bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Entner-Doudoroff pathway in
Pseudomonas aeruginosa
catheter-associated urinary tract infections
Authors: El Husseini Nour , Mekonnen Solomon A. , Hall Cherisse L. , Cole Stephanie J. , Carter Jared A. , Belew Ashton T. , El-Sayed Najib M. , Lee Vincent T. 
Published: December 2023

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic nosocomial pathogen responsible for a subset of catheter-associated urinary tract infections (CAUTI). In a murine model of
P. aeruginosa
CAUTI, we previously demonstrated that urea within urine suppresses quorum sensing and induces the Entner-Doudoroff (E-D) pathway. The E-D pathway consists of the genes
zwf
,
pgl
,
edd
, and
eda
. Zwf and Pgl convert glucose-6-phosphate into 6-phosphogluconate. Edd hydrolyzes 6-phosphogluconate to 2-keto-3-deoxy-6-phosphogluconate (KDPG). Finally, Eda cleaves KDPG to glyceraldehyde-3-phosphate and pyruvate, which enters the citric acid cycle. Here, we generated in-frame E-D mutants in the strain PA14 and assessed their growth phenotypes on chemically defined and complex media. These E-D mutants have a growth defect when grown on glucose or gluconate as the sole carbon source, which is similar to results previously reported for PAO1 mutants lacking E-D genes. RNA-sequencing following short exposure to urine revealed minimal gene regulation differences compared to the wild type. In a murine CAUTI model, virulence testing of E-D mutants revealed that two mutants lacking
zwf
and
pgl
showed minor fitness defects. Infection with the ∆
pgl
strain exhibited a 20% increase in host survival, and the ∆
zwf
strain displayed decreased colonization of the catheter and kidneys. Consequently, our findings suggest that the E-D pathway in
P. aeruginosa
is dispensable in this model of CAUTI.

IMPORTANCE

Prior studies have shown that the Entner-Doudoroff pathway is up-regulated when
Pseudomonas aeruginosa
is grown in urine. Pseudomonads use the Entner-Doudoroff (E-D) pathway to metabolize glucose instead of glycolysis, which led us to ask whether this pathway is required for urinary tract infection. Here, single-deletion mutants of each gene in the pathway were tested for growth on chemically defined media with single-carbon sources as well as complex media. The effect of each mutant on global gene expression in laboratory media and urine was characterized. The virulence of these mutants in a murine model of catheter-associated urinary tract infection revealed that these mutants had similar levels of colonization indicating that glucose is not the primary carbon source utilized in the urinary tract.
Ameliorative effects of aqueous extract from rosemary on oxidative stress and inflammation pathways caused by a high-fat diet in C57BL/6 mice
Authors: de Oliveira e Silva Ana Mara , Pereira Raquel Oliveira , Oliveira Anne Karoline de Souza , Harris Fernanda Santana , de Melo Illana Louise Pereira , Almeida-Souza Thiago Henrique , Yoshime Luciana Tedesco , dos Santos Melo Caroline , Lopes dos Santos Jymmys , de Andrade-Wartha Elma Regina Silva , Cogliati Bruno , Granato Daniel , Mancini-Filho Jorge 
Published: December 2023

Rosemary is an herb exhibits biological properties, attenuates inflammation, oxidative stress, and improves lipid profile. Here, we evaluated the effects of rosemary aqueous extract (RE) on mice fed with a high-fat diet (HFD). Male C57BL/6 mice were administered a control diet or HFD for 10 weeks. The treated groups received RE in the diet at different concentrations: 25, 250, and 500 mg/100 g. After 10 weeks, serum concentrations of glucose, lipid, insulin, leptin, adiponectin, and cytokines were evaluated and the oxygen radical absorbance capacity was determined. Histological analysis was performed to determine the concentrations of triacylglycerides (TG), total cholesterol, cytokines, and antioxidant enzymes as well as the expression of genes involved in lipid metabolism, oxidative stress, and inflammation. The dietary RE ameliorated HFD-induced weight gain, adipose tissue weight, glucose intolerance, and insulin, leptin, and free fatty acid levels. Reduction in hepatic TG deposition was observed. The levels of inflammatory cytokines decreased, and the expression of genes involved in lipid metabolism increased. RE mitigated oxidative stress and reduced the production of reactive oxygen species in HepG2 and 3T3-L1 cells. Therefore, RE is a potential therapeutic agent for the prevention of inflammation and oxidative stress outcomes associated with obesity.
From Embodiment to Super-Embodiment: An Approach to Open-Ended and Human Aligned Intelligence/Mind
Authors: Kuniyoshi Yasuo 
Published: December 2023

