bluuebunny/crossref_metadata_2025_split huggingface dataset:
A double-blinded randomized placebo-controlled non-inferiority trial protocol for postoperative infections associated with canine pyometra
Authors: Ylhäinen Anna , Mölsä Sari , Grönthal Thomas , Junnila Jouni , Rantala Merja , Laitinen-Vapaavuori Outi , Thomson Katariina 
Published: June 2023

AbstractBackgroundPyometra is a common infectious condition, especially in elderly bitches. In addition to an infected uterus, dogs may have concurrent urinary tract infection (UTI). The preferred treatment is surgical removal of the ovaries and uterus, whereupon the general prognosis is excellent. In addition, antimicrobial therapy is frequently prescribed for postoperative treatment. However, no research exists on the benefit of postoperative antimicrobial treatment in uncomplicated canine pyometra. Antimicrobial resistance has become a major challenge in treatment of bacterial infections. Diminishing overuse of antimicrobial agents is essential for controlling the development of antimicrobial resistance in both animals and humans.MethodsThis double-blinded, randomized, placebo-controlled two-arm clinical trial is designed to compare the incidence of postoperative infections associated with surgical treatment of uncomplicated pyometra followed by two different treatment protocols. For the study, 150 dogs presenting with an uncomplicated pyometra and that are to undergo surgical treatment will be recruited. Dogs with body weight < 3 or > 93 kg, complicated pyometra, primary disease increasing the risk of infection, or immunosuppressive medication will be excluded. All dogs will receive one dose of sulfadoxine-trimethoprim intravenously as an antimicrobial prophylaxis. Postoperatively, dogs will be randomized to receive either a five-day course of placebo or an active drug, sulfadiazine-trimethoprim orally. During the surgery microbiological samples will be taken from urine and uterine content. The follow-up includes a control visit in 12 days and an interview of the owner 30 days after surgery. If bacteriuria is detected at the time of surgery, a urinary sample will be cultured for bacterial growth at the control visit. The primary outcome is the incidence of a postoperative surgical site infection (SSI), and the secondary outcome is the occurrence of clinical UTI with bacteriuria. Intention-to-treat and per-protocol analyses will be performed to compare outcome incidences between the treatment groups.DiscussionResearch-based evidence is necessary to create treatment guidelines for judicious use of antimicrobials. The goals of this study are to provide evidence for reducing the use of antimicrobials and targeting the treatment to patients proven to benefit from it. Publishing the trial protocol will increase transparency and promote open science practices.
Proteomic analysis to identification of hypoxia related markers in spinal tuberculosis: a study based on weighted gene co-expression network analysis and machine learning
Authors: Wu Shaofeng , Liang Tuo , Jiang Jie , Zhu Jichong , Chen Tianyou , Zhou Chenxing , Huang Shengsheng , Yao Yuanlin , Guo Hao , Ye Zhen , Chen Liyi , Chen Wuhua , Fan Binguang , Qin Jiahui , Liu Lu , Wu Siling , Ma Fengzhi , Zhan Xinli , Liu Chong 
Published: June 2023

Abstract
Objective
This article aims at exploring the role of hypoxia-related genes and immune cells in spinal tuberculosis and tuberculosis involving other organs.

Methods
In this study, label-free quantitative proteomics analysis was performed on the intervertebral discs (fibrous cartilaginous tissues) obtained from five spinal tuberculosis (TB) patients. Key proteins associated with hypoxia were identified using molecular complex detection (MCODE), weighted gene co-expression network analysis(WGCNA), least absolute shrinkage and selection operator (LASSO), and support vector machine recursive feature Elimination (SVM-REF) methods, and their diagnostic and predictive values were assessed. Immune cell correlation analysis was then performed using the Single Sample Gene Set Enrichment Analysis (ssGSEA) method. In addition, a pharmaco-transcriptomic analysis was also performed to identify targets for treatment.

Results
The three genes, namely proteasome 20 S subunit beta 9 (PSMB9), signal transducer and activator of transcription 1 (STAT1), and transporter 1 (TAP1), were identified in the present study. The expression of these genes was found to be particularly high in patients with spinal TB and other extrapulmonary TB, as well as in TB and multidrug-resistant TB (p-value < 0.05). They revealed high diagnostic and predictive values and were closely related to the expression of multiple immune cells (p-value < 0.05). It was inferred that the expression of PSMB9, STAT 1, and TAP1 could be regulated by different medicinal chemicals.

