bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic structure of Spirometra mansoni (Cestoda: Diphyllobothriidae) populations in China revealed by a Target SSR-seq method
Authors: Xu Fang Fang , Chen Wen Qing , Liu Wei , Liu Sha Sha , Wang Yi Xing , Chen Jing , Cui Jing , Zhang Xi 
Published: December 2022

Abstract
Background
In China, the plerocercoid of the cestode Spirometra mansoni is the main causative agent of human and animal sparganosis. However, the population genetic structure of this parasite remains unclear. In this study, we genotyped S. mansoni isolates with the aim to improve current knowledge on the evolution and population diversity of this cestode.

Methods
We first screened 34 perfect simple sequence repeats (SSRs) using all available omic data and then constructed target sequencing technology (Target SSR-seq) based on the Illumina NovaSeq platform. Next, a series of STRUCTURE. clustering, principal component, analysis of molecular variance and TreeMix analyses were performed on 362 worm samples isolated from 12 different hosts in 16 geographical populations of China to identify the genetic structure.

Results
A total of 170 alleles were detected. The whole population could be organized and was found to be derived from the admixture of two ancestral clusters. TreeMix analysis hinted that possible gene flow occurred from Guizhou (GZ) to Sichuan (SC), SC to Jaingxi (JX), SC to Hubei (HB), GZ to Yunnan (YN) and GZ to Jiangsu (JS). Both neighbor-joining clustering and principal coordinate analysis showed that isolates from intermediate hosts tend to cluster together, while parasites from definitive hosts revealed greater genetic differences. Generally, a S. mansoni population was observed to harbor high genetic diversity, moderate genetic differentiation and a little genetic exchange among geographical populations.

Conclusions
A Target SSR-seq genotyping method was successfully developed, and an in-depth view of genetic diversity and genetic relationship will have important implications for the prevention and control of sparganosis.

Graphical Abstract
Metabarcoding of bacteria and parasites in the gut of Apodemus agrarius
Authors: Kim Soo Lim , Choi Jun Ho , Yi Myung-hee , Lee Seogwon , Kim Myungjun , Oh Singeun , Lee In-Yong , Jeon Bo-Young , Yong Tai-Soon , Kim Ju Yeong 
Published: December 2022

Abstract
Background
The striped field mouse Apodemus agrarius is a wild rodent commonly found in fields in Korea. It is a known carrier of various pathogens. Amplicon-based next-generation sequencing (NGS) targeting the 16S ribosomal RNA (rRNA) gene is the most common technique used to analyze the bacterial microbiome. Although many bacterial microbiome analyses have been attempted using feces of wild animals, only a few studies have used NGS to screen for parasites. This study aimed to rapidly detect bacterial, fungal and parasitic pathogens in the guts of A. agrarius using NGS-based metabarcoding analysis.

Methods
We conducted 18S/16S rDNA-targeted high-throughput sequencing on cecal samples collected from A. agrarius (n = 48) trapped in May and October 2017. Taxa of protozoa, fungi, helminths and bacteria in the cecal content were then identified.

Results
Among the protozoa identified, the most prevalent was Tritrichomonas sp., found in all of the cecal samples, followed by Monocercomonas sp. (95.8% prevalence; in 46/48 samples) and Giardia sp. (75% prevalence; in 36/48 samples). For helminths, Heligmosomoides sp. was the most common, found in 85.4% (41/48) of samples, followed by Hymenolepis sp. (10.4%; 5/48) and Syphacia sp. (25%; 12/48). The 16S rRNA gene analysis showed that the microbial composition of the cecal samples changed by season (P = 0.005), with the linear discriminant analysis effect size showing that in the spring Escherichia coli and Lactobacillus murinus were more abundant and Helicobacter rodentium was less abundant. Helicobacter japonicus was more abundant and Prevotella_uc was less abundant in males. The microbial composition changed based on the Heligmosomoides sp. infection status (P = 0.019); specifically, Lactobacillus gasseri and Lactobacillus intestinalis were more abundant in the Heligmosomoides sp.-positive group than in the Heligmosomoides sp.-negative group.

