bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-Driven Two-Stage Framework for Identification and Characterization of Different Antibiotic-Resistant Escherichia coli Isolates Based on Mass Spectrometry Data
Authors: Chung Chia-Ru , Wang Hsin-Yao , Yao Chun-Han , Wu Li-Ching , Lu Jang-Jih , Horng Jorng-Tzong , Lee Tzong-Yi
Published: April 2023

Based on a large amount of matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS) clinical data, comprising 37,918
Escherichia coli
isolates, a data-driven two-stage framework was established to evaluate the antimicrobial resistance of
E. coli
. Five antibiotics, including amoxicillin (AMC), ceftazidime (CAZ), ciprofloxacin (CIP), ceftriaxone (CRO), and cefuroxime (CXM), were considered for the two-stage model training, and the values of the area under the receiver operating characteristic curve (AUC) were 0.62 for AMC, 0.72 for CAZ, 0.87 for CIP, 0.72 for CRO, and 0.72 for CXM.
Pangenomic Study of Fusobacterium nucleatum Reveals the Distribution of Pathogenic Genes and Functional Clusters at the Subspecies and Strain Levels
Authors: Ma Xiaomei , Sun Tianyong , Zhou Jiannan , Zhi Mengfan , Shen Song , Wang Yushang , Gu Xiufeng , Li Zixuan , Gao Haiting , Wang Pingping , Feng Qiang
Published: April 2023

We used
F. nucleatum
as an example to analyze the genomic characteristics of oral pathogens at the species, subspecies, and strain levels and elucidate the similarities and differences in functional genes and virulence factors among different subspecies/strains of the same oral pathogen. We believe that the unique biological characteristics of each subspecies/strain can be attributed to the differences in functional gene clusters or the presence/absence of certain virulence genes.
Supplemental Material: Mechanical weakening of a mudrock seal by reaction with CO2-charged fluids
Authors: Busch Andreas , al. et
Published: April 2023

Methods used in this study, including nano-indentation tests, small and very small angle neutron scattering to obtain porosity and pore size distribution, and fracture analysis. Scanning electron microscopy summary is provided to support mineralogical changes of the mudrock. 
Rare manifestations of refractory extrapulmonary sarcoidosis
Authors: Teles Catarina , Teles Carolina , Moreira Sónia , Santos Lèlita
Published: April 2023

Sarcoidosis is a multisystemic disease, characterised by histopathologic presence of non-necrotising granulomas, primarily affecting the lungs (>90%). We present three cases predominantly characterised by uncommon extrapulmonary manifestations of sarcoidosis, where only one had pulmonary involvement. We describe three female patients, between the second and third decades of life, whose sarcoidosis was a diagnostic challenge due to their atypical extrapulmonary manifestations, from which we highlight: livedo reticularis and painful subcutaneous nodules with uncommon localisation, size and histology, being the first reported case of extensive subcutaneous nodules triggered by intramuscular penicillin; extensive symptomatic and refractory osseous involvement; and dispersed erythema nodosum affecting the entire body surface. All three patients required third-line treatment (antitumour necrosis factor agents) to achieve significant clinical and imagiological improvement. Through this case series, we highlight the importance of considering the rare and atypical presentations of sarcoidosis to avoid diagnostic delays and serious repercussions on the patient’s prognosis.
Investigating the hypoalgesic effects of spinal manipulative therapy using hidden pain conditioning and positive expectation in patients with chronic low back pain: protocol for a randomised controlled trial
Authors: Nogueira Carrer Helen Cristina , Lima Thamiris Costa de , George Steven Z , Reis Felipe José Jandre dos , Dias Deise Lilian Costa , Campanha Bianca Emanuelli Saes , Chaves Thaís Cristina
Published: April 2023

Introduction

Placebo effects are responses capable of modulating pain and influencing treatment response. Two mechanisms are commonly related to placebo effects: expectations and conditioning. However, the research in this field is focused on laboratory studies with healthy participants. This study aims to identify whether a conditioning procedure with positive induced expectations about spinal manipulative therapy (SMT) will result in greater hypoalgesic effects in adults with chronic low back pain (CLBP) in a clinical trial design.

Methods and analysis

This trial will enrol 264 patients with non-specific CLBP, aged 18–60 years. Patients will undergo a calibration test to determine the thermal pain threshold for the hidden pain conditioning procedure. Afterward, they will be randomised to one of the three groups: hidden pain conditioning with positive induced expectations—group one (G1); positive expectations—group two (G2) and neutral expectations—group three (G3). Patients will receive instructions to manipulate the expectations. The pretreatment heat pain test will be performed before the SMT and after the intervention patients will undergo again the heat pain intensity test. However, only patients in G1 will receive hidden pain conditioning to reinforce the association between SMT and pain intensity reduction. All patients will undergo five sessions of SMT. The outcomes will be assessed immediately after the last session and at the 6 weeks and 3-month follow-ups. All statistical analyses will be conducted following intention-to-treat principles, and the treatment effects will be determined with linear mixed models.

Ethics and dissemination

The Federal University of São Carlos approved this research (Process n° 52359521.1.0000.5504). All participants will give written informed consent. Dissemination of the results will include publications in peer-reviewed journals and presentations at conferences. If positive expectations and classical conditioning improve outcomes, it may support the administration of such intervention.

Trial registration number

NCT05202704.
Antibiotic resistance spectrum ofE. colistrains from different samples and age-grouped patients: a 10-year retrospective study
Authors: Wang Sipei , Zhao Sheng , Zhou Yangxiao , Jin Shanshan , Ye Tinghua , Pan Xinling
Published: April 2023

Objective

Escherichia coli(E. coli) is the most common opportunistic clinical micro-organism with high drug resistance. This study aimed to analyse the resistance pattern ofE. coliaccording to patient age and clinical sample type.

