bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel extraction-free dual HiFi-LAMP assay for detection of methicillin-sensitive and methicillin-resistant
Staphylococcus aureus
Authors: Zhao Xiuli , Zeng Yi , Yan Beibei , Liu Yanping , Qian Yueqin , Zhu Aiping , Zhao Yongjuan , Zhang Xiaoling , Zhang Chiyu , Wan Zhenzhou 
Published: February 2024

ABSTRACT

Staphylococcus aureus
(
S. aureus
) is a leading cause of bacteremia and blood stream infections. Methicillin-resistant
S. aureus
(MRSA) that first appeared in 1961 often caused hospital-acquired infections (HAIs) and community-acquired infections (CAIs) and was associated with high mortality rate. Accurate and rapid point-of-care testing (POCT) of MRSA is crucial for clinical management and treatment of MRSA infections, as well as the prevention and control of HAIs and CAIs. Here, we reported a novel extraction-free dual HiFi-LAMP assay for discriminative detection of methicillin-susceptible
S. aureus
and MRSA. The dual HiFi-LAMP assay can detect 30 copies/reaction of
nuc
and
mecA
genes with detection limits of 147 and 158 copies per 25 µL reaction, respectively. A retrospective clinical evaluation with 107 clinical
S. aureus
isolates showed both sensitivity and specificity of 100%. A prospective clinical evaluation with 35 clinical samples revealed a specificity of 100% and a sensitivity of 92.3%. The dual HiFi-LAMP assay can detect almost all
S. aureus
samples (141/142; 99.3%) within 20 min, implying that the entire HiFi-LAMP assay (including sample process) can be completed within 40 min, extremely significantly shorter than 3–5 days by the traditional clinical microbial culture and antibiotic susceptibility testing. The novel extraction-free dual HiFi-LAMP assay can be used as a robust POCT tool to promote precise diagnosis and treatment of MRSA infections in hospitals and to facilitate surveillance of MRSA at hospital and community settings.

IMPORTANCE

Methicillin-resistant
Staphylococcus aureus
(MRSA) was associated with high mortality rate and listed as a “priority pathogen” by the World Health Organization. Accurate and rapid point-of-care testing (POCT) of MRSA is critically required for clinical management and treatment of MRSA infections. Some previous LAMP-based POCT assays for MRSA might be questionable due to their low specificity and the lack of appropriate evaluation directly using clinical samples. Furthermore, they are relatively tedious and time-consuming because they require DNA extraction and lack multiplex detection capacity. Here, we reported a novel extraction-free dual HiFi-LAMP assay for discriminative detection of MRSA and methicillin-susceptible
S. aureus
. The assay has high specificity and sensitivity and can be completed within 40 min. Clinical evaluation with real clinical samples and clinical isolates showed excellent performance with 100% specificity and 92.3%–100% sensitivity. The novel extraction-free assay may be a robust POCT tool to promote precise diagnosis of MRSA infections and facilitate surveillance of MRSA at hospital and community settings.
Milk fat globule-epidermal growth factor 8 (MFGE8) prevents intestinal fibrosis
Authors: Lin Sinan , Wang Jie , Mukherjee Pranab K , Mao Ren , West Gail , Czarnecki Doug , Zhao Shuai , Nguyen Quang Tam , Elias Michael , Massey William J , Liu WeiWei , Wang Yan , Prasad Ankita , Banerjee Suhanti , Goren Idan , Chandra Jyotsna , Le Hongnga T , Dejanovic Dina , Li Jiannan , Chen Minhu , Holubar Stefan , Olman Mitchell , Southern Brian , Hu Shaomin , Gordon Ilyssa O , Atabai Kamran , Fiocchi Claudio , Rieder Florian 
Published: February 2024

Objective
Intestinal fibrosis is considered an inevitable consequence of chronic IBD, leading to stricture formation and need for surgery. During the process of fibrogenesis, extracellular matrix (ECM) components critically regulate the function of mesenchymal cells. We characterised the composition and function of ECM in fibrostenosing Crohn’s disease (CD) and control tissues.

Design
Decellularised full-thickness intestinal tissue platforms were tested using three different protocols, and ECM composition in different tissue phenotypes was explored by proteomics and validated by quantitative PCR (qPCR) and immunohistochemistry. Primary human intestinal myofibroblasts (HIMFs) treated with milk fat globule-epidermal growth factor 8 (MFGE8) were evaluated regarding the mechanism of their antifibrotic response, and the action of MFGE8 was tested in two experimental intestinal fibrosis models.