Conclusions
This study demonstrated that bacterial abundance changed based on the season and specific parasitic infection status of the trapped mice. These results highlight the advantages of NGS technology in monitoring zoonotic disease reservoirs.

Graphical Abstract
Levels of extracellular matrix metabolites are associated with changes in Ankylosing Spondylitis Disease Activity Score and MRI inflammation scores in patients with axial spondyloarthritis during TNF inhibitor therapy
Authors: Holm Nielsen Signe , Sun Shu , Bay-Jensen Anne C. , Karsdal Morten , Sørensen Inge Juul , Weber Ulrich , Loft Anne Gitte , Kollerup Gina , Thamsborg Gorm , Madsen Ole Rintek , Møller Jakob , Østergaard Mikkel , Pedersen Susanne Juhl 
Published: December 2022

Abstract
Background/purpose
In axial spondyloarthritis (axSpA) inflammation of the sacroiliac joints and spine is associated with local extracellular matrix (ECM) remodeling of affected tissues. We aimed to investigate the association of ECM metabolites with treatment response in axSpA patients treated with TNF-α inhibitory therapy for 46 weeks.

Methods
In a prospective clinical study of axSpA patients (n=55) initiating a TNF inhibitor (infliximab, etanercept, or adalimumab), serum concentrations of formation of type I (PRO-C1), type III (PRO-C3), and type VI (PRO-C6) collagen; turnover of type IV collagen (PRO-C4), and matrix-metalloproteinase (MMP)-degraded type III (C3M) collagen, MMP-degraded type IV (C4M), type VI (C6M), and type VII (C7M) collagen, and cathepsin-degraded type X collagen (C10C), MMP-mediated metabolite of C-reactive protein (CRPM), citrullinated vimentin (VICM), and neutrophil elastase-degraded elastin (EL-NE) were measured at baseline, week 2, week 22, and week 46.

Results
Patients were mostly males (82%), HLA-B27 positive (84%), with a median age of 40 years (IQR: 32–48), disease duration of 5.5 years (IQR: 2–10), and a baseline Ankylosing Spondylitis Disease Activity Score (ASDAS) of 3.9 (IQR: 3.0–4.5).
Compared to baseline, PRO-C1 levels were significantly increased after two weeks of treatment, C6M levels were significantly decreased after two and 22 weeks (repeated measures ANOVA, p=0.0014 and p=0.0015, respectively), EL-NE levels were significantly decreased after 2 weeks (p=0.0008), VICM levels were significantly decreased after two and 22 weeks (p=0.0163 and p=0.0374, respectively), and CRP were significantly decreased after two and 22 weeks (both p=0.0001). Baseline levels of PRO-C1, PRO-C3, C6M, VICM, and CRP were all associated with ASDAS clinically important and major improvement after 22 weeks (ΔASDAS ≥1.1) (Mann–Whitney test, p=0.006, p=0.008, p<0.001, <0.001, <0.001, respectively), while C6M, VICM and CRP levels were associated with ASDAS clinically important and major improvement after 46 weeks (ΔASDAS ≥2.0) (p=0.002, p=0.044, and p<0.001, respectively). PRO-C1 and C6M levels were associated with a Bath AS Disease Activity Score (BASDAI) response to TNF-inhibitory therapy after 22 weeks (Mann–Whitney test, p=0.020 and p=0.049, respectively). Baseline levels of PRO-C4 and C6M were correlated with the total SPARCC MRI Spine and Sacroiliac Joint Inflammation score (Spearman’s Rho ρ=0.279, p=0.043 and ρ=0.496, p=0.0002, respectively).