Design and setting

This retrospective observational study was conducted in a tertiary hospital in southeastern China.

Participants

E. colistrains were isolated from blood, urine and sputum of infected inpatients. The patients were divided into four age groups: children (0–14 years old, including neonatal and non-neonatal groups), youths (15–40 years old), middle-aged (41–60 years old) and old (>60 years old).

Results

A total of 7165E. colistrains were collected from all samples. Compared with urine and blood isolates, more sputum isolates were resistant against 12 tested antibiotics. Furthermore, urine isolates were more resistant to levofloxacin than sputum and blood isolates. Although the patients’ age was not associated with resistance rates ofE. colistrains isolated from blood, a larger proportion of urine-derived strains from youths were resistant to sulfamethoxazole-trimethoprim and piperacillin-tazobactam than those from old people. The sputum strains from the elderly were more resistant to most of the tested antibiotics compared with sputum strains isolated from children.

Conclusions

The resistance profile ofE. coliis different among age groups and specimen sources and should be considered duringE. coliinfection treatment.
Quality of life and its associated factors among home-dwelling older people residing in the District of Colombo, Sri Lanka: a community-based cross-sectional study
Authors: Wijesiri Hapuarachchige Sewvandi Maliga S K , Wasalathanthri Sudharshani , De Silva Weliange Shreenika , Wijeyaratne Chandrika N
Published: April 2023

Introduction

This community-based cross-sectional study explored the factors affecting overall and domain-specific (physical health, psychological health, social relationships and environmental) quality of life (QOL) of home-dwelling older residents of the District of Colombo, Sri Lanka.

Methods

A representative sample (n=723) of older adults aged >65 years was obtained by the multistage cluster sampling technique. QOL was assessed using the validated Sinhala version of WHOQOL BREF Questionnaire. Data analysis was done using SPSS V.20.

Results

The mean±SD age was 72.23±6.3 years with the overall QOL score being (mean±SD) 56.73±12.57/100. The mean±SD QOL score of physical health, psychological health, social relationships and environmental domains were 55.81±15.80, 59.25±14.68, 46.36±20.08 and 64.61±11.96, respectively. The overall QOL in the adjusted model showed a significant positive association with the educational status, living conditions (with spouse, with spouse and children), participation in religious activities, being visited by friends or relatives and financial independence. The overall QOL was negatively associated with limitations in activities of daily living and instrumental activities of daily living, chronic arthritis and heart disease in the adjusted model. Living with the spouse was positively associated with the psychological domain of QOL. Osteoporosis and chronic arthritis affected the physical health domain, while cancer and disabling stroke affected the psychological domain of QOL negatively. All statistical significances were considered at p<0.05.

Conclusion

The overall QOL of home-dwelling elders of the Colombo District is moderate, with the lowest score being in social relationships and the highest in the environmental domain. Educational status, engaging in religious activities and financial independence are key factors associated with a better QOL. Limitations in physical activity and chronic diseases are associated with a reduced QOL. Living with the spouse is a key factor associated with the psychological health domain.
Retrospective cohort study on treatment modalities and survival time after oesophageal fistula in patients with oesophageal cancer in a regional cancer care centre in China
Authors: Xu Wencai , Jiang Hui , Liu Yang , Liu Xiao , Jiang Yue
Published: April 2023

Background

Oesophageal fistula (perforation) is a devastating complication in patients with oesophageal cancer . The optimal treatment remains uncertain.

Objective

We sought to present real-world evidence on treatment modalities and survival postfistula in patients with oesophageal cancer.

Design, settings and main outcomes

This was a retrospective cohort study of patients with oesophageal cancer with oesophageal fistulae diagnosed between June 2010 and June 2020 in a regional cancer care centre in Zhengzhou, China (n=352). The treatment options included surgical resection, oesophageal stent grafting, gastrostomy, nasogastric tube and conservative care. The primary outcome was survival time (months) postfistula. Inverse probability of treatment weighting (IPTW) life regression was used to estimate the differences in survival time accounting for potential confounders.

Results

The median survival time was 2.3 months (IQR: 0.7–6.0 months). Survival times were shorter in patients of male sex, T4 stage and oesophagotracheal versus oesophageal-mediastinal fistulae, and longer for any treatment option versus conservative care. The IPTW life regression analyses showed that in patients with oesophagotracheal fistulae, survival times were longer for stent grafting (+0.90 (95% CI 0.60 to 1.19) months) or gastrostomy (+0.81 (95% CI 0.47 to 1.13) months) versus nasogastric tube. In patients with oesophageal-mediastinal fistulae, survival times were shorter for stent grafting versus nasogastric tube (−0.36 (95% CI –0.63 to –0.09) months) and gastric tube (−0.29 (95% CI −0.50 to –0.08) months). Surgical resection was recorded in nine patients with oesophageal-mediastinal fistulae, and it was associated with the longest survival time in these patients.

Conclusions

Stent grafting or gastrostomy may be preferable to nasogastric tube in survival prognosis for patients with oesophageal cancer with oesophagotracheal fistulae. In contrast, stent grafting may be not preferable to nasogastric tube or gastrostomy in survival prognosis for patients with oesophageal-mediastinal fistulae.
Use of norepinephrine in preterm neonates with dopamine-resistant shock: a retrospective single-centre cross-sectional study
Authors: Lu Pei , Sun Yifan , Gong Xiaohui , Li Zhiling , Hong Wenchao
Published: April 2023

Background

Norepinephrine (NE) is recommended for children and full-term neonates (born at >37 gestational weeks) with septic shock. Meanwhile, data on the effectiveness of NE in preterm neonates are still limited. This study aimed to evaluate the clinical efficacy of NE in preterm neonates with dopamine-resistant shock compared with that in full-term neonates.

