bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the potential of a prematurely aged immune phenotype in severely injured patients as predictor of risk of sepsis
Authors: Foster Mark A. , Bentley Conor , Hazeldine Jon , Acharjee Animesh , Nahman Ornit , Shen-Orr Shai S. , Lord Janet M. , Duggal Niharika A. 
Published: December 2022

AbstractBackgroundTraumatic injury elicits a hyperinflammatory response and remodelling of the immune system leading to immuneparesis. This study aimed to evaluate whether traumatic injury results in a state of prematurely aged immune phenotype to relate this to clinical outcomes and a greater risk of developing additional morbidities post-injury.Methods and findingsBlood samples were collected from 57 critically injured patients with a mean Injury Severity Score (ISS) of 26 (range 15–75 years), mean age of 39.67 years (range 20–84 years), and 80.7% males, at days 3, 14, 28 and 60 post-hospital admission. 55 healthy controls (HC), mean age 40.57 years (range 20–85 years), 89.7% males were also recruited. The phenotype and frequency of adaptive immune cells were used to calculate the IMM-AGE score, an indicator of the degree of phenotypic ageing of the immune system. IMM-AGE was elevated in trauma patients at an early timepoint (day 3) in comparison with healthy controls (p < 0.001), driven by an increase in senescent CD8 T cells (p < 0.0001), memory CD8 T cells (p < 0.0001) and regulatory T cells (p < 0.0001) and a reduction in naïve CD8 T cells (p < 0.001) and overall T cell lymphopenia (p < 0 .0001). These changes persisted to day 60. Furthermore, the IMM-AGE scores were significantly higher in trauma patients (mean score 0.72) that developed sepsis (p = 0.05) in comparison with those (mean score 0.61) that did not.ConclusionsThe profoundly altered peripheral adaptive immune compartment after critical injury can be used as a potential biomarker to identify individuals at a high risk of developing sepsis and this state of prematurely aged immune phenotype in biologically young individuals persists for up to two months post-hospitalisation, compromising the host immune response to infections. Reversing this aged immune system is likely to have a beneficial impact on short- and longer-term outcomes of trauma survivors.
Intensity modulated proton therapy for early-stage glottic cancer: high-precision approach to laryngeal function preservation with exceptional treatment tolerability
Authors: Held Thomas , Franke Henrik , Lang Kristin , Eichkorn Tanja , Regnery Sebastian , Weusthof Katharina , Bauer Lukas , Plath Karim , Dyckhoff Gerhard , Plinkert Peter K. , Harrabi Semi B. , Herfarth Klaus , Debus Jürgen , Adeberg Sebastian 
Published: December 2022

Abstract
Background
Due to the increasing expertise in transoral laser surgery and image-guided radiation therapy, treatment outcomes have recently improved in patients with early-stage glottic cancer. The objective of the current study was to evaluate intensity-modulated proton therapy (IMPT) as novel treatment option.

Methods
A total of 15 patients with T1-2N0 glottic squamous cell carcinoma, treated between 2017 and 2020, were evaluated. Toxicity was recorded according to the Common Terminology Criteria for Adverse Events (CTCAE) v4.03.

Results
The majority were T1a/b tumors (66.7%) and no patient had lymph node or distant metastases. The median total dose was 70 Gy relative biological effectiveness (RBE) (range 66–70 Gy RBE). The one- and two-year OS and metastases-free survival were 100%. One patient developed local failure and received salvage laryngectomy. No higher-grade acute or late toxicity was reported. The mean number of CTCAE grade I and II overall toxicity events per patient was 4.1 (95%-[confidence interval] CI 3.1–5.3) and 1.0 (95%-CI 0.5–1.5).

Conclusion
High-precision proton therapy of T1-2N0 glottic cancer resulted in exceptional treatment tolerability with high rates of laryngeal function preservation and promising oncological outcome. IMPT has the potential to become a standard treatment option for patients with early-stage laryngeal cancer.
Safety and efficacy of using portable coagulation monitor for INR examination after left-sided mechanical prosthetic valve replacement
Authors: Shen Yue , Zhong Fu-xiu , Huang Xue-shan 
Published: December 2022

Abstract
Background
Time in therapeutic range (TTR) is an index to assess the effectiveness of anticoagulation and is important to predict the risk of bleeding and thrombosis in patients taking warfarin. In recent years, the portable coagulation monitor, a point-of-care testing device for patients to perform self-management international normalized ratio (INR) examination, has provided an opportunity to improve the quality of oral warfarin treatment. In this study, we applied TTR to evaluate the safety and efficacy of the portable coagulation monitor for patients with oral anticoagulant warfarin after left-sided mechanical prosthetic valve (MPV) replacement.