Conclusions
Extracellular matrix metabolites were associated with ASDAS response, MRI inflammation, and clinical treatment response during TNF-inhibitory treatment in patients with axSpA.
Neuronal CRMP2 phosphorylation inhibition by the flavonoid, naringenin, contributes to the reversal of spinal sensitization and arthritic pain improvement
Authors: Jiang Yue-Peng , Wang Song , Lai Wei-Dong , Wu Xue-Qing , Jin Yan , Xu Zheng-Hao , Moutal Aubin , Khanna Rajesh , Park Ki Duk , Shan Zhi-Ming , Wen Cheng-Ping , Yu Jie 
Published: December 2022

Abstract
Background
Rheumatoid arthritis patients usually suffer from arthritic chronic pain. However, due to an incomplete understanding of the mechanisms underlying autoimmune disorders, the management of arthritic pain is unsatisfactory. Here, we investigated the analgesic effect and underlying mechanism of the natural flavonoid naringenin (NAR) in collagen-induced arthritis (CIA) pain.

Methods
NAR was injected (i.p.) once per day for 42 days after initial immunization, and rats were sacrificed on the 28th (the 21st day after final immunization, PID 21) and 42nd days (PID 35). The inflammatory factors, central sensitization indicators, and CRMP2 phosphorylation, as well as the anti-rheumatoid activity and analgesic effect of NAR, were further investigated.

Results
We found that NAR decreased the arthritis score and paw swelling, as well as the mechanical and thermal pain. The immunofluorescence results also showed a dose dependent effect of NAR on reducing the expressions of spinal cFos, IBA-1, and GFAP on the 28th (PID 21) and 42nd day (PID 35). NAR decreased the phosphorylation of CRMP2 S522 and the expression of the kinase CDK5 in the spinal dorsal horn, but pCRMP2 Y479 was unchanged. In addition, CRMP2 was co-localized with NEUN, but not IBA-1 or GFAP, indicating the involvement of neural CRMP2 phosphorylation in CIA-related pain. Finally, CRMP2 S522 phosphorylation selective inhibitor (S)-lacosamide also alleviated arthritic pain.

Conclusions
Taken together, our results demonstrate that NAR alleviates inflammation and chronic pain in CIA model, which might be related to its inhibition of neuronal CRMP2 S522 phosphorylation, potentially mitigating the central sensitization. Our study provide evidence for the potential use of NAR as non-opioid-dependent analgesia in arthritic pain.
Multiparametric autoantibody analysis: a new paradigm for the diagnosis of connective tissue diseases
Authors: Bizzaro Nicola , Villalta Danilo , Bini Vittorio , Migliorini Paola , Franceschini Franco , Piantoni Silvia , Garrafa Emirena , Riccieri Valeria , Fioravanti Antonella , Bellisai Francesca , Tampoia Marilina , Fornaro Marco , Iannone Florenzo , Ghirardello Anna , Zen Margherita , Palterer Boaz , Parronchi Paola , Infantino Maria , Benucci Maurizio , Rigon Amelia , Arcarese Luisa , Del Rosso Stefania , Canti Valentina , Bartoloni Elena , Gerli Roberto ,   FIRMA Collaborators, Bistoni Onelia , Cafaro Giacomo , Perricone Carlo , Topini Fabiana , Cavazzana Ilaria , Fredi Micaela , Masneri Stefania , Cheleschi Sara , Bacarelli Maria-Romana , Cammelli Daniele , Manfredi Mariangela , Giacomelli Roberto , Querini Patrizia Rovere 
Published: December 2022

Abstract
Background
In patients affected by connective tissue diseases (CTDs), the identification of wide autoantibody profiles may prove useful in early diagnosis, in the evaluation of prognosis (risk stratification), and in predicting response to therapy. The aim of the present study was to evaluate the utility of multiparametric autoantibody analysis performed by a new fully automated particle-based multi-analyte technology (PMAT) digital system in a large multicenter cohort of CTD patients and controls.