Methods

This was a single-centre, retrospective (January 2010–December 2020) cohort study of neonates with persistent shock despite adequate fluid resuscitation and dopamine or dobutamine administration at ≥10 μg/kg/min. Medical records of neonates treated with NE were retrospectively reviewed to collect respiratory and haemodynamic parameters and results of arterial blood gas (ABG) tests before and 8 hours after NE infusion. The effectiveness of NE was assessed using changes in clinical parameters and multiple regression models for mortality among subgroups of preterm and full-term neonates.

Results

Ninety-two neonates (76% preterm) who received NE infusion were included in the study. NE infusion was started after a median of 7 hours (IQR 2–19 hours) after shock onset. Among the preterm neonates, the maximum dose of NE infusion was 0.5 (IQR 0.3–1.0) µg/kg/min with a median duration of 45 (IQR 24.0–84.5) hours. Haemodynamic dysfunction was ameliorated with increased blood pressure, decreased heart rate and improved ABG results. Preterm neonates with septic shock tended to have a reduced response to NE; however, preterm neonates with persistent pulmonary hypertension of the newborn tended to have a better response. Thirty-four (37%) neonates died in our cohort. The timing, dose and duration of NE use were not associated with neonatal mortality.

Conclusions

Although using NE effectively improves clinical parameters in preterm neonates with dopamine-resistant shock, our study is underpowered to identify the association between NE infusion and mortality in preterm neonates with dopamine-resistant shock.
Characterization of the endotheliopathy, innate-immune activation and hemostatic imbalance underlying CAR-T cell toxicities: laboratory tools for an early and differential diagnosis
Authors: Moreno-Castaño Ana Belen , Fernández Sara , Ventosa Helena , Palomo Marta , Martinez-Sanchez Julia , Ramos Alex , Ortiz-Maldonado Valentín , Delgado Julio , Fernández de Larrea Carlos , Urbano-Ispizua Alvaro , Penack Olaf , Nicolás J M , Téllez Adrian , Escolar Gines , Carreras Enric , Fernández-Avilés Francesc , Castro Pedro , Diaz-Ricart Maribel
Published: April 2023

Background

Chimeric antigen receptor (CAR)-T cell-based immunotherapy constitutes a revolutionary advance for treatment of relapsed/refractory hematological malignancies. Nevertheless, cytokine release and immune effector cell-associated neurotoxicity syndromes are life-threatening toxicities in which the endothelium could be a pathophysiological substrate. Furthermore, differential diagnosis from sepsis, highly incident in these patients, is challenging. Suitable laboratory tools could be determinant for their appropriate management.

Methods

Sixty-two patients treated with CAR-T cell immunotherapy for hematological malignancies (n=46 with CD19-positive diseases, n=16 with multiple myeloma) were included. Plasma samples were obtained: before CAR-T cell infusion (baseline); after 24–48 hours; at suspicion of any toxicity onset and 24–48 hours after immunomodulatory treatment. Biomarkers of endothelial dysfunction (soluble vascular cell adhesion molecule 1 (sVCAM-1), soluble TNF receptor 1 (sTNFRI), thrombomodulin (TM), soluble suppression of tumorigenesis-2 factor (ST2), angiopoietin-2 (Ang-2)), innate immunity activation (neutrophil extracellular traps (NETs), soluble C5b-9 (sC5b-9)) and hemostasis/fibrinolysis (von Willebrand Factor antigen (VWF:Ag), ADAMTS-13 (A13), α2-antiplasmin (α2-AP), plasminogen activator inhibitor-1 antigen (PAI-1 Ag)) were measured and compared with those in cohorts of patients with sepsis and healthy donors.

Results

Patients who developed CAR-T cell toxicities presented increased levels of sVCAM-1, sTNFRI and ST2 at the clinical onset versus postinfusion values. Twenty-four hours after infusion, ST2 levels were good predictors of any CAR-T cell toxicity, and combination of ST2, Ang-2 and NETs differentiated patients requiring intensive care unit admission from those with milder clinical presentations. Association of Ang-2, NETs, sC5b-9, VWF:Ag and PAI-1 Ag showed excellent discrimination between severe CAR-T cell toxicities and sepsis.

Conclusions

This study provides relevant contributions to the current knowledge of the CAR-T cell toxicities pathophysiology. Markers of endotheliopathy, innate immunity activation and hemostatic imbalance appear as potential laboratory tools for their prediction, severity and differential diagnosis.
Understanding the burden of injury in children from conflict: an analysis of radiological imaging from a Role 3 hospital in Afghanistan in 2011
Authors: Sargent Will , Mahoney P , Clasper J , Bull A , Reavley P , Gibb I
Published: April 2023

Introduction

There is a need for quality medical care for children injured in conflict, but a description of injuries and injury burden from blast and ballistic mechanisms is lacking. The radiology records of children imaged during the war in Afghanistan represent a valuable source of information about the patterns of paediatric conflict injuries.

Methods

The UK military radiological database was searched for all paediatric presentations to Camp Bastion during 2011. Reports and original images were reviewed to determine location and severity of injuries sustained. Additional information was obtained from imaging request forms and the Joint Theatre Trauma Register, a database of those treated at UK medical facilities in Iraq and Afghanistan.