Embodiment is a key to solving the reliability and alignment issues in the current AI. This is because it imposes consistent constraints on the entire agent-environment interactions and accompanying information without specifying their actual contents, and the constraints are common to those with similar embodiment. The concept of embodiment should be generalized beyond mechanical properties of the body and information structure of sensory signals, encompassing internal organs and metabolism, mental processes, and inter-agent interactions, to “super-embodiment”. It can address sensibilities, values and morals toward artificial humanity, which will be critically important for the next generation AI. [Y. Kuniyoshi, Open-ended intelligence arises from emergence and development from embodiment, J. Robotics Soc. Jpn. 41(7) (2023) 585–590 (in Japanese); Y. Kuniyoshi, Fusing autonomy and sociality via embodied emergence and development of behaviour and cognition from fetal period, Philos. Trans. R. Soc. B: Biol. Sci. 374 (2019) 20180031].
Modelling and Explaining IR System Performance Towards Predictive Evaluation
Authors: Faggioli Guglielmo 
Published: December 2023

Information Retrieval (IR) systems play a fundamental role in many modern commodities, including search engines (SEs), digital libraries, recommender systems, and social networks.
The IR task is particularly challenging because of the volatility of IR systems performance: users' information needs change daily, and so do the documents to be retrieved and the concept of what is relevant to a given information need. Therefore, the empirical offline evaluation of an IR system is a costly and slow post-hoc procedure, that happens after the system deployment. Given the challenges linked to empirical IR evaluation, predicting a system's performance before its deployment would add significant value to the development of an IR system.
In this manuscript, we place the cornerstone for the prediction of IR performance, by considering two closely related areas: the modeling of IR systems performance and the Query Performance Prediction (QPP). The former area allows us to identify those features that impact the most on the performance and that can be used as predictors, while the latter provides us with a starting point to instantiate the predictive task in IR.
Concerning the modeling of IR performance, we first investigate one of the most popular statistical tools, ANOVA. In particular, we compare traditional ANOVA with a recent approach, bootstrap ANOVA, and observe the different conclusions that can be achieved using these two different statistical tools [Faggioli and Ferro, 2021]. Secondly, using ANOVA, we study the concept of topic difficulty and observe that the topic difficulty is not an intrinsic property of the information need but stems from the formulation used to represent the topic [Culpepper et al., 2022]. Finally, we show how to use Generalized Linear Models (GLMs) as an alternative to the traditional linear modeling of IR performance [Faggioli et al., 2022]. We show how GLMs provide more powerful inference with comparable stability.
Our analyses on the QPP domain start with developing a predictor used to select among a set of reformulations for the same information need, the best-performing one for the systematic review task [Di Nunzio and Faggioli, 2021]. Secondly, we investigate how to classify queries as either semantic or lexical to predict whether neural models will perform better than lexical ones. Finally, given the challenges shown in the evaluation of the previous approaches, we devise a new evaluation procedure, dubbed sMARE [Faggioli et al., 2021]. sMARE allows moving from a single point estimation of the performance to a distributional one, allowing us to achieve improved comparisons between QPP models and more precise analyses.

Awarded by:
University of Padova, Padova, Italy on 20 March 2023.

Supervised by:
Nicola Ferro.

Available at:
https://www.research.unipd.it/handle/11577/3472979.
TROP2 Is Associated with Primary Resistance to Immune Checkpoint Inhibition in Patients with Advanced Non–Small Cell Lung Cancer
Authors: Bessede Alban , Peyraud Florent , Besse Benjamin , Cousin Sophie , Cabart Mathilde , Chomy François , Rey Christophe , Lara Oren , Odin Ophélie , Nafia Imane , Vanhersecke Lucile , Barlesi Fabrice , Guégan Jean-Philippe , Italiano Antoine 
Published: December 2023

Abstract

Purpose:
Mechanisms of primary resistance to inhibitors of the programmed cell death-1 (PD-1)/programmed death-ligand 1 (PD-L1) signaling axis in non–small cell lung cancer (NSCLC) are still poorly understood. While some studies suggest the involvement of trophoblast cell surface antigen 2 (TROP2) in modulating tumor cell resistance to therapeutic drugs, its specific role in the context of PD-1/PD-L1 axis blockade is not definitively established.

