bluuebunny/crossref_metadata_2025_split huggingface dataset:
Split-Cre-mediated GFP expression as a permanent marker for flagellar fusion of
Trypanosoma brucei
in its tsetse fly host
Authors: Etzensperger Ruth , Benninger Mattias , Pozzi Berta , Rehmann Ruth , Naguleswaran Arunasalam , Schumann Gabriela , Van Den Abbeele Jan , Roditi Isabel 
Published: December 2024

ABSTRACT

Trypanosomes have different ways of communicating with each other. While communication via quorum sensing, or by the release and uptake of extracellular vesicles, is widespread in nature, the phenomenon of flagellar fusion has only been observed in
Trypanosoma brucei
. We showed previously that a small proportion of procyclic culture forms (corresponding to insect midgut forms) can fuse their flagella and exchange cytosolic and membrane proteins. This happens reproducibly in cell culture. It was not known, however, if flagellar fusion also occurs in the tsetse fly host, and at what stage of the life cycle. We have developed a split-Cre-Lox system to permanently label trypanosomes that undergo flagellar fusion. Specifically, we engineered trypanosomes to contain a GFP gene flanked by Lox sites in the reverse orientation to the promoter. In addition, the cells expressed inactive halves of the Cre recombinase, either N-terminal Cre residues 1–244 (N-Cre) or C-terminal Cre residues 245–343 (C-Cre). Upon flagellar fusion, these Cre halves were exchanged between trypanosomes, forming functional full Cre and flipping reverse-GFP into its forward orientation. We showed that cells that acquired the second half Cre through flagellar fusion were permanently modified and that the cells and their progeny constitutively expressed GFP. When tsetse flies were co-infected with N-Cre and C-Cre cells, GFP-positive trypanosomes were observed in the midgut and proventriculus 28–34 days post-infection. These results show that flagellar fusion not only happens in culture but also during the natural life cycle of trypanosomes in their tsetse fly host.

IMPORTANCE

We have established a procedure to permanently label pairs of trypanosomes that transiently fuse their flagella and exchange proteins. When this occurs, a reporter gene is permanently flipped from the “off” to the “on” position, resulting in the production of green fluorescent protein. Crucially, green trypanosomes can be detected in tsetse flies co-infected with the two cell lines, proving that flagellar fusion occurs in the host. To our knowledge, we are the first to describe a split-Cre-Lox system for lineage tracing and selection in trypanosomes. In addition to its use in trypanosomes, this system could be adapted for other parasites and in other contexts. For example, it could be used to determine whether flagellar fusion occurs in related parasites such as Leishmania and
Trypanosoma cruzi
or to monitor whether intracellular parasites and their hosts exchange proteins.
Genome sequences of two
Klebsiella
phages isolated from wastewater treatment samples that infect a clinical
Klebsiella
isolate
Authors: Lewis Jessica M. , Arens Daniel K. , Quaye Abraham , Calvopina-Chavez Diana G. , Jensen Kyson T. , Miller Ashley K. , Moss Melinda M. , Warren M. Elizabeth , Tavana Justina P. , Johnson Steven M. , Grose Julianne H. 
Published: December 2024

ABSTRACT

We announce the complete genomes of
Klebsiella
phages ValerieMcCarty03 and ValerieMcCarty04 isolated from wastewater treatment plant samples that infect a multidrug-resistant
Klebsiella oxytoca
clinical isolate. These phages belong to the T4-like cluster and fall within the
Jiaodavirus
genus.
Draft genome of
Talaromyces
sp. UPCC 4333, from
Senna alata
flowers, displayed a remarkable diversity of potentially novel biosynthetic gene clusters
Authors: Eugenio Rafael B. , Gloria Paul Christian T. , Relucio-San Diego Mary Ann Cielo V. 
Published: December 2024

ABSTRACT

Here, we report the draft genome of
Talaromyces
sp. UPCC 4333, isolated from
Senna alata
flowers, with a size of 31.3 Mb and 92.9% BUSCO completeness. The genome contains at least 39 secondary metabolite biosynthetic gene clusters which merit further investigation in the future.
Draft genome sequence of endophyte
Bacillus amyloliquefaciens
strain Apn01R, isolated from the roots of
Alhagi pseudalhagi
(Bieb.) Fisch
Authors: Chebotar Vladimir K. , Myskova Anna V. , Khudyaeva Margarita , Keleinikova Oksana V. , Baganova Maria E. , Zaplatkin Alexander N. , Pishchik Veronika N. , Chizhevskaya Elena P. 
Published: December 2024