Results

Radiology was available for 219 children. 71% underwent CT scanning. 46% suffered blast injury, 22% gunshot wounds (GSWs), and 32% disease and non-battle injuries (DNBIs). 3% had penetrating head injury, 11% penetrating abdominal trauma and 8% lower limb amputation, rates far exceeding those found in civilian practice. Compared with those with DNBI, those with blast or GSW were more likely to have serious (Abbreviated Injury Score, AIS, ≥3) injuries (median no. AIS ≥3 injuries were 1 for blast, 1 for GSW and 0 for DNBI, p<0.05) and children exposed to blast were more likely to have multiple body regions with serious injuries (OR for multiple AIS ≥3 injuries for blast vs DNBI=5.811 CI [1.877 to 17.993], p<0.05).

Conclusions

Paediatric conflict injuries are severe, and clinicians used only to civilian practice may be unprepared for the nature and severity of injuries inflicted on children in conflict. Whole-body CT for those with conflict-related injuries, especially blast, is hugely valuable. We recommend that CT is used for paediatric assessment in blast and ballistic incidents and that national imaging guidelines amend the threshold for doing so.
Minor injury turns into major problem in severe acute kidney injury: a propensity matched analysis
Authors: Ahmed Nasim , Kuo Yen-Hong , Mathew Roy O , Asif Arif
Published: April 2023

Objective

Severe acute kidney injury (sAKI) has been associated with a higher mortality in trauma patients, and severity of trauma often correlates with risk of sAKI. Whether minor to moderate trauma is associated with sAKI is less clear. The purpose of the study was to examine the outcomes of minor to moderate trauma patients who developed sAKI.

Methods

The National Trauma Database participant use files of 2017 and 2018 were accessed for the study. All patients aged 18 years old and above who sustained an Injury Severity Score (ISS) of <16 and who were brought to a level I or level II trauma center were included in the study. sAKI was defined as an abrupt decrease in kidney function either three times increase in serum creatinine (SCr) level from the baseline or increase in SCr to ≥4.0 mg/dL (≥353.6 µmol/L), initiation of renal replacement therapy, or anuria for ≥12 hours. Propensity matching analysis was performed between the groups who developed sAKI and without sAKI. Outcome of interest was in-hospital mortality.

Results

A total of 655 872 patients fulfilled the inclusion criteria with complete information, of which 1896 patients were found to have sAKI. There were significant differences between the two groups on baseline characteristics. The propensity score matching eliminated all the differences and created 1896 pairs of patients. The median hospital length of stay was longer in patients with sAKI when compared with patients who did not develop sAKI (14 (13 to 15) vs. 5 (5 to 5), days p<0.001) . The overall in-hospital mortality was 20.6% in patients with sAKI compared with 2.1% without sAKI (p<0.001).

Conclusion

The occurrence of sAKI in minor to moderate trauma patients was less than 0.5%. There was a three times longer hospital stay in patients with sAKI and 10-fold increase in mortality when compared with patients who did not develop sAKI.

Level of evidence

IV.

Study type

Observational cohort study.
Evaluation of biochemical profile and oxidative damage to lipids and proteins in patients with lysosomal acid lipase deficiency
Authors: Guerreiro Gilian , Deon Marion , Vargas Carmen Regla
Published: April 2023

Lysosomal acid lipase deficiency (LALD) is an inborn error of metabolism that lacks satisfactory treatment, which leads to the development of severe hepatic and cardiac complications and may even lead to death. In this sense, knowledge of the mechanisms involved in the pathophysiology of this disorder becomes essential to allow the search for new therapeutic strategies. There are no studies in the literature investigating the role of reactive species and inflammatory processes in the pathophysiology of this disorder. Therefore, the aim of this work was to investigate parameters of oxidative and inflammatory stress in LALD patients. In this work, we obtained results that demonstrate that LALD patients are susceptible to oxidative stress caused by an increase in the production of free radicals, observed by the increase of 2-7-dihydrodichlorofluorescein. The decrease in sulfhydryl content reflects oxidative damage to proteins, as well as a decrease in antioxidant defenses. Likewise, the increase in urinary levels of di-tyrosine observed also demonstrates oxidative damage to proteins. Furthermore, the determination of chitotriosidase activity in the plasma of patients with LALD was significantly higher, suggesting a pro-inflammatory state. An increase in plasma oxysterol levels was observed in patients with LALD, indicating an important relationship between this disease and cholesterol metabolism and oxidative stress. Also, we observed in LALD patients increased levels of nitrate production. The positive correlation found between oxysterol levels and activity of chitotriosidase in these patients indicates a possible link between the production of reactive species and inflammation. In addition, an increase in lipid profile biomarkers such as total and low-density lipoprotein cholesterol were demonstrated in the patients, which reinforces the involvement of cholesterol metabolism. Thus, we can assume that, in LALD, oxidative and nitrosative damage, in addition to inflammatory process, play an important role in its evolution and future clinical manifestations. In this way, we can suggest that the study of the potential benefit of the use of antioxidant and anti-inflammatory substances as an adjuvant tool in the treatment will be important, which should be associated with the already recommended therapy.
Speaking the same language: Aligning project designations to clarify communication in restoration ecology
Authors: Gerwing Travis G. , Hawkes Virgil C. , Murphy Stephen D.
Published: April 2023