Methods
It is a single-centre cohort study. From September 2019 to June 2021, a total of 243 patients who returned to our institution for outpatient clinic revisit at 3 months after left-sided MPV replacement, met the inclusion criteria and agreed to be followed up were included. Self-management group used portable coagulation monitor for INR examination, and patients in the conventional group had their INR monitored in routine outpatient visits. Clinical data of the patients would be recorded for the next 12 months, and results were compared between the two groups to assess the effect of the coagulation monitor on TTR and complications related to bleeding and thrombosis in patients with left-sided MPV replacement.

Results
A total of 212 individuals provided complete and validated INR data spanning of 1 year. Those who applied the portable coagulation monitor had higher TTR values and larger number of tests for INR. No significant differences were seen between the two groups in postoperative bleeding and thromboembolic complications, but portable coagulation monitor showed a trend toward fewer bleeding events.

Conclusion
Portable devices for coagulation monitoring are safe and can achieve a higher TTR. Patients who use the portable coagulation monitor for home INR self-management can achieve a safe and effective warfarin therapy.
Comparison of oocyte vitrification using a semi-automated or a manual closed system in human siblings: survival and transcriptomic analyses
Authors: Barberet Julie , Ducreux Bastien , Bruno Céline , Guilleman Magali , Simonot Raymond , Lieury Nicolas , Guilloteau Adrien , Bourc’his Déborah , Fauque Patricia 
Published: December 2022

Abstract
Background
Indications of oocyte vitrification increased substantially over the last decades for clinical and ethical reasons. A semi-automated vitrification system was recently developed making each act of vitrification reproducible. In this study, we evaluated the efficiency of the semi-automated technique of oocyte vitrification by survival rate, morphometric assessment and resistance to empty micro-injection gesture as compared with a manual method. Additionally, we intended to evaluate transcriptomic consequences of both techniques using single-cell RNA-seq technology.

Results
Post-warming survival rate, oocyte surfaces and resistance to empty micro-injection were comparable between semi-automated and manual vitrification groups. Both oocyte vitrification techniques showed limited differences in the resulting transcriptomic profile of sibling oocytes since only 5 differentially expressed genes were identified. Additionally, there was no difference in median transcript integrity number or percentage of mitochondrial DNA between the two groups. However, a total of 108 genes were differentially expressed between fresh and vitrified oocytes (FDR < 0.05) and showed over-represented of genes related to important cellular process.

Conclusions
Our results provide reassurance about the influence of semi-automation as compared with the manual vitrification method. Concerning oocyte vitrification itself, no tight common transcriptomic signature associated has been observed across studies.

Trial registration
NCT03570073.
Evolution of breast cancer incidence in young women in a French registry from 1990 to 2018: Towards a change in screening strategy?
Authors: Hassaine Yanis , Jacquet Emmanuelle , Seigneurin Arnaud , Delafosse Patricia 
Published: December 2022

Abstract
Background
The worldwide incidence of invasive breast cancer in women is increasing according to several studies. This increase in incidence seems to be higher in young women (< 40 years). However, the reasons for this trend are poorly understood. This article aims to provide the most recent estimates of this trend and assess whether there is indeed an increase in the incidence of breast cancer among young women to strengthen prevention campaigns.

Methods
We collected data from the Isere cancer registry in France of all invasive breast cancers from January 1990 to December 2018. The standardized incidence rate was calculated for four age groups (< 40 years, 40–49 years, 50–74 years, ≥ 75 years) for this period. The 10-year relative survival was evaluated for each age group age for two periods (1990–1999 and 2000–2008). From 2011 to 2013, we analyzed the incidence and 5-year relative survival by tumor subtype (triple negative, luminal, HER2 amplified) for each age group.

Results
A total of 23,703 cases were selected, including 1343 young women (< 40 years). The incidence of invasive breast cancer increased annually by 0,8% (95% CI 0,7; 1) in all age groups combined from 1990 to 2018. The highest incidence increase is found among young women, by 2,1% annually (95% CI 1,3; 2,8). Regarding tumor subtypes from 2011 to 2018, the incidence of triple negatives increases higher in young women (+ 1,4% by year, 95% CI − 8,2; 11) and those over 75 years (+ 4% by year, 95% CI − 5,1; 13,2), but the results are not statistically significant. 10-year relative survival in young women increased from 74,6% (95% CI 69,6; 78,9) to 78,3%(95% CI 73,7; 82,1) between 1990–1999 and 2000–2008, respectively. Five-year relative survival is better in young women among triple negative and HER2 amplified.