ABSTRACT

In this article, we announce the sequence and draft analysis of the genome of endophyte
Bacillus amyloliquefaciens
strain Apn01R, isolated from the roots of
Alhagi pseudalhagi
(Bieb.) Fisch. Our results show genes that may be crucial to defy abiotic stress and repel bacterial and fungal pathogens.
Draft genome sequence and analysis of endophyte
Bacillus amyloliquefaciens
strain Can02R isolated from the roots of
Chenopodium album
L.
Authors: Chebotar Vladimir K. , Myskova Anna V. , Khudyaeva Margarita , Keleinikova Oksana V. , Baganova Maria E. , Zaplatkin Alexander N. , Pishchik Veronika N. , Chizhevskaya Elena P. 
Published: December 2024

ABSTRACT

In this study, we sequence, assemble, and analyze the genome of endophyte
Bacillus amyloliquefaciens
Can02R isolated from the roots of the resurrection plant host,
Chenopodium album
. The assembly of the strain’s genome amounts to 3,965,760 bp and contains 3,989 coding sequences, among which synthetic antibiotic clusters and multidrug resistance transporters can be found.
A nonstandard Standard Model
Authors: LaChapelle J. 
Published: December 2024

This paper examines the Standard Model under the strong–electroweak symmetry group [Formula: see text] subject to the Lie algebra condition [Formula: see text]. Physically, the condition ensures that all electroweak gauge bosons interact with each other prior to symmetry breaking — as one might expect from [Formula: see text] invariance. This represents a crucial shift in the identification of physical gauge bosons: Unlike the Standard Model which posits a change of Lie algebra basis induced by spontaneous symmetry breaking, here the basis is unaltered and A, [Formula: see text], [Formula: see text] represent the physical bosons both before and after spontaneous symmetry breaking. Our choice of [Formula: see text] requires some modification of the matter field representation of the Standard Model. The group [Formula: see text] admits two pertinent defining representations, [Formula: see text] and its [Formula: see text]-conjugate [Formula: see text], related by a large gauge transformation. Accordingly, the product group structure calls for strong–electroweak degrees of freedom in the [Formula: see text] and the [Formula: see text] of [Formula: see text] that possess integer electric charge just like leptons. These degrees of freedom play the role of quarks, and they lead to a modified Lagrangian that nevertheless reproduces transition rates and cross-sections equivalent to the Standard Model. In particular, they reproduce the fractional electric charge of quark currents. The close resemblance between quark and lepton electroweak doublets in this picture suggests a mechanism for a speculative phase transition between quarks and leptons that stems from the product structure of the symmetry group. Our hypothesis is that the strong and electroweak bosons see each other as a source of decoherence. In effect, lepton representations get identified with the [Formula: see text]-trace-reduced quark representations. This mechanism allows for possible extensions of the Standard Model that do not require large inclusive multiplets of matter fields and might explain the Higgs as a pseudo Nambu–Goldstone boson.
An Innovative Collaboration-Based Ozone and Aerosol Observation Network in Northeast Asia
Authors: Ji Dongsheng , Zhang Miao , Liu Yu , Xu Yang , Cong Chunhua , He Jun , Wang Lili , Tang Guiqian , Liu Zirui , Gao Wenkang , Li Yan , Zhang Xiaolin , Cui Jinmeng , Chen Jinmin , Wang Yuesi 
Published: December 2024