As we enter the United Nations Decade of Ecosystem Restoration, the need to engage in restoration activities has never been greater. Included within this need is a requirement for clear communication between researchers, practitioners, policymakers, stakeholders, and community members. To facilitate the discussion and assessment of restorative activities, we propose two decision trees to differentiate between key restoration terms (Reclamation, Rehabilitation, Ecological Restoration, Rewilding, Landscape Restoration, Intra-Ecosystem Restoration, Reference Condition Restoration, and Ecological Reclamation) and to clarify how they relate to each other, based upon project scope and desired/intended project outcomes. Continued use of unclear terminology impedes practitioners or researchers from using the literature efficiently, to find precedents that could assist their current efforts. As such, increasing clarity of communications will ensure restoration is discussed within a framework of well-defined and agreed upon terms. It is our hope that this suggested framework will contribute to the ongoing and much needed terminology debate and help enhance cohesion on the use of key terms within the restoration focused literature. Given the increased focus upon restoration projects of any kind, especially during the UN's decade of ecosystem restoration, it is more important than ever that restoration practitioners speak the same language.
A viable $$A_4$$ 3HDM theory of quark mass matrices
Authors: Brée Iris , Carrôlo Sérgio , Romão Jorge C. , Silva João P.
Published: April 2023

It is known that a three Higgs doublet model (3HDM) symmetric under an exact $$A_4$$

A
4

symmetry is not compatible with nonzero quark masses and/or non-block-diagonal CKM matrix. We show that a 3HDM with softly broken $$A_4$$

A
4

terms in the scalar potential does allow for a fit of quark mass matrices. Moreover, the result is consistent with $$m_h=125\,\text {GeV}$$

m
h

=
125

GeV

and the $$h \rightarrow WW,ZZ$$

h
→
W
W
,
Z
Z

signal. We also checked numerically that, for each point that passes all the constraints, the minimum is a global minimum of the potential.
Fuzzy Fractional Order Proportional Integral Derivative Controller Design for Higherorder Time Delay Processes
Authors: Anuja R. , Sivarani T. S. , Nisha M. Germin
Published: April 2023

Process control is the interested domain of interest as the industrial high-order applications require an effective control mechanism with higher robustness. Since the conventional method of proportional integral derivative (PID) controller remains inadequate for the higher-order processes, this research concentrates on the fuzzy fractional-order controllers, that more and more attention nowadays in various research areas of science and engineering specifically, on the areas of tuning, design, implementation, and analysis of these controllers. Accordingly, this research marks a milestone for the control industry through introducing a robust controller, fuzzy fractional-order (FO) PI[Formula: see text]D[Formula: see text] (fuzzy FOPID) for higher-order applications with dead time. The fractional-order controller requires the fractional orders for the derivative term [Formula: see text] and integral term [Formula: see text]. The results of the proposed fuzzy FOPID controller is analyzed and compared with the comparative methods, such as a proportional integral derivative (PID) controller and fractional order PID controller (FOPID). Accordingly, the time-domain specifications are evaluated in the presence/absence of the disturbances is analyzed and in addition, the time domain optimal integral metrics are determined. Simulations are carried out using MATLAB/SIMULINK.
Why Do We Need to Learn about Citational Practices? Recognizing Knowledge Production from the Global Souths and Beyond
Authors: Ogan Amy , van Amstel Frederick , León Gabriela Molina , Maestre Juan Fernando , Williams Kristin , Bidwell Nicola J , Reynolds-Cuéllar Pedro , Savage Saiph , Oswal Sushil , Sharma Vishal
Published: April 2023

How do you decide which papers to cite, how many, and from which particular sources? We reflect and discuss the implications of these critical questions based on our experiences in the panel and workshops on the topic of citational justice that took place at CSCW, CLIHC, and India HCI in 2021.
Electrolytic reduction of Gd2O3-ZnO in NaCl-CaCl2 Molten Salt
Authors: Chen Hao , Peng Hao , Ji Nan , Huang Wei
Published: April 2023

The electrochemical behaviors of Gd2O3, ZnO and Gd2O3-ZnO in NaCl-CaCl2 molten salt was studied by cyclic voltammetry and square wave voltammetry, and the corresponding constant potential electrolysis and XRD analysis indicated that the reduction processes were in agreement with the process that 3PI (metal∣oxide∣electrolyte three-phase interline) expanded with time from surface to interior of the cathode. Moreover, the addition of ZnO could promote the electrochemical reduction of Gd2O3. According to the electrochemical behavior (CV) and the characterization (XRD and SEM-EDS) of electrolytic product, the intermetallic compounds, GdZn12, Gd2Zn17 and Gd13Zn58, were generated during the electrolysis of Gd2O3-ZnO cathode without dendritic deposits.
Probing Mechanical, Thermoelectric, and Magnetic Properties of ACr2O4 (A = Hg, Cd) Spinel Oxides for Energy Storage Applications
Authors: Mahmood Asif , Ramay Shahid M. , Al-Masry Waheed
Published: April 2023

DFT calculations are employed to examine the half-metallic, thermoelectric, as well as electronics properties of Cr-based spinels ACr2O4 (A = Hg, Cd). The structural and elastic properties are calculated using the PBEsol-GGA, a modified Perdew–Burke–Ernzerhof plus generalized gradient approach (mBJ + GGA). The modified-Becke Johnson (mBJ) potential is also employed to examine the electronics and thermoelectric properties. In the ferromagnetic (FM) phase, the stability of the structures is validated through energy differences calculations among the ferromagnetic (FM) and non-magnetic (NM) periods. Additionally, the Chopin technique is used to examine in detail the elastic properties. The 2p-states of chalcogenide and the 3d-states of Cr atoms, which result in significant Fermi-level hybridization, provide the total magnetic moments. Furthermore, it is found that the examined spinels may be employed potentially in thermoelectric devices by looking into transport characteristics like the power factor, Seebeck coefficient, and thermal and electrical conductance.
Bivalves Improved Water Quality by Changing Bacterial Composition in Sediment and Water in an IMTA System
Authors: Kong Shuo , Chen Zhao , Ghonimy Abdallah , Li Jian , Zhao Fazhen
Published: April 2023