Experimental Design:
We performed high-throughput analysis of transcriptomic data from 891 NSCLC tumors from patients treated with either the PD-L1 inhibitor atezolizumab or chemotherapy in two large randomized clinical trials. To confirm our results at the protein level, we complemented this transcriptional approach by performing a multiplex immunofluorescence analysis of tumor tissue samples as well as a proteomic profiling of plasma.

Results:
We observed a significant association of TROP2 overexpression with worse progression-free survival and overall survival on PD-L1 blockade, independent of other prognostic factors. Importantly, we found increased TROP2 expression to be predictive of survival in patients treated with atezolizumab but not chemotherapy. TROP2 overexpression was associated with decreased T-cell infiltration. We confirmed these results at the proteomic level both on tumor tissue and in plasma.

Conclusions:
Our results suggest an important contribution of TROP2 expression to the primary resistance to PD-L1 blockade in NSCLC. TROP2-biomarker–based strategy may be relevant in selecting patients with NSCLC who are more likely to benefit from a combination of immunotherapy and an anti-TROP2 agent.
Cardiac Abnormalities in Hispanic/Latina Women With Prior De Novo Hypertensive Disorders of Pregnancy
Authors: Quesada Odayme , Kulandavelu Shathiyah , Vladutiu Catherine J. , DeFranco Emily , Minissian Margo B. , Makarem Nour , Bello Natalie A. , Wong Melissa S. , Pabón Maria A. , Chandra Alvin A. , Avilés-Santa Larissa , Rodríguez Carlos J. , Bairey Merz C. Noel , Sofer Tamar , Hurwitz Barry E , Talavera Gregory A. , Claggett Brian L. , Solomon Scott D. , Cheng Susan 
Published: December 2023

BACKGROUND:
Hypertensive disorders of pregnancy (HDP) are associated with long-term maternal risks for cardiovascular disease for reasons that remain incompletely understood.

METHODS:
The HCHS/SOL (Hispanic Community Health Study/Study of Latinos), a multi-center community-based cohort of Hispanic/Latino adults recruited 2008 to 2011, was used to evaluate the associations of history of de novo HDP (gestational hypertension, preeclampsia, eclampsia) with echocardiographic measures of cardiac structure and function in Hispanic/Latina women with ≥1 prior pregnancy and the proportion of association mediated by current hypertension (>140/90 mm Hg or antihypertensive therapy).

RESULTS.
The study cohort included 5168 Hispanic/Latina women with an average age (SD) of 58.7 (9.7) years at time of echocardiogram. Prior de novo HDP was reported by 724 (14%) of the women studied and was associated with lower left ventricle (LV) ejection fraction −0.66 (95% confidence interval [CI], −1.21 to −0.11), higher LV relative wall thickness 0.09 (95% CI, 0–0.18), and 1.39 (95% CI, 1.02–1.89) higher risk of abnormal LV geometry after adjusting for blood pressure and other confounders. The proportion of the association mediated by current hypertension between HDP and LV ejection fraction was 0.09 (95% CI, 0.03–0.45), LV relative wall thickness was 0.28 (95% CI, 0.16–0.51), abnormal LV geometry was 0.14 (95% CI, 0.12–0.48), concentric left ventricular hypertrophy was 0.31 (95% CI, 0.19–0.86), and abnormal LV diastolic dysfunction was 0.58 (95% CI, 0.26–0.79).