Conclusion
PSMB9, STAT1, and TAP1, might play a key role in the pathogenesis of TB, including spinal TB, and the protein product of the genes can be served as diagnostic markers and potential therapeutic target for TB.
Outcomes and survival following thoracic endovascular repair in patients with aortic aneurysms limited to the descending thoracic aorta
Authors: Fankhauser Katharina , Wamala Isaac , Penkalla Adam , Heck Roland , Hammerschmidt Robert , Falk Volkmar , Buz Semih 
Published: June 2023

Abstract
Background
Thoracic endovascular aortic repair (TEVAR) is a well-established therapy for descending aortic aneurysms (DTA). There is a paucity of large series reporting the mid- and long-term outcomes from this era. The main aim of this study was to evaluate the outcomes of TEVAR with regards to the effect of aortic morphology and procedure-related variables on survival, reintervention and freedom from endoleaks.

Methods
In this retrospective single center study, we evaluated the clinical outcomes among 158 consecutive patients with DTA than underwent TEVAR between 2006 and 2019 at our center. The cohort included 51% patients with device landing zones proximal to the subclavian artery and 25.9% patients undergoing an emergent or urgent TEVAR. The primary outcome was survival, and secondary outcomes were reintervention and occurrence of endoleaks.

Results
Median follow-up was 33 months [IQR 12 to 70] while 50 patients (30.6%) had longer than 5-year follow-up. With a median patient age of 74 years, post-operative Kaplan Meyer survival estimates were 94.3% (95%CI 90.8–98.0, SE 0.018%) at 30 days, 76.4% (95%CI 70.0–83.3, SE 0.034%) at one year and, 52.9% (95%CI 45.0–62.2, SE 0.043%) at five years. Freedom from reintervention at 30 days, one year, and five years was 92.9% (95%CI 89.0–97.1, SE 0.021%), 80.0% (95%CI 72.6–88.1, SE 0.039%), and 52.8% (95%CI 41.4–67.4, SE 0.065%), respectively. On cox regression analysis greater aneurysm diameter, and the use of device landing zones in aortic regions 0–1 were associated with an increased probability of all-cause mortality, and with reintervention during follow-up. Independent of aneurysm size undergoing urgent or emergent TEVAR was associated with higher mortality risk for the first three years post-operative but not on long-term follow-up.

Conclusions
Larger aneurysms and those requiring stent-graft landing in aortic zones 0 or 1, are associated with higher risk for mortality and reintervention. There remains a need to optimize clinical management and device design for larger proximal aneurysms.
International differences and inaccuracies in the public advertising about calcaneal apophysitis: an audit of websites originating in Australia, UK and USA
Authors: Liu Sue , Williams Cylie M. , Welch James J. 
Published: June 2023

AbstractBackgroundCalcaneal apophysitis is a common condition in childhood. Parents often seek online information for children's' health care concerns prior to seeking care. Therefore, we aimed to evaluate the credibility, readability, and accuracy of calcaneal apophysitis advertising on popular websites in three countries.MethodsWe used content analysis of publicly accessible data. This involved identifying the top 50 websites in each country from their hit rates. We used elements of validated tools to audit and determine frequencies relevant to credibility (e.g. publisher), readability (e.g. literacy score) and accuracy (e.g. alignment with evidence). Data were analysed quantitatively and reported against each element.ResultsWebsites were predominantly hosted by private health services (n = 118, 79%). The mean (SD) SMOG (readability) score was 9.3 (4.5). The majority of websites (n = 140, 93%) provided at least one treatment recommendation, and less than 10% (n = 11) of websites advertised treatments fully aligned with evidence. Use of treatment modalities without evidence and with high risk to children were also found including surgery, extracorporeal shock wave therapy and laser.ConclusionsCalcaneal apophysitis online advertising is mostly curated by clinicians. Clinicians should consider revising online advertising to increase understandability and accuracy to reduce health care wastage, risk, and low value care.
A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL
Authors: Galgonek Jakub , Vondrášek Jiří 
Published: June 2023

AbstractCurrent biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database systems and databases stored in them to be interoperable with each other. One of the possible solutions to address this issue is to use systems based on Semantic Web technologies, namely on the Resource Description Framework (RDF) to express data and on the SPARQL query language to retrieve the data. Many existing biological and chemical databases are stored in the form of a relational database (RDB). Converting a relational database into the RDF form and storing it in a native RDF database system may not be desirable in many cases. It may be necessary to preserve the original database form, and having two versions of the same data may not be convenient. A solution may be to use a system mapping the relational database to the RDF form. Such a system keeps data in their original relational form and translates incoming SPARQL queries to equivalent SQL queries, which are evaluated by a relational-database system. This review compares different RDB-to-RDF mapping systems with a primary focus on those that can be used free of charge. In addition, it compares different approaches to expressing RDB-to-RDF mappings. The review shows that these systems represent a viable method providing sufficient performance. Their real-life performance is demonstrated on data and queries coming from the neXtProt project.
Joint ISAR imaging and azimuth scaling under low SNR using parameterized compensation and calibration method with entropy minimum criterion
Authors: He Tingting , Tian Biao , Wang Yu , Li Shuai , Xu Shiyou , Chen Zengping 
Published: June 2023