Integrated multitrophic aquaculture (IMTA) maximises the nitrogen cycle between system components, including bacteria. In order to maximise the bacterial role in nitrogen elimination in an IMTA system, we investigated the effect of bivalve culture on water quality and bacterial community structure in overlying water and sediment in the “shrimp-crab-bivalve-fish” IMTA system. The bacterial composition in overlying water and sediment was measured by Illumina -MiSeq high-throughput sequencing technology. The results show that dissolved oxygen was higher in the bivalve culture area. Ammonia and nitrite in the bivalve culture area were lower than those in the nonbivalve culture area; however, the nitrate and phosphate in the bivalve culture area were higher than those in the nonbivalve culture area. The Chao1, Shannon, and Ace indexes were higher in the bivalve area. More bacteria with nitrification and denitrification functions were detected in bivalve culture areas, such as Ruegeria (1.05%–4.79%), Thalassobius (0.11%–0.69%), Limibaculum (0.07%–0.69%), HIMB11 (0.13%–0.21%), and Rubellimicrobium (0.01%–0.16%). More Cyanobacteria were detected in bivalve culture areas with higher phosphate concentrations. To sum up, bivalves can release phosphorus through bioturbation, increasing the abundance of Cyanobacteria, which release dissolved oxygen into overlying water through photosynthesis, enhance nitrification (mainly ammonia oxidation), and improve the ammonia nitrogen removal capacity of the system. Meanwhile, bivalves can increase bacterial diversity and abundance by regulating dissolved oxygen. This study provided insight into bivalve interaction with bacterial activity in the IMTA system.
An Enhanced Phrase Matching Method Based on Cross‐Attention
Authors: Pang Guoqing , Fu Qiming , Chen Jianping , Wang Yunzhe , Lu You , Wu Hongjie
Published: April 2023

Text matching is a core problem in the field of natural language understanding. It aims to analyze and judge the semantic relevance or similarity between two texts. In the past, much work on text matching focused on long text and little on phrase optimization. However, phrase matching also has essential application scenarios. Compared with long texts, phrases have difficulties covering less semantics and polysemy, and because of the weak expression ability of phrases, it is hard to match phrases accurately. On the Kaggle patent phrase matching dataset, due to the few words in the phrase and the repeated occurrences under different patent classification numbers, it is difficult to match each other accurately. In the data‐processing stage, this work proposes aggregating related targets for data fusion, expanding the background semantic information, and enhancing the expression ability of phrases. In the training stage, this work considers adding a cross‐attention network to the model to make the additional related targets better used and learned. The added cross‐attention network makes the model pay more attention to the most related information. The proposed method has experimented on pretrained language models such as BERT‐for‐patent, DeBERTa, and RoBERTa. The results show that the proposed method in this work improves by 2–4 points more than the general method without any information or additional network layers in its evaluation metric called the Pearson correlation, which enhances the performance in short‐text matching.
Keloid Core Factor CTRP3 Overexpression Significantly Controlled TGF-β1-Induced Propagation and Migration in Keloid Fibroblasts
Authors: He Lin , Zhu Chan , Dou Huicong , Yu Xueyuan , Jia Jing , Shu Maoguo
Published: April 2023

Purpose. Keloid is a type of benign fibrous proliferative tumor characterized by excessive scarring. C1q/TNF-related protein 3 (CTRP3) has been proven to possess antifibrotic effect. Here, we explored the role of CTRP3 in keloid. In the current research, we examined the influence of CTRP3 on keloid fibroblasts (KFs) and investigated the potential molecular mechanism. Methods. KF tissue specimens and adjacent normal fibroblast (NF) tissues were collected cultured from 10 keloid participants. For the TGF-β1 stimulation group, KFs were processed with human recombinant TGF-β1. Cell transfection of pcDNA3.1-CTRP3 or pcDNA3.1 was performed. The siRNA of CTRP3 (si-CTRP3) or negative control siRNA (si-scramble) was transfected into KFs. Results. CTRP3 was downregulated in keloid tissues and KFs. CTRP3 overexpression significantly controlled TGF-β1-induced propagation and migration in KFs. Col I, α-SMA, and fibronectin mRNA and protein levels were enhanced by TGF-β1 stimulation, whereas they were inhibited by CTRP3 overexpression. In contrast, CTRP3 knockdown exhibited the opposite effect. In addition, CTRP3 attenuated TGF-β receptors TRI and TRII in TGF-β1-induced KFs. Furthermore, CTRP3 prevented TGF-β1-stimulated nuclear translocation of smad2 and smad3 and suppressed the expression levels of p-smad2 and p-smad3 in KFs. Conclusion. CTRP3 exerted an antifibrotic role through inhibiting proliferation, migration, and ECM accumulation of KFs via regulating TGF-β1/Smad signal path.
Data from UBE2C-mediated autophagy inhibition via ubiquitination of SIRT1 contributes to endometrial cancer progression
Authors: Zhao Rong , Liu Yan , Wang Ziwei , Zhang Jun , Zhang Wei , Zhou Xing , Tsedendorj Sevjid , Enkhtur Amarsanaa , Feng Dilu , Wang Hongbo
Published: April 2023