CONCLUSIONS.
In a large cohort of Hispanic/Latina women those with history of de novo HDP had detectable and measurable subclinical alterations in cardiac structure and both systolic and diastolic dysfunction that were only partially mediated by current hypertension.
Fortresses as Ideological Images of Power
Authors: Spalinger Anthony 
Published: December 2023

This paper is a discussion of the essential, indeed the key, element of New Kingdom pictorial representations of warfare in Asia surrounding the depiction of the enemy citadel-fortress. We appear to find this depiction from the early stages of the 18th Dynasty onwards, but its inclusion as well as absence needs further specification, and that is the aim of this study. Based on earlier analyses of images of warfare, the following contribution carries the vector of imagery and historical development. The contrast of these urban scenes with Libyan and Nubian combat depictions, frequently touched upon in scholarship, will be partially limned in this paper. [Formula: see text]
Rituximab as add-on therapy in patients with resistant lupus nephritis who have failed induction or maintenance therapy with other agents: A real-world experience from a single center in Mumbai
Authors: Yadav Sandeep , Balakrishnan C , Mangat Gurmeet , Kothari Jatin 
Published: December 2023

Background Lupus nephritis (LN) is associated with poor outcomes and a significant risk of progression to end-stage renal disease (ESRD). Some patients with resistant LN do not respond adequately to current treatment options and need alternative strategies or therapies. Objective The objective is to evaluate the efficacy and safety of rituximab as a re-induction therapy (Re-RTX) followed by maintenance therapy for patients with resistant LN. Methods Twenty-four patients with resistant LN (failed initial induction therapy or severe relapse after remission) were analyzed. Re-RTX was co-administered with other immunosuppressants. The primary KDIGO criteria outcomes included renal response (complete and partial), disease progression, relapses, and infections. Results The median age was 28 years (IQR 24.5–42), and the female-to-male ratio was 11:1. All patients had active LN, and 91.3% had proliferative LN. Baseline creatinine was 1.075 mg% (IQR 0.7–1.38), and mean urine protein-to-creatinine ratio (UPCR) was 4.9 (IQR 2.8–6.65). Of the patients receiving RTX as re-induction therapy, 66.6% (16/24) had failed initial induction therapy with other immunosuppressants, whereas 33.3% (8/24) had severe relapse during maintenance therapy. Re-RTX had a favorable renal response at 6 months, with 91.7% of the patients responding (20.8% complete response and 70.8% partial response). At 12 months, 58.3% of the patients maintained a renal response (25% complete response and 33.3% partial response). Approximately one-third of patients relapsed within a year. Fourteen patients (58.3%) continued RTX maintenance therapy with two different treatment regimens. At 6 months, Regimen-1 (500 mg every 6 months) resulted in a partial response in 43% (3/7) and relapse in 57% (4/7) of patients. Regimen 2 (1 g dose per year) achieved a complete response in 28.5% (2/7) and a partial response in 71.5% (5/7) with no relapses at 6 months. At a median follow-up of 29 months, adverse renal outcomes were observed in 29.16% of the patients with progression to advanced chronic kidney disease (CKD) or end-stage renal disease (ESRD). The overall use of Re-RTX was considered safe, with a reported infection prevalence of 16%, which is comparable to the existing data. Conclusion Re-RTX demonstrated efficacy and safety as an induction therapy for resistant LN. However, the response waned after 1 year, underscoring the need for optimized maintenance therapy.
Do upright radiograph findings affect treatment plans for patients with thoracic and lumbar spine injuries?
Authors: Ragoowansi Henna , Young Brian , Young Steven , Young Jeffrey 
Published: December 2023

Background After spinal trauma, upright radiographs are commonly used to evaluate spinal stability. However, the benefits and risks of upright films have not yet been thoroughly studied. This study aimed to elucidate the effect that upright imaging has on patients with thoracic and/or lumbar spinal injuries by evaluating the impact on treatment decisions. Methods A retrospective review of all adult patients who suffered traumatic spine injuries and received thoracic and/or lumbar spine imaging between April 2019 and March 2021 in a Level 1 University Trauma Center. Patients’ charts were reviewed, and those patients who received upright films as a final dynamic evaluation of their spine before clearance for standing were identified. Fractures due to infection or malignancy were excluded as were 17 patients who only received post-operative upright films. We examined whether upright films modified the treatment strategy. Results Of the 353 upright radiographs conducted on patients without prior surgical intervention, 27 (7.6%) of these studies provided information not known from prior imaging; the remaining 92.4% of upright films were considered “unchanged” or “stable.” Of the 27 patients who had changes in uprights, in only 7 cases (2.0%) did the new findings affect the treatment plans. In 6/7 cases, upright films showed increased vertebral body height loss and/or worsening fractures—suggestive of instability—in previously known T12-L1 fractures. Conclusions We studied 353 patients who received T and/or L uprights after suffering a traumatic spine injury and before receiving any surgical interventions. Of these patients, 98.0% did not gain substantial benefit from the additional imaging as the upright radiographs did not affect the treatment strategy. In 2% of cases a significant change in management was indicated following the upright films; virtually all of these were in T11-L2 fractures. The utility of upright films should be re-evaluated and more studies directed to potentially clarify which subgroups of patients will benefit from these radiographs.
Machine Learning and Deep Learning Techniques Applied to Diabetes Research: A Bibliometric Analysis
Authors: García-Jaramillo Maira , Luque Carolina , León-Vargas Fabian 
Published: December 2023

