11) was slightly higher than ST23 (36.4%, 4/11). All of the ST218 and ST23 strains presented with the virulence genes combination of iucA + iroB + peg344 + rmpA + rmpA2. Interestingly, the virulence score of ST218 was lower than ST23, whereas one ST218 strain (pPEKP3107) exhibited resistance to carbapenems, cephalosporins, β-lactamase/inhibitors and quinolones and harbored an ~ 59-kb IncN type MDR plasmid carrying resistance genes including blaNDM-1, dfrA14 and qnrS1. Importantly, blaNDM-1 and qnrS1 were flanked with IS26 located within the plasmid that could successfully transfer into E. coli J53. Additionally, PEKP2044 harbored an ~ 41-kb resistance plasmid located within tetA indicating resistance to doxycycline.

Conclusion
The emergence of blaNDM-1 revealed that there is great potential for ST218 Kp to become a high-risk clone for MDR-hvKp, indicating the urgent need for enhanced genomic surveillance.
Identification of candidate genes and residues for improving nitrogen use efficiency in the N-sensitive medicinal plant Panax notoginseng
Authors: Cun Zhu , Li Xia , Zhang Jin-Yan , Hong Jie , Gao Li-Lin , Yang Jing , Ma Su-Yun , Chen Jun-Wen 
Published: February 2024

Abstract
Background
Nitrogen (N) metabolism-related key genes and conserved amino acid sites in key enzymes play a crucial role in improving N use efficiency (NUE) under N stress. However, it is not clearly known about the molecular mechanism of N deficiency-induced improvement of NUE in the N-sensitive rhizomatous medicinal plant Panax notoginseng (Burk.) F. H. Chen. To explore the potential regulatory mechanism, the transcriptome and proteome were analyzed and the three-dimensional (3D) information and molecular docking models of key genes were compared in the roots of P. notoginseng grown under N regimes.

Results
Total N uptake and the proportion of N distribution to roots were significantly reduced, but the NUE, N use efficiency in biomass production (NUEb), the recovery of N fertilizer (RNF) and the proportion of N distribution to shoot were increased in the N0-treated (without N addition) plants. The expression of N uptake- and transport-related genes NPF1.2, NRT2.4, NPF8.1, NPF4.6, AVP, proteins AMT and NRT2 were obviously up-regulated in the N0-grown plants. Meanwhile, the expression of CIPK23, PLC2, NLP6, TCP20, and BT1 related to the nitrate signal-sensing and transduction were up-regulated under the N0 condition. Glutamine synthetase (GS) activity was decreased in the N-deficient plants, while the activity of glutamate dehydrogenase (GDH) increased. The expression of genes GS1-1 and GDH1, and proteins GDH1 and GDH2 were up-regulated in the N0-grown plants, there was a significantly positive correlation between the expression of protein GDH1 and of gene GDH1. Glu192, Glu199 and Glu400 in PnGS1 and PnGDH1were the key amino acid residues that affect the NUE and lead to the differences in GDH enzyme activity. The 3D structure, docking model, and residues of Solanum tuberosum and P. notoginseng was similar.

Conclusions
N deficiency might promote the expression of key genes for N uptake (genes NPF8.1, NPF4.6, AMT, AVP and NRT2), transport (NPF1.2 and NRT2.4), assimilation (proteins GS1 and GDH1), signaling and transduction (genes CIPK23, PLC2, NLP6, TCP20, and BT1) to enhance NUE in the rhizomatous species. N deficiency might induce Glu192, Glu199 and Glu400 to improve the biological activity of GS1 and GDH, this has been hypothesized to be the main reason for the enhanced ability of N assimilation in N-deficient rhizomatous species. The key genes and residues involved in improving NUE provide excellent candidates for the breeding of medicinal plants.
The complete plastomes of thirteen Libanotis (Apiaceae, Apioideae) plants: comparative and phylogenetic analyses provide insights into the plastome evolution and taxonomy of Libanotis
Authors: Liu Li-Jia , Liu Chang-Kun , Cai Jing , Deng Jiao-Jiao , He Xing‑Jin , Zhou Song‑Dong 
Published: February 2024

Abstract
Background
The genus Libanotis Haller ex Zinn, nom. cons., a contentious member of Apiaceae, encompasses numerous economically and medicinally significant plants, comprising approximately 30 species distributed across Eurasia. Despite many previous taxonomic insights into it, phylogenetic studies of the genus are still lacking. And the establishment of a robust phylogenetic framework remains elusive, impeding advancements and revisions in the taxonomic system for this genus. Plastomes with greater variability in their genetic characteristics hold promise for building a more robust Libanotis phylogeny.