Abstract
Recent studies have shown that autophagy plays an important role in gynecological tumours, and ubiquitin modification of autophagy regulatory components is essential to regulate autophagic. In this study, we found that UBE2C affects endometrial cancer cell apoptosis and proliferation by inhibiting autophagy. Electron microscopy observation of cell ultrastructure and experimental biochemical analysis showed that EC cells with UBE2C expression knocked down display typical autophagic characteristics. Cells were cotreated with the autophagy pharmacological inhibitors chloroquine and/or bafilomycin A1, and mRFP-GFP-LC3 assays were performed to monitor autophagic flux and determine whether UBE2C suppresses the autophagy program. Investigation of the corresponding mechanism by which UBE2C inhibits autophagy revealed that UBE2C induces K48-linked SIRT1 ubiquitination and promotes ubiquitination-dependent degradation of SIRT1, subsequently reducing H4K16 deacetylation levels and epigenetically inhibiting the expression of autophagy-related genes. The results of CCK-8, Hoechst staining, and immunofluorescence assays further indicated that deletion of the autophagy-related gene BECN1 significantly attenuates UBE2C knockdown-induced cell apoptosis. Moreover, overexpression of UBE2C promoted tumor growth in the xenograft mice model. While, the introduction of rapamycin, an agonist of autophagy, successfully reversed tumor growth and apoptosis inhibition mediated by UBE2C overexpression in vitro and in vivo. Taken together, our results suggested that UBE2C-mediated ubiquitination and degradation of SIRT1 contribute to the malignant progression of endometrial cancer through epigenetic inhibition of autophagy.
Implications: Our study highlights the tumorigenic role and regulatory mechanism of UBE2C in EC; UBE2C inhibits EC cell apoptosis through autophagy-related mechanisms and our findings provide new insights into the treatment of endometrial cancer.
Data from Downregulation of BASP1 Promotes Temozolomide Resistance in Gliomas via Epigenetic Activation of the FBXO32/NF-κB/MGMT Axis
Authors: Liao Xinyi , Li Ziwen , Zheng Haiqing , Qian Wanying , Zhang Shuxia , Chen Suwen , Li Xincheng , Tang Miaoling , Xu Yingru , Yu Ruyuan , Li Man , Song Libing , Li Jun
Published: April 2023

Abstract
The chemoresistance of temozolomide-based therapy is a serious limitation for lasting effective treatment of gliomas, while the underlying mechanisms remain unclear. In this study, we showed that downregulation of BASP1 correlated negatively with the response to temozolomide therapy and disease-free survival (DFS) of patients with gliomas. Silencing BASP1 significantly enhanced the temozolomide resistance of glioma cells both in vitro and in vivo through repair of temozolomide-induced DNA damage via activation of the FBXO32/NF-κB/MGMT axis in both MGMT-methylated and -unmethylated gliomas. We demonstrated that loss of BASP1 resulted in removal of TRIM37/EZH2 complex–induced repressive histone modifications, including H2A-ub and H3K27me3, but addition of WDR5/MLL complex–mediated active histone modifications, including H3K4me3 and H3K9ac, on the FBXO32 promoter, which elicited in FBXO32 upregulation and further activated NF-κB/MGMT signaling via ubiquitin-dependent degradation of IκBα. Importantly, treatment with OICR-9429, an antagonist of the WDR5–MLL interaction, impaired the FBXO32/NF-κB/MGMT axis–mediated repair of temozolomide-induced DNA damage, leading to significant apoptosis of BASP1-downregulated glioma cells. These findings shed light on the molecular mechanism underlying BASP1-mediated epigenetic transcriptional repression and may represent a potential strategy in the fight against temozolomide-resistant gliomas.
Implications:
BASP1 downregulation promotes temozolomide resistance in gliomas through WDR5/MLL complex–mediated epigenetic activation of the FBXO32/NF-κB/MGMT axis, providing new target for improving outcomes in patients with temozolomide-resistant gliomas.
Data from Interdependence of SS18-SSX–driven YAP1 and β-Catenin Activation in Synovial Sarcoma
Authors: Isfort Ilka , Berthold Ruth , Heinst Lorena , Wardelmann Eva , Larsson Olle , Trautmann Marcel , Hartmann Wolfgang
Published: April 2023

Abstract
Synovial sarcoma, a rare malignant soft tissue tumor, is characterized by a specific chromosomal translocation t(X;18). The resulting chimeric SS18-SSX fusion protein drives synovial sarcoma pathogenesis by integrating into the BAF complex and dysregulating gene transcription. Because previous functional analyses revealed a connection between SS18-SSX and the activity of the transcriptional coregulators YAP1/TAZ and β-catenin, respectively, this study examined a potential interdependence between these essential effector proteins in synovial sarcoma. In a large cohort of synovial sarcoma tissue specimens, IHC analyses revealed a substantial subset of synovial sarcoma with concurrent nuclear accumulation of YAP1/TAZ and β-catenin. In vitro, small-molecule inhibitor treatment, RNAi-mediated knockdown, and vector-based overexpression assays demonstrated that YAP1, TAZ, and β-catenin transcriptional activity is not only stimulated by the SS18-SSX fusion protein, but that they also mutually enhance each other's activation. These analyses showed the highest cooperative effect with overexpression of YAP1 in combination with β-catenin. Coimmunoprecipitation experiments detected nuclear interactions between YAP1, β-catenin, and the SS18-SSX fusion protein, the latter being an integral part of the BAF complex. Disruption of BAF complex assembly affected the coregulation of YAP1 and β-catenin, indicating that this chromatin remodeling complex plays a crucial role for interdependent YAP1 and β-catenin activation in synovial sarcoma cells.
Implications:
This study provides deeper insights into synovial sarcoma tumor biology demonstrating a mutual dependence between YAP1/TAZ and β-catenin transcriptional activity and a complex interplay with the SS18-SSX fusion protein within the BAF complex.
Data from FOXA1 reprogramming dictates retinoid X receptor response in ESR1 mutant breast cancer
Authors: Wu Yang , Li Zheqi , Wedn Abdalla M. , Casey Allison N. , Brown Daniel , Rao Shalini V. , Omarjee Soleilmane , Hooda Jagmohan , Carroll Jason S. , Gertz Jason , Atkinson Jennifer M. , Lee Adrian V. , Oesterreich Steffi
Published: April 2023