Results
We established and validated an optimal decellularisation protocol for intestinal IBD tissues. Matrisome analysis revealed elevated MFGE8 expression in CD strictured (CDs) tissue, which was confirmed at the mRNA and protein levels. Treatment with MFGE8 inhibited ECM production in normal control HIMF but not CDs HIMF. Next-generation sequencing uncovered functionally relevant integrin-mediated signalling pathways, and blockade of integrin αvβ5 and focal adhesion kinase rendered HIMF non-responsive to MFGE8. MFGE8 prevented and reversed experimental intestinal fibrosis in vitro and in vivo.

Conclusion
MFGE8 displays antifibrotic effects, and its administration may represent a future approach for prevention of IBD-induced intestinal strictures.
Diagnostic challenges of the idiopathic plasmacytic lymphadenopathy (IPL) subtype of idiopathic multicentric Castleman disease (iMCD): Factors to differentiate from IgG4-related disease
Authors: Nishikori Asami , Nishimura Midori Filiz , Fajgenbaum David C , Nishimura Yoshito , Maehama Kanna , Haratake Tomoka , Tabata Tetsuya , Kawano Mitsuhiro , Nakamura Naoya , Momose Shuji , Sumiyoshi Remi , Koga Tomohiro , Yamamoto Hidetaka , van Rhee Frits , Kawakami Atsushi , Sato Yasuharu 
Published: February 2024

Aims and methodsIdiopathic multicentric Castleman disease (iMCD) is currently considered to be classified into three clinical subtypes, including idiopathic plasmacytic lymphadenopathy (IPL), thrombocytopaenia, anasarca, fever, reticulin fibrosis/renal dysfunction, organomegaly (TAFRO) and not otherwise specified (NOS). Among the three, iMCD-IPL closely mimics IgG4-related disease (IgG4-RD). In diagnosing IgG4-RD, it is sometimes challenging to distinguish iMCD-IPL patients that also meet the histological diagnostic criteria for IgG4-RD. In this study, we focused on the number of IgG4-positive cells in the lymph nodes and analysed the relationship with laboratory findings to distinguish iMCD-IPL from IgG4-RD. Thirty-nine patients with iMCD-IPL and 22 patients with IgG4-RD were included.ResultsAmong the cases considered to be iMCD-IPL, 33.3% (13/39) cases also met the histological diagnostic criteria for IgG4-RD and serum IgG4 levels were not different between the two groups. However, the serum IgG4/IgG ratio was significantly higher in IgG4-RD, with a cut-off value of 19.0%. Additionally, a significant positive correlation between serum IgG levels and the number of IgG4-positive cells was observed in iMCD-IPL (p=0.001). The serum IgG cut-off value for distinguishing iMCD-IPL meeting histological criteria for IgG4-RD from other iMCD-IPL was 5381 mg/dL.ConclusionsiMCD-IPL cases with high serum IgG levels (>5000 mg/dL) were likely to meet the diagnostic criteria for IgG4-RD because of the numerous IgG4-positive cells observed. A combination of clinical presentations, laboratory values including the serum IgG4/IgG ratios and histological analysis is crucial for diagnosis of IgG4-RD and iMCD-IPL.
An “on-off-on” fluorescent sensor based on TSPP-gallic acid: Visual detection of S2− in actual samples
Authors: Liu Yuanyuan , Ma Tianfeng , Li Jing , Shi Lin , Xu Xiaohua , Wang Huan 
Published: February 2024

A novel “on-off-on” switches fluorescence sensor based on TSPP-gallic acid (GA) for S[Formula: see text]-detecting was designed in this article. 5,10,15,20- (4-sulphonatophenyl) porphyrin (TSPP) was synthesized by a modified “one-pot” method. The synthesized TSPP was used as a fluorescence probe for the construction of a fluorescence sensing system. At room temperature, the maximum fluorescence emission wavelength could be obtained at 642 nm when the excitation wavelength was 515 nm when the fluorescence signal was in the “on” mode. The TSPP solution appeared pink in color at this moment. When GA was introduced into the TSPP solution, the fluorescence signal was turned off (fluorescence intensity was quenched) due to the protonation of TSPP, which was caused by the weak acidity of GA. The color of the TSPP solution changed from pink to green. Following that, an acid-base reaction between S[Formula: see text]and GA was initiated when S[Formula: see text]was introduced into the TSPP-GA system, leading to the liberation of TSPP and restoration of fluorescence intensity. The solution color reverted to red, indicating that the fluorescence sensing system had returned to the “on” mode. The TSPP-GA system had good selectivity and sensitivity to S[Formula: see text], the linear range was 4.52 × 10[Formula: see text] M [Formula: see text] 4.34 × 10[Formula: see text] M, and the detection limit (LOD) was 0.87 [Formula: see text] M. It could be used to detect sulfur ions in actual samples with satisfactory recoveries and RSD values.
BUSTLE: A Versatile Tool for the Evolutionary Learning of STL Specifications from Data
Authors: Pigozzi Federico , Nenzi Laura , Medvet Eric 
Published: February 2024