Results
During our research, we sequenced, assembled, and annotated complete plastomes for twelve Libanotis species belong to three sections and two closely related taxa. We conducted a comprehensive comparative analysis through totally thirteen Libanotis plastomes for the genus, including an additional plastome that had been published. Our results suggested that Libanotis plastome was highly conserved between different subclades, while the coding regions were more conserved than the non-coding regions, and the IR regions were more conserved than the single copy regions. Nevertheless, eight mutation hotspot regions were identified among plastomes, which can be considered as candidate DNA barcodes for accurate species identification in Libanotis. The phylogenetic analyses generated a robustly framework for Libanotis and revealed that Libanotis was not a monophyletic group and their all three sections were polygenetic. Libanotis schrenkiana was sister to L. sibirica, type species of this genus, but the remainders scattered within Selineae.

Conclusion
The plastomes of Libanotis exhibited a high degree of conservation and was effective in enhancing the support and resolution of phylogenetic analyses within this genus. Based on evidence from both phylogeny and morphology, we propose the recognition of "Libanotis sensu stricto" and provide taxonomic recommendations for other taxa that previously belonged to Libanotis. In conclusion, our study not only revealed the phylogenetic position and plastid evolution of Libanotis, but also provided new insights into the phylogeny of the family Apiaceae and phylogenetic relationships within the tribe Selineae.
Association between Internet use and depressive symptoms among older adults in two regions of Myanmar: a cross-sectional study
Authors: Sasaki Yuri , Shobugawa Yugo , Nozaki Ikuma , Takagi Daisuke , Nagamine Yuiko , Shirakura Yuki , Lwin Kay Thi , Zin Poe Ei , Bo Thae Zarchi , Sone Tomofumi , Win Hla Hla 
Published: February 2024

Abstract
Background
Internet use has both positive and negative effects on mental health. However, few studies have examined the association between internet use and mental health among older adults in developing countries. This study aimed to investigate the association between Internet use and depressive symptoms among older adults in two regions of Myanmar.

Methods
Data based on a visit to 1,200 older adults in urban and rural Myanmar were obtained through stratified random sampling using the cross-sectional baseline survey of the longitudinal study titled “Healthy and Active Aging in Myanmar.”
Our analysis included 1,186 participants. The dependent variable was depressive symptoms, and the 15-item version of the Geriatric Depression Scale (GDS) was used as a continuous variable; the higher the score, the more likely a person was to be depressed. Internet use (one of the questions about household property ownership) was used as an independent variable. After confirming the absence of multicollinearity, we adjusted for age, gender, educational background, activities of daily living, residential area, and frequency of meeting friends, and stratified by subjective economic status (above or below average). We also examined the interaction between internet use and subjective economic status. A linear regression analysis was performed.

Results
Among the 1,186 participants included in the analysis (women: 59.5%; median age: 68 years old), 202 (17.0%) were Internet users (95% Confidential Interval [CI]: 0.15, 0.19), and they had significantly lower GDS scores than the participants who did not use the Internet (B: -1.59, 95% CI: -2.04, -1.13).GDS showed a negative association with Internet use even in the multivariate analysis (B: -0.95, 95% CI: -1.41, -0.50). However, the interaction term for GDS between Internet use and subjective economic status was not significantly associated (B: 0.43, 95% CI: -1.11, 1.98).

Conclusions
Internet use and depressive symptoms were associated especially among the older adults. However, there were no significant interaction between Internet use and subjective economic status for GDS.
Six dilemmas for stakeholders inherently affecting data sharing during a zoonotic (re-)emerging infectious disease outbreak response
Authors: van Roode Martine Y. , dos S. Ribeiro Carolina , Farag Elmoubasher , Nour Mohamed , Moustafa Aya , Ahmed Minahil , Haringhuizen George , Koopmans Marion P.G. , van de Burgwal Linda H.M. 
Published: February 2024

Abstract
Background
Timely access to outbreak related data, particularly in the early events of a spillover, is important to support evidence based control measures in response to outbreaks of zoonotic Emerging Infectious Diseases (EID). Yet, this is impeded by several barriers that need to be understood to promote timely sharing of data. Using the MERS epidemic as a model for a zoonotic EID outbreak, this study sought to provide an in-depth understanding of data sharing practices.