Abstract
Situated in close proximity to the Korea Peninsula and the Japan Islands, Shandong Province in China (SDP) has emerged as a focal point for global attention due to its significant surface ozone (O3) and aerosol pollution. Despite this attention, there are notable gaps in knowledge across various interconnected research domains, encompassing climate change, atmospheric circulation, anthropogenic emissions, and the chemistry of O3 and aerosols. The impact of frequent heat waves on regional O3 and aerosol pollution remains unclear, while our comprehension of atmospheric circulation dynamics and the chemistry involved with O3 and aerosols is still hampered by substantial limitations. The unique topography and geographical setting of SDP, with its complex interplay of factors like sea–land breezes, mountain–valley winds, and urban heat islands, make it an ideal location for investigating the dynamics of O3 and aerosol chemistry. Moreover, it is essential to explore the effects of transboundary transport on O3 and aerosol pollution and delve into the underlying mechanisms contributing to their combined pollution effects. To bridge these knowledge gaps, the Innovative Collaboration-Based Ozone and Aerosol Observation Network in Northeast Asia has been established through collaborative efforts involving the Bureaus of Ecology and Environment, Meteorology in SDP, and the Chinese Academy of Sciences. This network encompasses various components, including air quality and weather stations, a network of low-cost air quality sensors, monitoring stations focused on atmospheric photochemical smog and aerosol chemical speciation, and vertical measurement systems targeting O3 and its precursor gases (utilizing light detection and ranging, balloon sounding, and drone-based measurements), as well as measurements conducted via vehicles and ships. Additionally, preliminary findings from this comprehensive observational campaign will be shared.
Accelerating Community-Wide Evaluation of AI Models for Global Weather Prediction by Facilitating Access to Model Output
Authors: Radford Jacob T. , Ebert-Uphoff Imme , Stewart Jebb Q. , Musgrave Kate D. , DeMaria Robert , Tourville Natalie , Hilburn Kyle 
Published: December 2024

Abstract
Numerous artificial intelligence-based weather prediction (AIWP) models have emerged over the past 2 years, mostly in the private sector. There is an urgent need to evaluate these models from a meteorological perspective, but access to the output of these models is limited. We detail two new resources to facilitate access to AIWP model output data in the hope of accelerating the investigation of AIWP models by the meteorological community. First, a 3-yr (and growing) reforecast archive beginning in October 2020 containing twice daily 10-day forecasts for FourCastNet v2-small, Pangu-Weather, and GraphCast Operational is now available via an Amazon Simple Storage Service (S3) bucket through NOAA’s Open Data Dissemination (NODD) program (https://noaa-oar-mlwp-data.s3.amazonaws.com/index.html). This reforecast archive was initialized with both the NOAA’s Global Forecast System (GFS) and ECMWF’s Integrated Forecasting System (IFS) initial conditions in the hope that users can begin to perform the feature-based verification of impactful meteorological phenomena. Second, real-time output for these three models is visualized on our web page (https://aiweather.cira.colostate.edu) along with output from the GFS and the IFS. This allows users to easily compare output between each AIWP model and traditional, physics-based models with the goal of familiarizing users with the characteristics of AIWP models and determine whether the output aligns with expectations, is physically consistent and reasonable, and/or is trustworthy. We view these two efforts as a first step toward evaluating whether these new AIWP tools have a place in forecast operations.
From trauma to chronicity: Understanding the incidence and early immune changes of chronic complications in polytrauma patients
Authors: Zhang Cong , Chen Deng , Wan Qian , Yin Gang , Liu Yang , Luo Jialiu , Chen Shunyao , Lin Zhiqiang , Gu Shuaipeng , Li Hui , Chang Teding , Dong Liming , Zhang Peidong , Tang Zhaohui 
Published: December 2024