Abstract
Describing the properties of complex systems that evolve over time is a crucial requirement for monitoring and understanding them. Signal Temporal Logic (STL) is a framework that proved to be effective for this aim because it is expressive and allows state properties as human-readable formulae. Crafting STL formulae that fit a particular system is, however, a difficult task. For this reason, a few approaches have been proposed recently for the automatic learning of STL formulae starting from observations of the system. In this paper, we propose BUSTLE (Bi-level Universal STL Evolver), an approach based on evolutionary computation for learning STL formulae from data. BUSTLE advances the state of the art because it (i) applies to a broader class of problems, in terms of what is known about the state of the system during its observation, and (ii) generates both the structure and the values of the parameters of the formulae employing a bi-level search mechanism (global for the structure, local for the parameters). We consider two cases where (a) observations of the system in both anomalous and regular state are available, or (b) only observations of regular state are available. We experimentally evaluate BUSTLE on problem instances corresponding to the two cases and compare it against previous approaches. We show that the evolved STL formulae are effective and human-readable: the versatility of BUSTLE does not come at the cost of lower effectiveness.
Breaking Disciplinary Boundaries in Studies of Audience Experience of Engagement with Art and Immersive Virtual Stories
Authors: Wlazeł Agnieszka 
Published: February 2024

Abstract
This paper examines the audience experience of engagement with immersive virtual stories and art in general, positioning it within the broader context of audience art engagement studies. The literature review indicates that the audience's experience of engagement is a process in specific artistic and personal contexts. Yet, audience studies lack an approach to empirically study the complexity and dynamics of directed (in narrative stages) engagement. This paper presents an exploratory pilot study of the experience of immersive VR theatre. The comparison of the data of different participants experiencing the same art project demonstrates that even a simple research design integrating bodily data and audience reflection in the context of the specific artwork can bring insights valuable for practitioners and researchers. The paper endorses the use of the mixed-method design in engagement studies.
Gender-Diverse Patients’ Awareness and Utilization of Gender-Affirming Laryngological Services
Authors: Madzia Jules L. , Stryker Shanna D. , Bamford Leigh M. , Pickle Sarah , McKenna Victoria S. 
Published: February 2024

Objective: Despite gender-affirming laryngological services (GALS; eg, voice therapy or surgery) being available nationwide, there is a discrepancy between the number of transgender and gender diverse (TGD) people with vocal incongruence and those who pursue services. Primary care is an important setting for accessing gender-affirming care, including learning about GALS. The purpose of this study was to understand the relationship between access to primary care and utilization of GALS. Methods: An anonymous cross-sectional online survey was developed in REDCap. Between June-November 2022, 187 TGD respondents answered all questions related to this analysis. We assessed the relationship between having a primary care provider (PCP) and use of GALS via logistic regression. Results: Of the 167 individuals who reported having a PCP, 54% reported familiarity with GALS, compared to 45% of individuals without a PCP. Compared to the group without a PCP, a greater proportion of individuals with a PCP had received professional voice therapy (21% vs 5%) and voice surgery (3% vs 0%). Logistic regression models did not demonstrate a significant effect of primary care access on either familiarity with, or use of, GALS. Conclusion: Most respondents (89%) were linked to the medical community through a PCP. A greater proportion of respondents with a PCP had accessed professional voice therapy and voice surgery compared with respondents without a PCP, though this difference was not statistically significant. Increased communication between GALS providers and PCPs would raise awareness of available services and may strengthen the referral pipeline to increase access to vocal care. Level of Evidence: Level III.
Characterizing Aging-Related Health in Older Women with a History of Incarceration: Multimorbidity, Polypharmacy, Mortality, Frailty, and Depression
Authors: Emerson Amanda , Li Xinyang , Zaller Nick , Ramaswamy Megha 
Published: February 2024