AbstractIn general, the method of conventional motion compensation for inverse synthetic aperture radar (ISAR) imaging is divided into translational motion compensation (TMC) and rotational motion compensation (RMC) in sequence. TMC is the premise of rotational compensation and the most critical procedure is range alignment. However, the deviation of echo correlation results in the poor performance of range alignment under low signal-to-noise ratio (SNR). Therefore, a new high-resolution ISAR imaging and azimuth scaling method under low SNR using parameterized compensation and calibration is proposed in this paper. Firstly, the target motion is modeled, in which translational motion is modeled as formula of the polynomial coefficient vector. In addition, entropy minimization corresponding to echo signal with compensation term based on coefficients is taken as objective function. Moreover, the particle swarm optimization (PSO) algorithm is utilized to search the global optimal parameters to be estimated precisely and efficiently to implement joint motion compensation and azimuth scaling. The experimental results from both simulated and real data verify the effectiveness and robustness of the method.
Pathological ultrastructural alterations of myelinated axons in normal appearing white matter in progressive multiple sclerosis
Authors: Oost Wendy , Huitema Allard J. , Kats Kim , Giepmans Ben N. G. , Kooistra Susanne M. , Eggen Bart J. L. , Baron Wia 
Published: June 2023

AbstractMultiple sclerosis (MS) pathophysiology includes inflammation, demyelination and neurodegeneration, but the exact mechanisms of disease initiation and progression are unknown. A major feature of lesions is lack of myelin, which increases axonal energy demand and requires adaptation in number and size of mitochondria. Outside lesions, subtle and diffuse alterations are observed in normal appearing white matter (NAWM) and normal appearing grey matter (NAGM), including increased oxidative stress, reduced axon density and changes in myelin composition and morphology. On an ultrastructural level, only limited data is available on alterations in myelinated axons. We generated large scale 2D scanning transmission electron microscopy images (‘nanotomy’) of non-demyelinated brain tissue of control and progressive MS donors, accessible via an open-access online repository. We observed a reduced density of myelinated axons in NAWM, without a decrease in cross-sectional axon area. Small myelinated axons were less frequently and large myelinated axons were more frequently present in NAWM, while the g-ratio was similar. The correlation between axonal mitochondrial radius and g-ratio was lost in NAWM, but not in NAGM. Myelinated axons in control GM and NAGM had a similar g-ratio and radius distribution. We hypothesize that axonal loss in NAWM is likely compensated by swelling of the remaining myelinated axons and subsequent adjustment of myelin thickness to maintain their g-ratio. Failure of axonal mitochondria to adjust their size and fine-tuning of myelin thickness may render NAWM axons and their myelin more susceptible to injury.
Graphical Abstract
Use of Fourier phase characteristics and effective stress analyses for post-earthquake ground motion estimation: application to ESG6 blind prediction steps 2&3 dataset and JMA accelerometric data
Authors: Nozu Atsushi 
Published: June 2023

AbstractAfter the occurrence of a large earthquake, engineering seismologists are often requested to estimate strong ground motions at a site where strong motion data were not obtained. The goal of this study was to test the ability of a class of methods that uses Fourier phase characteristics for the post-earthquake ground motion estimation, making use of the precious opportunity provide by the ESG6 Blind Prediction Steps 2&3. It was also part of the goal of this study to test the performance of the effective stress analyses to account for soil nonlinearity. In addition to the dataset provided by the organizer of the blind prediction, the author used additional accelerometric data from a nearby JMA site. To simulate ground motions for an M5.9 earthquake at the target site “KUMA”, the Fourier amplitude spectrum was estimated from the spectral ratio between KUMA and the nearby JMA site. The Fourier phase spectrum was approximated by the spectrum of another event at KUMA. Comparison between the estimated and recorded ground motions after the blind prediction revealed that the estimated ground motions were fairly consistent with the observed ground motions, indicating the effectiveness of the method when the rupture process of the target event is simple and the soil nonlinearity at the target site is not significant. To simulate ground motions at KUMA for the M6.5 foreshock and the M7.3 mainshock of the 2016 Kumamoto earthquake sequence, the author conducted effective stress analyses using a program called “FLIP” to account for soil nonlinearity. Comparison between the estimated and recorded ground motions after the blind prediction indicated that the low-frequency components were overestimated and the high-frequency components were underestimated. The strong soil nonlinearity considered in the effective stress analyses was the main cause of the discrepancy. One explanation for this result could be that the nonlinear soil behavior at KUMA during the foreshock and the mainshock was not a strong one. Another explanation could be that the effect of soil nonlinearity was already included in the records at JMA and the effect of soil nonlinearity was double counted in the results submitted by the author.Graphical Abstract
High-resolution three-dimensional azimuthal velocity anisotropy of S-waves in southern-central Japan, based on ambient noise tomography
Authors: Nthaba Bokani , Ikeda Tatsunori , Tsuji Takeshi , Iio Yoshihisa 
Published: June 2023