Objective Polytrauma is a complex condition associated with poor outcomes and high mortality rates resulting from severe damage and complicated complications. This study sought to ascertain the incidence of chronic complications in polytrauma patients, as well as the early immune changes and risk factors. Methods A multicenter, prospective and observational cohort study was conducted at the emergency surgery or traumatic intensive care unit (TICU) of the Advanced Trauma Center from August 2020 to July 2023. A total of 2033 consecutive trauma patients were included in the study. In the first 1, 7, and 14 days after admission, flow cytometry and immunoassay kits were used to examine cytokine release and lymphocyte count. Results Trauma patients were reported 33.8% (687/2033) chronic complication rates, with monotrauma patients reported 8.1% (55/683) and polytrauma patients reported 59.4% (802/1350). And the four most frequent chronic complications in polytrauma patients were chronic musculoskeletal pain (30.4%), post-traumatic osteoarthritis (27.2%), chronic wound (21.6%), and chronic lung injury (14.1.%) .There were significant differences in lymphocyte ratios and cytokine levels, at 1, 7, and 14 day of admission between chronic complication groups (CCP) and not chronic complication groups (N-CCP) in polytrauma. Polytrauma patients with characteristics of higher ratio of Ts7d ratio (95% CI: 2.01–6.21), Treg14d (95% CI: 1.12–5.43) and level of IL-67d (95% CI: 1.22–4.43), TNF-α7d (95% CI: 1.05–3.83), IL-1014d (95% CI: 2.01–6.84) were found to have a higher likelihood of experiencing a chronic complication. Conversely, a higher ratio of Tc1d (95% CI: 0.53–0.86), Th1d (95% CI: 0.64–0.95) and Th/Ts14d (95% CI: 0.21–0.64) were identified as independent protective factors against a chronic complication event. Conclusion Polytrauma patients exhibit a notable prevalence of chronic complications. Some immune and inflammatory indicators can be observed early in combination after injury to predict the risk of chronic complications after polytrauma.
Combined CAR-T/HSCT approach in a patient with refractory acute lymphoblastic leukemia and cystic fibrosis
Authors: Di Majo Benedetta E , Vendemini Francesca , Bonanomi Sonia , Casartelli Pietro , Napolitano Sara , Ottaviano Giorgio , Prunotto Giulia , Verna Marta , Sala Alessandra , Migliorino Guglielmo M , Petrella Francesco , Rosso Lorenzo , Claut Laura , Rafaniello Raviele Paola , Rizzari Carmelo , Biondi Andrea , Balduzzi Adriana , Lucchini Giovanna 
Published: December 2024

Introduction: The association of acute lymphoblastic leukaemia (ALL) and cystic fibrosis (CF) is rare. We present the case of a paediatric patient affected by CF and refractory B-cell precursor (BCP) ALL, who was treated with combined chimeric antigen receptor T-cells (CAR-T) and allogeneic haematopoietic stem cell transplantation (HSCT). Case description: Autologous-CD19 targeting CAR-T allowed to achieve molecular remission and spare chemo-related toxicity. As B-cell aplasia was not achieved, the patient underwent HSCT after total body irradiation (TBI)-based conditioning. The course after HSCT was complicated by veno-occlusive disease, status epileptic and pulmonary invasive fungal infection which showed progressive radiological worsening despite aggressive treatment. Five months after HSCT a left upper lobe lobectomy was successfully performed. Thirteen months after HSCT the patient is in complete disease remission with normal lung function. Conclusions: CAR-T cell therapy bridge-to-HSCT may be an effective approach in paediatric refractory ALL in the context of multiple comorbidities as observed in CF.
LRP1B mutation is associated with lymph node metastasis in endometrial carcinoma: A clinical next-generation sequencing study
Authors: Zheng Yunfeng , Yang Fan , Wu Jie 
Published: December 2024

Background This study aims to investigate the mutation status and protein expression of low-density lipoprotein receptor-related protein 1B (LRP1B) in endometrial cancer, and analyze its association with lymph node metastasis (LNM) in endometrial cancer. Methods Targeted next-generation sequencing (NGS) was conducted on both tumor tissues and paired blood DNA obtained from 94 endometrial cancer patients, followed by comprehensive analysis. Additionally, immunohistochemistry (IHC) was used to explore the correlation between LRP1B protein expression levels, its gene mutation status, and LNM. Results LRP1B mutation was observed in 19 patients (20.2%). Our results revealed that LRP1B mutation frequencies were significantly different between endometrial cancer with or without LNM ( P = 0.038). Multivariate analysis indicated that LRP1B mutation was a favorable predictor (odds ratio 0.09; 95% confidence interval 0.01–0.95; P = 0.045) for LNM in endometrial cancer. Further analysis revealed that combination of LRP1B mutation with clinical variants (LVSI and histological subtype) yielded a higher area under the curve value of 0.871) and patients harboring LRP1B mutated-type were less likely to develop LNM. On integrated analysis, the concordance between LRP1B NGS and LRP1B IHC was 73.3%. Conclusions This study utilizes targeted NGS to uncover the relationship between LRP1B mutation and LNM status, contributing to the development of primary prevention and proactive treatment strategies.
Clinical efficacy of proximal femoral nail anti-rotation in elderly patients with intertrochanteric fractures with negative medial cortical support: A comparison of lithotomy and scissor position techniques
Authors: Lin Zhe , Chen Weidong , Zhou Wenchao 
Published: December 2024