Background: The use of machine learning and deep learning techniques in the research on diabetes has garnered attention in recent times. Nonetheless, few studies offer a thorough picture of the knowledge generation landscape in this field. To address this, a bibliometric analysis of scientific articles published from 2000 to 2022 was conducted to discover global research trends and networks and to emphasize the most prominent countries, institutions, journals, articles, and key topics in this domain. Methods: The Scopus database was used to identify and retrieve high-quality scientific documents. The results were classified into categories of detection (covering diagnosis, screening, identification, segmentation, among others), prediction (prognosis, forecasting, estimation), and management (treatment, control, monitoring, education, telemedicine integration). Biblioshiny and RStudio were used to analyze the data. Results: A total of 1773 articles were collected and analyzed. The number of publications and citations increased substantially since 2012, with a notable increase in the last 3 years. Of the 3 categories considered, detection was the most dominant, followed by prediction and management. Around 53.2% of the total journals started disseminating articles on this subject in 2020. China, India, and the United States were the most productive countries. Although no evidence of outstanding leadership by specific authors was found, the University of California emerged as the most influential institution for the development of scientific production. Conclusion: This is an evolving field that has experienced a rapid increase in productivity, especially over the last years with exponential growth. This trend is expected to continue in the coming years.
Postoperative Management of Osteochondral Lesions of the Ankle: A Survey Among German-Speaking Foot and Ankle Surgeons
Authors: Matthias Aurich , Becher Christoph , Ettinger Sarah , Gottschalk Oliver , Guenther Daniel , Klos Kajetan , Ahrend Marc-Daniel , Körner Daniel , Plaass Christian , Walther Markus 
Published: December 2023

Objective To assess the current treatment of osteochondral lesions of the ankle (OCLA) by German-speaking foot and ankle surgeons, focusing on the management of postoperative care and rehabilitation. Design A questionnaire was created by a panel of 4 experienced foot and ankle surgeons on behalf of the “Clinical Tissue Regeneration” (CTR) working group of the German Society of Orthopaedics and Trauma Surgery (DGOU), and distributed electronically to members of the CTR, participants of the German Cartilage Registry (Knorpelregister DGOU©), and members of 6 German-speaking orthopedics or sports medicine societies. Results were classified depending on the consensus within the answers (agreement ≥75% “strong tendency,” 50%-74% “tendency,” 25%-49% “weak tendency,” <25% “no tendency”). Results A total of 60 participants returned the questionnaire. The main results are as follows: regarding the frequency of surgical procedures for OCLA, refixation of the fragment, retrograde drilling, and bone marrow stimulation with or without using a matrix were performed by at least 75% of the surgeons and was considered a strong tendency. There was a strong tendency to stabilize the ankle (76.7%) and perform corrective osteotomies (51.7%). In total, 75.5% and 75% of the surgeons performed bone marrow stimulation with and without using a matrix, respectively. Corrective osteotomy and ankle stabilization were performed in 64.5% and 65.2% cases, respectively. Most participants included published recommendations on postoperative rehabilitation and the return to sports activities in their postoperative management. The main surgical procedures were considered the most critical factor in influencing the postoperative management by 81% of the participants (strong tendency). Adjunct surgical procedures such as corrective osteotomy and stabilization of the ankle were considered important by 67.8% of the respondents (tendency). Conclusions The management of OCLA varies among German-speaking foot and ankle surgeons. Therefore, guidelines remain essential to standardize the management of OCLA, to achieve improved and stable results. This survey will assist clinicians and patients with rehabilitation to return to sports after treating the ankle’s cartilage injury.