Conclusion
Our study confirms the current trend of increasing the incidence of breast cancer in young women, associated with improved survival very likely attributable to earlier diagnosis due to increased awareness, and improvements in treatment. A better individualized risk-based screening strategy is needed for these patients. Additional studies will be needed to more accurately assess the risk of developing breast cancer and improve diagnostic performance.
Aurora kinase a promotes the progression of papillary thyroid carcinoma by activating the mTORC2-AKT signalling pathway
Authors: Zhao Zewei , Wang Huijuan , Kang Ning , Wang Zhongyu , Hou Xiukun , Hu Linfei , Qie Shuo , Guo Jianping , Wei Songfeng , Ruan Xianhui , Zheng Xiangqian 
Published: December 2022

Abstract
Background
Treatment failure is the main cause of death from papillary thyroid carcinoma (PTC). It is urgent to look for new intervention targets and to develop new therapies for treating PTC. Aurora-A kinase (AURKA) functionally regulates cell mitosis and is closely related to the occurrence and development of a variety of tumours. However, the expression and potential functions of AURKA in PTC remain largely elusive.

Results
Clinicopathologically, AURKA is highly expressed in PTC tissues compared to normal tissues and is correlated with lymph node metastasis, TNM stage and patient prognosis. Biologically, AURKA functions as an oncoprotein to promote the proliferation and migration of PTC cells. Mechanistically, AURKA directly binds to SIN1 and compromises CUL4B-based E3 ligase-mediated ubiquitination and subsequent degradation of SIN1, leading to hyperactivation of the mTORC2-AKT pathway in PTC cells.

Conclusions
We found that AURKA plays critical roles in regulating the progression of PTC by activating the mTORC2-AKT pathway, highlighting the potential of targeting AURKA to treat PTC.
On the chaotic nature of the Rabinovich system through Caputo and Atangana–Baleanu–Caputo fractional derivatives
Authors: Deressa Chernet Tuge 
Published: December 2022

AbstractThe Rabinovich system can describe different physical interactions, including waves in plasmas, a convective fluid flow inside a rotating ellipsoid, and Kolmogorov’s flow interactions. This study considers the Rabinovich system through Caputo and Atangana–Baleanu fractional derivatives to detect its chaotic nature. First, the existence and uniqueness of the solutions of the fractional-order systems are proved using the combination of the Picard–Lindelöf theorem and the Banach contraction principle. Then, a numerical approximation of the fractional systems is developed. The fractional Rabinovich system is found to exhibit a chaotic behavior verified via Lyapunov exponents. However, the fractional-order models do not enter into chaotic behavior at the same fractional-derivative order. Bifurcation diagrams referring to variation of the fractional-order derivatives are provided. Chaotic attractors for both cases of the fractional-derivative representation of the system are depicted. The two fractional-order models of the system show sensitivity to initial conditions. A master–response synchronization was developed in the context of the Atangana–Baleanu fractional derivative. The master and the response systems showed a strong correlation, proving the system’s applicability in solving real problems, including secure communications.
Determinants of women participation in income generating activities: evidence from Ethiopia
Authors: Alemu Abera , Woltamo Tesfaye , Abuto Aklilu 
Published: December 2022

AbstractThis paper aims to examine the major determinants and challenges of women's participation in income-generating activities focusing on rural women of Ethiopia. To carry out this study, both primary and secondary data were used. Randomly selected 161 households were the source of primary data for this study. Secondary data were collected from the review of related literature. A binary logistic regression econometric model was implemented to identify major determinants of women's participation in income-generating activities. The finding of this study revealed that in the study area, women are not allowed by their husbands to participate in high-income earning activities. They are considered a housewife and only husband are expected to participate in high income-generating activities due to the local customs. In the study area, women's participation in the income-generating activity is determined by age, husband’s education, women's education, family size, land size, market distance, livestock holding, and access to credit. This paper contributes to the literature on women's participation challenges in income-generating activities, giving emphasis to rural women's perspectives. It provides the basis for further studies aimed at challenges hindering women's participation in high-income earning activities, particularly in developing countries.
Low secondary attack rate after prolonged exposure to sputum smear positive miliary tuberculosis in a neonatal unit
Authors: Pop Roxana , Kaelin Marisa B. , Kuster Stefan P. , Sax Hugo , Rampini Silvana K. , Zbinden Reinhard , Relly Christa , Zacek Bea , Bassler Dirk , Fontijn Jehudith R. , Berger Christoph 
Published: December 2022

Abstract
Background
Several neonatal intensive care units (NICU) have reported exposure to sputum smear positive tuberculosis (TB). NICE guidelines give support regarding investigation and treatment intervention, but not for contact definitions. Data regarding the reliability of any interferon gamma release assay (IGRA) in infants as a screening test for TB infection is scarce. We report an investigation and management strategy and evaluated the viability of IGRA (T-Spot) in infants and its concordance to the tuberculin skin test (TST).