Methods
Serum samples from 787 patients with CTD (166 systemic lupus erythematosus; 133 systemic sclerosis; 279 Sjögren’s syndrome; 106 idiopathic inflammatory myopathies; 103 undifferentiated CTD), 339 patients with other disorders (disease controls) (118 infectious diseases, 110 organ-specific autoimmune diseases, 111 other rheumatic diseases), and 121 healthy subjects were collected in 13 rheumatologic centers of the FIRMA group. Sera were analyzed with the Aptiva-PMAT instrument (Inova Diagnostics) for a panel of 29 autoantibodies.

Results
Multiparametric logistic regression showed that enlarged antibody profiles have a higher diagnostic efficiency than that of individual antibodies or of antibodies that constitute classification criteria for a given disease and that probability of disease increases with multiple positive autoantibodies.

Conclusions
This is the first study that analyzes the clinical and diagnostic impact of autoantibody profiling in CTD. The results obtained with the new Aptiva-PMAT method may open interesting perspectives in the diagnosis and sub-classification of patients with autoimmune rheumatic diseases.
Perceptions towards biologic and biosimilar therapy of patients with rheumatic and gastroenterological conditions
Authors: Khoo Thomas , Sidhu Navkiran , Marine Franca , Lester Susan , Quinlivan Alannah , Rowett Debra , Buchbinder Rachelle , Hill Catherine L. 
Published: December 2022

Abstract
Background
Biologic and targeted synthetic disease modifying agents (b/tsDMARDs) have broadened the treatment landscape for autoimmune diseases particularly in patients refractory to conventional DMARDs. More recently, the introduction of biosimilars has reduced the price of bDMARDs, potentially improving accessibility. Though efficacy and safety have been described, patient attitudes to b/tsDMARDs are not well-understood. We aim to investigate patients’ beliefs about biologic and biosimilar therapy, and the factors influencing their perceptions.

Methods
Patient consumer groups (Arthritis Australia, Crohn’s and Colitis Australia) assisted in advertising an online questionnaire for people with a self-reported diagnosis of inflammatory arthritis (IA) or inflammatory bowel disease (IBD). The questionnaire incorporated the Belief about Medicines Questionnaire (BMQ) and the single-item literacy screener (SILS). Sources and favourability of biologic/biosimilar information were analysed, using the chi-square and a non-parametric trend test for unordered and ordered categorical variables respectively, comparing respondents with IA and IBD.

Results
Eight hundred and thirty eight people (686–IA, 144–IBD, 8 both) responded. 658 (79%) used b/tsDMARDs. The BMQ demonstrated high necessity belief (median 4.2) with moderate concerns (median 2.8) about biologics. 95% of respondents obtained medication information from specialists though most used multiple sources (median 4). The most positive resources were specialists and specialist nurses. 73/141 (52%) respondents with IBD obtained information from specialist nurses compared with 202/685 (29%) with IA (p = 0.012). Respondents with limited reading ability on SILS were more likely to discuss information with a general practitioner or pharmacist. Younger respondents and those with higher BMQ concern scores more frequently consulted less reliable sources (e.g. social media). 502 respondents (60%) answered the biosimilar questions. Only 23 (4.6%) reported currently using a biosimilar and 336 (66.9%) were unsure if biosimilars were available in Australia. Specialist recommendation was the most frequent factor that would influence a patient to change from originator to biosimilar (352/495, 71.1%).

Conclusions
There is a high level of trust in specialists’ recommendations about b/tsDMARDs, although most people also utilise additional information sources. Contextual factors influencing resource selection include age, reading ability and degree of concern about medicines. People with IA and IBD have similar attitudes though those with IBD more frequently access specialist nurse advice.
Promising biological agents represented in Bacillus velezensis 33RB and Aspergillus niger 46SF endophytic isolates for controlling Populus tomentosa wilt and anthracnose diseases
Authors: Dawwam Ghada E. , Sehim Amira E. 
Published: December 2022

Abstract
Background
Poplar fungal infections are difficult to control and result in severe economic loss. As a viable alternative to chemical pesticides, biocontrol is an effective safe method for disease control.