Methods
Semi-structured interviews with 25 experts were conducted, along with Focus Group Discussions with 15 additional experts. A root-cause analysis was performed to examine the causal relationships between barriers. Enablers were mapped to the root-cause analysis to understand their influence on the barriers. Finally, root causes were placed in context of core dilemmas identified from the qualitative analysis.

Findings
Eight barriers to data sharing were identified, related to collaboration, technical preparedness, regulations, and (conflict of) interests, and placed in the context of six dilemmas inherent to the multi-stakeholder collaboration required for a zoonotic outbreak response. Fourteen identified enablers showed the willingness of stakeholders to overcome or circumvent these barriers, but also indicated the inherent trial and error nature of implementing such enablers.

Interpretation
Addressing the barriers requires solutions that must consider the complexity and interconnectedness of the root causes underlying them, and should consider the distinct scopes and interests of the different stakeholders. Insights provided by this study can be used to encourage data sharing practices for future outbreaks

Funding
Wellcome Trust and UK Aid; EU-H2020 Societal Challenges (grant agreement no. 643476), Nederlandse Organisatie voor Wetenschappelijk Onderzoek (VI.Veni.201S.044)
Patterns of antibiotic administration in Chinese neonates: results from a multi-center, point prevalence survey
Authors: Zhang Jiaosheng , Lin Li , Lu Gen , Wu Keye , Tian Daiyin , Tang Lanfang , Ma Xiang , Wang Yajuan , Liu Gang , Li Yanqi , Qian Jing , Wang Ping , Cao Qing , Zhang Wenshuang , Wu Lijuan , Si Ligang , Wu Yue , Zheng Yuejie , Shen Kunling , Deng Jikui , Li Defa , Yang Yonghong 
Published: February 2024

Abstract
Objectives
In this study, we describe the patterns of antibiotic prescription for neonates based on World Health Organization’s (WHO) Essential Medicines List Access, Watch, and Reserve (AWaRe), and the Management of Antibiotic Classification (MAC) Guidelines in China.

Methods
One-day point-prevalence surveys (PPS) on antimicrobial prescriptions were conducted on behalf of hospitalized neonates in China from September 1 and November 30, annually from 2017 to 2019.

Results
Data was collected for a total of 2674 neonatal patients from 15 hospitals in 9 provinces across China of which 1520 were newborns who received at least one antibiotic agent. A total of 1943 antibiotic prescriptions were included in the analysis. The most commonly prescribed antibiotic was meropenem (11.8%). The most common reason for prescribing antibiotic to neonates was pneumonia (44.2%). There were 419 (21.6%), 1343 (69.1%) and 6 (0.3%) antibiotic prescriptions in the Access, Watch and Reserve groups, respectively. According to MAC Guidelines in China, there were 1090 (56.1%) antibiotic agents in the Restricted and 414 (21.3%) in the Special group.

Conclusion
Broad-spectrum antibiotics included in the Watch and Special groups were likely to be overused in Chinese neonates.
Prevalence and outcomes of chronic comorbid conditions in patients with sepsis in Korea: a nationwide cohort study from 2011 to 2016
Authors: Kang Christine , Choi Seongmi , Jang Eun Jin , Joo Somin , Jeong Jae Hoon , Oh Seung-Young , Ryu Ho Geol , Lee Hannah 
Published: February 2024

Abstract
Background
Chronic comorbid conditions are common in patients with sepsis and may affect the outcomes. This study aimed to evaluate the prevalence and outcomes of common comorbidities in patients with sepsis.

Methods
We conducted a nationwide retrospective cohort study. Using data from the National Health Insurance Service of Korea. Adult patients (age ≥ 18 years) who were hospitalized in tertiary or general hospitals with a diagnosis of sepsis between 2011 and 2016 were analyzed. After screening of all International Classification of Diseases 10th revision codes for comorbidities, we identified hypertension, diabetes mellitus (DM), liver cirrhosis (LC), chronic kidney disease (CKD), and malignancy as prevalent comorbidities.