Abstract
Estrogen receptor alpha (ER/ESR1) mutations occur in 30-40% of endocrine resistant ER-positive (ER+) breast cancer. Forkhead Box A1 (FOXA1) is a key pioneer factor mediating ER-chromatin interactions and endocrine response in ER+ breast cancer, but its role in ESR1 mutant breast cancer remains unclear. Our previous FOXA1 ChIP-seq identified a large portion of redistributed binding sites in T47D genome-edited Y537S and D538G ESR1 mutant cells. Here, we further integrated FOXA1 genomic binding profile with the isogenic ER cistrome, accessible genome and transcriptome data of T47D cell model. FOXA1 redistribution was significantly associated with transcriptomic alterations caused by ESR1 mutations. Furthermore, in ESR1 mutant cells, FOXA1 binding sites less frequently overlapped with ER, and differential gene expression was less associated with the canonical FOXA1-ER axis. Motif analysis revealed a unique enrichment of retinoid X receptor (RXR) motifs in FOXA1 binding sites of ESR1 mutant cells. Consistently, ESR1 mutant cells were more sensitive to growth stimulation with the RXR agonist LG268. The mutant-specific response was dependent on two RXR isoforms, RXR-α and RXR-β, with a stronger dependency on the latter. In addition, T3, the agonist of thyroid receptor also showed a similar growth-promoting effect in ESR1 mutant cells. Importantly, RXR antagonist HX531 blocked growth of ESR1 mutant cells and a patient derived xenograft (PDX)-derived organoid with an ESR1 D538G mutation. Collectively, our data support evidence for a stronger RXR response associated with FOXA1 reprogramming in ESR1 mutant cells, suggesting development of therapeutic strategies targeting RXR pathways in breast tumors with ESR1 mutation.
Implications: It provides comprehensive characterization of the role of FOXA1 in ESR1 mutant breast cancer and potential therapeutic strategy through blocking RXR activation.
Data from Netrin-1 Promotes the Immunosuppressive Activity of MDSCs in Colorectal Cancer
Authors: Xia Xueli , Mao Zhenwei , Wang Wenxin , Ma Jie , Tian Jie , Wang Shengjun , Yin Kai
Published: April 2023

Abstract
Myeloid-derived suppressive cells (MDSC) inhibit antitumor immunity and confer a survival advantage for tumor evasion. Tumor cells also support MDSC expansion and recruitment by secreting multiple growth factors and cytokines, but the mechanisms by which tumors affect MDSC function are not completely understood. Here, we found that the neuronal guidance protein netrin-1 was selectively secreted by MC38 murine colon cancer cells, which could enhance the immunosuppressive activity of MDSCs. MDSCs predominantly expressed one type of netrin-1 receptor, adenosine receptor 2B (A2BR). Netrin-1 interacted with A2BR on MDSCs to activate the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) signaling pathway, which ultimately increased CREB phosphorylation in MDSCs. Furthermore, netrin-1 knockdown in tumor cells inhibited the immunosuppressive activity of MDSCs and restored antitumor immunity in MC38 tumor xenograft mice. Intriguingly, high netrin-1 in the plasma correlated with MDSCs in patients with colorectal cancer. In conclusion, netrin-1 significantly enhanced the immunosuppressive function of MDSCs through A2BR on MDSCs, thus promoting the development of tumors. These findings highlight that netrin-1 may regulate the abnormal immune response in colorectal cancer and may become a potential target for immunotherapy.
Supplementary Table S2 from Structurally Complex Osteosarcoma Genomes Exhibit Limited Heterogeneity within Individual Tumors and across Evolutionary Time
Authors: Rajan Sanjana , Zaccaria Simone , Cannon Matthew V. , Cam Maren , Gross Amy C. , Raphael Benjamin J. , Roberts Ryan D.
Published: April 2023

Characteristics of patient samples obtained from Childhood Solid Tumor Network
Data from Mitochondrial metabolism drives low-density lipoprotein-induced breast cancer cell migration
Authors: Nóbrega-Pereira Sandrina , Santos Francisco , Santos Miguel Oliveira , Serafim Teresa L. , Patrícia Lopes Ana , Coutinho Diogo , Carvalho Filipa S. , Domingues Rosário M. , Domingues Pedro , Bernardes de Jesus Bruno , Morais Vanessa A , Dias Sérgio
Published: April 2023

Abstract
Most cancer related deaths are due to metastases. Systemic factors, such as lipid-enriched environments (as low-density lipoprotein (LDL)-cholesterol), favor breast cancer, including triple negative breast cancer (TNBC) metastasis formation. Mitochondria metabolism impacts TNBC invasive behavior but its involvement in a lipid-enriched setting is undisclosed. Here we show that LDL increases lipid droplets, induces CD36 and augments TNBC cells migration and invasion in vivo and in vitro. LDL induces higher mitochondrial mass and network spread in migrating cells, in an actin remodeling-dependent manner, and transcriptomic and energetic analyses revealed that LDL renders TNBC cells dependent on fatty acids (FAs) usage for mitochondrial respiration. Indeed, engagement on FA transport into the mitochondria is required for LDL-induced migration and mitochondrial remodeling. Mechanistically, LDL treatment leads to mitochondrial long chain fatty acid (LCFA) accumulation and increase reactive oxygen species (ROS) production. Importantly, CD36 or ROS blockade abolished LDL-induced cell migration and mitochondria metabolic adaptations. Our data suggest that LDL induces TNBC cells migration by reprogramming mitochondrial metabolism, revealing a new vulnerability in metastatic breast cancer.