Results
Inhibitory activity of Bacillus velezensis 33RB and Aspergillus niger 46SF was evaluated against numerous phytopathogens. The bacterial strain displayed the highest inhibitory activity toward Colletotrichum gloeosporioides BJ02 and Fusarium oxysporum 20RF (61.2 and 49.4%, respectively). Also, the maximum inhibitory activity of A. niger 46SF was exhibited (75.51 and 70.83%) against C. gloeosporioides BJ02 and F. oxysporum 20RF, respectively. The minimum volume (6.25 ml) of sterilized cultural filtrate of bacterial and fungal strains significantly inhibited the growth of C. gloeosporioides BJ02 by 73.3 and 83.3%, respectively, and F. oxysporum 20RF reached 40.4 and 78.8%, respectively. B. velezensis 33RB and A. niger 46SF displayed the highest inhibition toward C. gloeosporioides BJ02 and F. oxysporum 20RF at neutral pH and pH 5, respectively. Moreover, the highest inhibitory activity of B. velezensis 33RB and A. niger 46SF was achieved at 37 °C and 28 °C, respectively. Pathogenicity tests on sterilized detached leaves indicated that these isolates could potentially affect anthracnose and fusarium wilt diseases. Several secondary bioactive metabolites that assured the biocontrol efficacy of tested microbes were detected by liquid chromatography–mass spectrometry (LC–MS). The most detectable compounds included organic acids such as fumaric, DL-malic, citric, isobutyric, and glutamic acids. Also, numerous fatty acids such as lauric, linoleic, oleic, stearic, and myristic acids with diverse biological functions, including antimicrobial properties, were determined.

Conclusions
Bacillus velezensis 33RB and A. niger 46SF were potential alternatives to chemical pesticides as biological control agents for the phytopathogens C. gloeosporioides BJ02 and F. oxysporum with environmentally friendly and sustainable properties.
Neurophysiologic evaluation of patients with cervical spondylotic myelopathy
Authors: Jawad Zahraa Y. , Hamdan Farqad B. , Nema Ihssan S. 
Published: December 2022

Abstract
Background
Cervical spondylotic myelopathy (CSM) is a neurodegenerative disease caused by repetitive spinal cord damage that has resulted in significant clinical morbidity. The clinical evaluation of signs and symptoms, as well as neuroimaging and several neurophysiological tests, are used to make the diagnosis.

Objectives
To investigate changes in the cutaneous silent period (CuSP), cortical silent period (CoSP), and H-reflex in CSM patients, and to correlate these tests with the Japanese Orthopedic Association (JOA) score and Nurick’s grading, as well as to determine the diagnostic value of each of them.

Methods
Twenty patients (14 males and 6 females) with CSM were clinically diagnosed and documented by magnetic resonance imaging (MRI), and they were paired with another 20 healthy volunteers (13 males and 7 females) as a control group. CuSP, CoSP, and H-reflex tests were performed on both groups.

Results
In CSM patients, CuSP latency and duration are substantially longer and shorter in CSM patients, respectively. The degree of changes in CuSP latency is well correlated with the severity of the disease. Further, CoSP duration is significantly shortened. The H-reflex parameters did not differ significantly between the patient and control groups.

Conclusion
The shortened CoSP’s duration and the prolonged CuSP's latency suggest malfunction of the inhibitory and excitatory circuits in the spinal cord. The CuSP is more sensitive and specific than the CoSP in the diagnosis of a patient with CSM.
Diagnostic accuracy of hysterosalpingo-lidocaine-foam sonography combined with power Doppler (HyLiFoSy-PD) compared to laparoscopy and dye testing in tubal patency assessment in cases of infertility
Authors: Sharaf Marwa F. , Fawzy Ibrahim , Elkhateb Islam T. , Elmahgoub Yassin , Idris Omaima , Aboulghar Mona 
Published: December 2022