Methods
We performed an outbreak investigation of incident TB infection in a NICU after prolonged exposure to sputum smear positive miliary TB by an infant’s mother. We defined individual contact definitions and interventions and assessed secondary attack rates. In addition, we evaluated the technical performance of T-Spot in infants and compared the results with the TST at baseline investigation.

Results
Overall, 72 of 90 (80%) exposed infants were investigated at baseline, in 51 (56.7%) of 54 (60%) infants, follow-up TST at the age of 6 months was performed. No infant in our cohort showed a positive TST or T-Spot at baseline. All blood samples from infants except one responded to phytohemagglutinin (PHA), which was used as a positive control of the T-Spot, demonstrating that cells are viable and react upon stimulation. 149 of 160 (93.1%) exposed health care workers (HCW) were investigated. 1 HCW was tested positive, having no other reason than this exposure for latent TB infection. 5 of 92 (5.5%) exposed primary contacts were tested positive, all coming from countries with high TB incidences. In total, 1 of 342 exposed contacts was newly diagnosed with latent TB infection. The secondary attack rate in this study including pediatric and adult contacts was 0.29%.

Conclusion
This investigation highlighted the low transmission rate of sputum smear positive miliary TB in a particularly highly susceptible population as infants. Our expert definitions and interventions proved to be helpful in terms of the feasibility of a thorough outbreak investigation. Furthermore, we demonstrated concordance of T-Spot and TST. Based on our findings, we assume that T-Spot could be considered a reliable investigation tool to rule out TB infection in infants.
Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments
Authors: Ruscheweyh Hans-Joachim , Milanese Alessio , Paoli Lucas , Karcher Nicolai , Clayssen Quentin , Keller Marisa Isabell , Wirbel Jakob , Bork Peer , Mende Daniel R. , Zeller Georg , Sunagawa Shinichi 
Published: December 2022

AbstractBackgroundTaxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both “known” and “unknown” species based on a set of select marker genes.ResultsWe present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6–11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43–63%) or even the majority (pig, fish, cattle: 60–80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.ConclusionsWe developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at:https://github.com/motu-tool/mOTUs.
Landslide disasters in eastern Uganda: post-traumatic stress disorder and its correlates among survivors in Bududa district
Authors: Kabunga Amir , Okalo Ponsiano , Nalwoga Viola , Apili Brenda 
Published: December 2022

Abstract
Background
Post-traumatic stress disorder is the commonly reported psychiatric morbidity among the survivors of natural disasters. However, its prevalence particularly in Bududa, Eastern Uganda is largely unknown.

Aims and objectives
To assess the prevalence and correlates of post-traumatic stress disorder among Bududa landslide survivors.

Methods
A community-based cross-sectional study was conducted on a sample of 587 participants. The study setting was the Bududa district, with a multistage sampling method. Pre-tested, administered interviewer PTSD Checklist–civilian version was used as screening tools between 4th and April 29th 2022. Data were analyzed using descriptive and binary logistic approaches at a 5% level of significance.

Results
Of the study participants, 276 (46.8%) had PTSD symptoms. Among the respondents, 250 (42.6%) were in the age range of 40 and above, 396 (67.3%) were female, 284 (48.4%) had no formal education, and 333 (56.7%) were married. Results showed that male gender (AOR: 0.47; 95% CI 0.31–0.73; p = 0.001), widowhood (AOR: 0.44; 95% CI 0.21–0.94; p = 0.034), lack of counseling (AOR: 0.44; 95% CI 0.21–0.94; p = 0.001), and duration since the landslide (AOR: 0.35; 95% CI 0.23–0.52; p = 0.001) were associated with an increased likelihood of screening for PTSD in landslide survivors.

Conclusion
Landslides pose significant effects on the mental health of survivors. In the present study, the extent of PTSD among survivors is substantially high. male gender,, widowhood, lack of counselling, low social support, and duration since the landslide were significantly associated with PTSD. Effective screening and awareness programs among survivors should be strengthened for the prevention and treatment of psychiatric morbidity among the survivors of landslides.