Background Femoral intertrochanteric fractures are a prevalent type of hip fracture among the elderly population. And proximal femoral nail anti-rotation (PFNA) is the leading surgical technique for managing femoral intertrochanteric fractures in this patient population. Objective This study aimed to evaluate the clinical efficacy of proximal femoral nail anti-rotation (PFNA) in managing intertrochanteric fractures in elderly patients with negative medial cortical support. Additionally, the outcomes associated with two different nail positioning techniques were investigated. Methods Elderly patients with femoral intertrochanteric fractures with negative medial cortical support, treated between January 2017 and January 2021, were included. A retrospective analysis of their clinical data was conducted. Patients were categorized into two groups based on the positioning technique: lithotomy position group (n = 40) and scissor position group (n = 40). Baseline characteristics, perioperative indicators, hidden blood loss, and Harris hip scores were compared. Results The groups exhibited no significant differences in baseline characteristics, incision length, or postoperative tip-apex distance. The scissor position group experienced fewer fluoroscopies, shorter surgical durations, and lower Visual Analogue Scale (VAS) scores for the unaffected limb on postoperative day 1 compared to the lithotomy position group. No significant differences in hidden blood loss were observed between the groups. The Harris hip score for the unaffected side showed no significant differences between the scissor position group on postoperative day 1 and postoperative month 1. However, in the lithotomy position group, the Harris hip score of the unaffected side on postoperative day 1 was significantly lower than that at postoperative month 1. Additionally, the Harris hip score for the unaffected side on postoperative day 1 was substantially higher in the scissor position group compared to the lithotomy position group, although there were no significant differences between the two groups at postoperative month 1. Conclusion PFNA in the scissor position demonstrated advantages over the lithotomy position, including reduced fluoroscopy usage, shorter surgical duration, and less trauma to the unaffected limb. These findings indicate its effectiveness in managing intertrochanteric fractures in elderly patients with negative medial cortical support.
Drug overdose deaths among women 1999–2021 in the United States: Differences by race, ethnicity, and age
Authors: Jones Abenaa A , Segel Joel E , Skogseth Emma M , Apsley Hannah B , Santos-Lozada Alexis R 
Published: December 2024

Background: The U.S. drug overdose epidemic is increasingly severe and steep increases have been seen among women. Objective: To explore trends in drug overdose deaths among women in the United States by race, ethnicity, and age group. Design: This study is a retrospective observational study of drug overdose deaths among U.S. women from 1999 to 2021. Methods: We use CDC WONDER Multiple Causes of Death files data using International Classification of Diseases, 10th Revision (ICD-10) codes X40–X44, X60–X64, X85, and Y10–Y14 to identify overall drug overdose deaths, T40.5 for cocaine-related deaths, T40.0–T40.4, T40.6 for opioid-related deaths, T42.4 for benzodiazepines, and T43.6 to identify psychostimulants. Race and ethnicity were defined as non-Hispanic Black, White, American Indian/Alaska Native (AI/AN), Asian, and Hispanic. We calculated overdose death rates per 100,000 women for all overdose deaths and for specific drugs by year, stratified by race and ethnicity. Results: From 1999 to 2021, overdose deaths among all women in the United States increased by 480%. Overdose deaths rose 750% for non-Hispanic AI/AN women, 490% for non-Hispanic Black women, 450% for non-Hispanic White women, 325% for Hispanic women, and 150% for non-Hispanic Asian or Pacific Islander women. Women ages 35–44 and 45–54 saw the largest increases in overall overdose deaths. Cocaine-related deaths were more prevalent among non-Hispanic Black women, opioid and methamphetamine-related deaths were more prevalent among non-Hispanic AI/AN women, and benzodiazepine-related deaths were more prevalent among non-Hispanic White women. Conclusion: Increases in overdose deaths were noted in all races, ethnicities, and age groups, with deaths continuing to accelerate in 2021. Our study highlights a need for interventions expanding access to medications for opioid use disorder, naloxone, fentanyl test strips, and contingency management while accounting for gendered roles and vulnerabilities.