Results
Overall, 373,539 patients diagnosed with sepsis were hospitalized in Korea between 2011 and 2016. Among them, 46.7% had hypertension, 23.6% had DM, 7.4% had LC, 13.7% had CKD, and 30.7% had malignancy. In-hospital mortality rates for patients with hypertension, DM, LC, CKD, and malignancy were 25.5%, 25.2%, 34.5%, 28.0%, and 33.3%, respectively, showing a decreasing trend over time (P < 0.001). After adjusting for baseline characteristics, male sex, older age, use of mechanical ventilation, and continuous renal replacement therapy, LC, CKD, and malignancy were significantly associated with in-hospital mortality.

Conclusions
Hypertension is the most prevalent comorbidity in patients with sepsis, and it is associated with an increased survival rate. Additionally, liver cirrhosis, chronic kidney disease, and malignancy result in higher mortality rates than hypertension and DM, and are significant risk factors for in-hospital mortality in patients with sepsis.
Risk factors of adverse birth outcomes among a cohort of pregnant women in Coastal Kenya, 2017–2019
Authors: Mirieri Harriet , Nduati Ruth , Dawa Jeanette , Okutoyi Lydia , Osoro Eric , Mugo Cyrus , Wamalwa Dalton , Jin Hafsa , Mwaengo Dufton , Otieno Nancy , Marwanga Doris , Shabibi Mufida , Munyua Peninah , Kinuthia John , Clancey Erin , Widdowson Marc-Alain , Njenga M. Kariuki , Verani Jennifer R. , Inwani Irene 
Published: February 2024

Abstract
Introduction
Adverse birth outcomes particularly preterm births and congenital anomalies, are the leading causes of infant mortality globally, and the burden is highest in developing countries. We set out to determine the frequency of adverse birth outcomes and the risk factors associated with such outcomes in a cohort of pregnant women in Kenya.

Methods
From October 2017 to July 2019, pregnant women < 28 weeks gestation were enrolled and followed up until delivery in three hospitals in coastal Kenya. Newborns were examined at delivery. Among women with birth outcome data, we assessed the frequency of congenital anomalies defined as gastroschisis, umbilical hernia, limb abnormalities and Trisomy 21, and adverse birth outcomes, defined as either stillbirth, miscarriage, preterm birth, small for gestational age, or microcephaly. We used log-binomial regression to identify maternal characteristics associated with the presence of at least one adverse outcome.

Results
Among the 2312 women enrolled, 1916 (82.9%) had birth outcome data. Overall, 402/1916 (20.9%; 95% confidence interval (CI): 19.1–22.8) pregnancies had adverse birth outcomes. Specifically, 66/1916 (3.4%; 95% CI: 2.7–4.4) were stillbirths, 34/1916 (1.8%; 95% CI: 1.2–2.4) were miscarriages and 23/1816 (1.2%; 95% CI: 0.8–1.9) had congenital anomalies. Among the participants with anthropometric measurements data, 142/1200 (11.8%; 95% CI: 10.1 − 13.8) were small for gestational age and among the participants with ultrasound records, 143/1711 (8.4%; 95% CI: 7.1–9.8) were preterm. Febrile illnesses in current pregnancy (adjusted risk ratio (aRR): 1.7; 95% CI: 1.1–2.8), a history of poor birth outcomes in prior pregnancy (aRR: 1.8; 95% CI: 1.3–2.4) and high blood pressure in pregnancy (aRR: 3.9, 95% CI: (1.7–9.2) were independently associated with adverse birth outcomes in a model that included age, education, human immunodeficiency virus status and high blood pressure at enrolment.

Conclusion
We found similar rates of overall adverse birth outcomes, congenital anomalies, and small for gestational age but higher rates of stillbirths and lower rates of prematurity compared to the rates that have been reported in the sub-Saharan Africa region. However, the rates of adverse birth outcomes in this study were comparable to other studies conducted in Kenya. Febrile illnesses during the current pregnancy, previous history of poor birth outcomes and high blood pressure in pregnancy are predictive of an increased risk of adverse birth outcomes.