Abstract
Background
Tubal patency testing is an essential part of female subfertility evaluation. Hysterosalpingogram is less invasive and less expensive compared to laparoscopy and dye testing (LDT), i.e., laparoscopic chromopertubation. Hysterosalpingo-foam sonography (HyFoSy) uses commercial echogenic gel foam that is easily visible on ultrasound to assess the tubes. It offers a safer and less painful alternative to HSG, with no radiation exposure. Hysterosalpingo-lidocaine-foam sonography with power Doppler (HyLiFoSy-PD) uses lidocaine-made gel foam as a contrast medium. It was postulated to as to be less painful and easier to detect on ultrasound, compared with hysterosalpingo-foam sonography using other contrast media and that it can also be used whenever the commercial gel used with HyFoSy is not available or is relatively expensive.

Methodology
This prospective diagnostic accuracy study was carried out between February 2018 and 2020 at the Cairo Fetal Medicine Unit, Department of Obstetrics and Gynecology, Cairo University. One hundred twenty-two infertile patients, who were already scheduled for LDT as a part of their infertility work-up, were consecutively recruited for this study. The HyLiFoSy-PD (index test) was performed 1 week before the scheduled LDT for these patients. Using an intrauterine pediatric Folley’s balloon catheter, 20 ml of lidocaine-made gel foam was slowly infused intrauterine, while observing their flow in both fallopian tubes using a grayscale and power Doppler transvaginal two-dimensional ultrasound system. All patients then underwent LDT (reference test). The results of HyLiFoSy-PD were compared with those of LDT to determine the accuracy of HyLiFoSy-PD in tubal patency assessment. We also assessed the procedure duration, associated pain, and other complications.

Results
Comparing HyLiFoSy-PD with LDT in the 115 patients who completed the procedure, results showed 98.1% sensitivity, 90% specificity, 99% positive predictive value, 81.8% negative predictive value, 9.81 positive likelihood ratio, 0.02 negative likelihood ration, and 97.4% overall accuracy in the assessment of tubal patency (odds ratio = 463.5 with confidence interval = 79.39–2706; P-value: 0.687). The median procedure duration was 11 min. All patients experienced some degree of pain during the procedure with 91 patients (79%) reported mild pain and 24 patients (21%) reported moderate pain.

Conclusion
HyLiFoSy-PD was found to be an accurate tool in tubal patency assessment. It was also found to be safe and well-tolerated.
Hereditary Endocrine Tumor Registries
Authors: Moore Edwina C , Ioannou Liane , Ruseckaite Rasa , Serpell Jonathan , Ahern Susannah 
Published: December 2022

Abstract

Context
Endocrine neoplasia syndromes are phenotypically complex, and there is a misconception that they are universally rare. Genetic alterations are increasingly recognized; however, true prevalence is unknown. The purpose of a clinical registry is to monitor the quality of health care delivered to a specified group of patients through the collection, analysis, and reporting of relevant health-related information. This leads to improved clinical practice, decision-making, patient satisfaction, and outcome.

Objective
This review aims to identify, compare, and contrast active registries worldwide that capture data relevant to hereditary endocrine tumors (HETs).

Methods
Clinical registries were identified using a systematic approach from publications (Ovid MEDLINE, EMBASE) peer consultation, clinical trials, and web searches. Inclusion criteria were hereditary endocrine tumors, clinical registries, and English language. Exclusion criteria were institutional audits, absence of clinical data, or inactivity. Details surrounding general characteristics, funding, data fields, collection periods, and entry methods were collated.

Results
Fifteen registries specific for HET were shortlisted with 136 affiliated peer-reviewed manuscripts.

Conclusion
There are few clinical registries specific to HET. Most of these are European, and the data collected are highly variable. Further research into their effectiveness is warranted. We note the absence of an Australian registry for all HET, which would provide potential health and economic gains. This review presents a unique opportunity to harmonize registry data for HET locally and further afield.