AbstractTo investigate the dominant deformational patterns and stress conditions in the upper crustal structure of the Kinki region, southern-central Japan, we constructed a high-resolution 3D azimuthal anisotropy model to a depth of ~ 11 km. We used 6-month-long ambient noise data recorded by the densely distributed permanent and temporary stations. From this dataset, cross-correlations were retrieved. We then obtained a 3D isotropic velocity model by inverting Rayleigh wave dispersion data, followed by a direct joint inversion for both 3D azimuthal anisotropy and additional isotropic velocity perturbation. The resolved 3D azimuthal anisotropy reveals significant contrasts of anisotropy across the Kinki region. The predominant fast axes observed in the northwestern Kinki region align with the direction of the maximum horizontal compressional stress and the principal strain rate axes, suggesting that the observed anisotropy is mainly stress-induced. In the southern part of the study area, furthermore, the predominant fast axes trend NE–SW and near E–W, also indicating the presence of stress-induced anisotropy. On the depth profile of the anisotropy, we found depth-dependent variation of azimuthal anisotropy. There exists a significant consistency between the anisotropy observed beneath 3 km depth and the dense distribution of earthquake hypocenters. This interrelationship between anisotropy and seismicity demonstrates that the observed anisotropy could be linked to local crustal stress or fractures relevant to earthquake ruptures. Our 3D anisotropy model therefore contributes towards understanding the locations and features of the seismicity region.
Graphical Abstract
IRES-mediated Pichia pastoris cell-free protein synthesis
Authors: Wang Yanan , Wang Ting , Chen Xinjie , Lu Yuan 
Published: June 2023

AbstractCell-free protein synthesis (CFPS) system is an ideal platform for fast and convenient protein research and has been used for macromolecular assembly, unnatural amino acid embedding, glycoprotein production, and more. To realize the construction of an efficient eukaryotic CFPS platform with the advantages of low cost and short time, a CFPS system based on the yeast Pichia pastoris was built in this study. The internal ribosomal entry site (IRES) can independently initiate translation and thus promote protein synthesis. The Kozak sequences can facilitate translation initiation. Therefore, the screening of IRES and its combination with Kozak was performed, in which cricket paralysis virus (CRPV) exhibited as the best translation initiation element from 14 different IRESs. Furthermore, the system components and reaction environment were explored. The protein yield was nearly doubled by the addition of RNase inhibitor. The cell extract amount, energy regeneration system (phosphocreatine and phosphocreatine kinase), and metal ions (K+ and Mg2+) were optimized to achieve the best protein synthesis yield. This P. pastoris CFPS system can extend the eukaryotic CFPS platform, providing an enabling technology for fast prototyping design and functional protein synthesis.
Graphical Abstract
Social phobia and evasiveness: trial protocol for a randomized controlled feasibility and superiority trial of the effect of Modified Collaborative Assessment vs. standard assessment on patients’ readiness for psychotherapy (CO-ASSM-RCT)
Authors: Hovmand Oliver Rumle , Reinholt Nina , Dichmann Kirstine , Borisov Radoslav , Arnfred Sidse 
Published: June 2023

Abstract
Background
Evasive personality disorder (AvPD) and social phobia (SP) have substantial costs for patients and their families and great economic costs to the society. While psychotherapy can be an efficacious treatment, many patients drop out during treatment. Increased knowledge on how to decrease dropout from psychotherapy is warranted, including how to increase a patient’s readiness for psychotherapy.

Methods
We describe a randomized controlled feasibility and superiority trial of 42 individuals with a clinical diagnosis of either SP or AvPD, who are to initiate psychotherapeutic treatment in Danish outpatient mental health services. They will be randomized in a 1:1 ratio to either assessment-as-usual and receive no further assessment or to a Modified Collaborative Assessment (MCA) provided as a pre-treatment intervention before psychotherapy initiation. MCA will include a battery of psychological tests designed to thoroughly assess the patients’ psychopathology. The tests are administered in collaboration with the patient, including detailed oral and written feedback. We hypothesize that the intervention is feasible regarding patient’s acceptance and adherence. We further hypothesize that patients randomized to MCA will reach higher levels of readiness for psychotherapy as assessed with the University of Rhode Island Change Assessment Scale (URICA).

Discussion
This protocol assesses the feasibility, efficacy, acceptability, and safety of an intervention aimed at changing the readiness for participation in psychotherapy of patients with SP and AvPD. Results from this feasibility study could guide the development of future large-scale trials of MCA and procedures for MCA treatment fidelity assessment.

Trial registration
NCT2021001.