Older women with criminal legal system involvement (CLSI) face aging-related challenges to health earlier and with fewer resources than other women. Few studies focus on their health status and aging-related health needs. Objective To characterize aging-related health in women with past CLSI and compare with women with no-CLSI. Method Health and Retirement Study Wave 11 and 12 data from women age >50 with CLSI were compared with data from women age >50 with no-CLSI. Generalized linear models were estimated for aging-related health outcomes. Results The group with CLSI ( n = 230) was significantly younger than the no-CLSI group ( n = 8035) yet had more physical, functional, and mental health challenges and fewer resources. Incarceration significantly predicted aging-related outcomes of multimorbidity, polypharmacy, mortality, frailty, and depression. Discussion Earlier onset of physical and functional health conditions in women with past CLSI has implications for health education and promotion, clinical practice, and intervention design.
Effects of atropine eyedrops at ten different concentrations for myopia control in children: A systematic review on meta-analysis
Authors: Wang Jin-Da , Liu Mei-Rui , Chen Chang-Xi , Cao Kai , Zhang Yun , Zhu Xiao-Hong , Wan Xiu-Hua 
Published: February 2024

Purpose To estimate the effect of atropine eyedrops at different concentrations for myopia control in children. Methods We conducted a Bayesian random-effects network meta-analysis based on randomized controlled trials (RCT). Primary outcomes include changes in spherical equivalent error (SER) and changes in axial length (AL), mean difference (MD) together with 95% credible interval (CrI) were used to evaluate the efficacy. Results 28 RCTs (6608 children) were included in this review. Comparing ten atropine eyedrops (0.0025%, 0.005%, 0.01%, 0.02%, 0.025%, 0.05%, 0.1%, 0.25%, 0.5% and 1% concentrations) with the placebo, the MDs and 95%CrIs of changes in SER are −0.006 (−0.269, 0.256) D, 0.216 (−0.078, 0.508) D, 0.146 (0.094, 0.199) D, 0.167 (0.039, 0.297) D, 0.201 (0.064, 0.341) D, 0.344 (0.251, 0.440) D, 0.255 (0.114, 0.396) D, 0.296 (0.140, 0.452) D, 0.331 (0.215, 0.447) D, and 0.286 (0.195, 0.337) D, respectively. The MDs and 95%CrIs of changes in AL are −0.048 (−0.182, 0.085) mm, −0.078 (−0.222, 0.066) mm, −0.095 (−0.130, −0.060) mm, −0.096 (−0.183, −0.009) mm, −0.083 (−0.164, −0.004) mm, −0.114 (−0.176, −0.056) mm, −0.134 (−0.198, −0.032) mm, −0.174 (−0.315, −0.061) mm, −0.184 (−0.291, −0.073) mm, and −0.171 (−0.203, −0.097) mm, respectively.Whether evaluated by SER or AL, 1% concentration ranks first in efficacy, but the risk of photophobia is 17 times higher than 0.01% concentration. Conclusions 0.01% or higher concentration atropine eyedrops are effective for myopia control, while 0.0025% and 0.005% concentrations may not. As the concentration increases, the effect tends to increase, 1% concentration may have the strongest effect.
Increasing trends in the use of the Precivia® intravitreal injection assist device across the UK
Authors: Ahmed Ibrar , Maghsoudlou Panayiotis , Shah Nimish 
Published: February 2024

Background Intravitreal anti-VEGF injections are the most frequently performed outpatient procedure in the UK, the need for which continues to rise. To meet this demand, injection assist devices such as Precivia® are increasingly adopted to aid in their prompt and safe delivery. We present data on the usage of Precivia® intravitreal injection assist device across two district general hospitals and its distribution across the UK over five years. Methods A retrospective review was undertaken of all Precivia® assisted intravitreal injections delivered at Great Western Hospitals NHS Trust (GWH), and Gloucestershire and Cheltenham Hospitals NHS Trust (GCH) between 2015–2020. Data were also obtained from the Precivia® device UK distributor; Veni Vidi Medical. Results In GCH, 47,968 intravitreal injections were administered with Precivia®: 5947 in year 1; 7058 in year 2; 9893 in year 3; 11,503 in year 4 and 13,567 injections in year 5, observing a 128.13% increase in the use of Precivia® over the five-year-period. In GWH, 26,923 injections were administered with Precivia®: 4232 in year 1; 5117 in year 2; 5437 in year 3; 5878 in year 4 and 6259 in year 5, observing a 47.89% increase in Precivia® injections over a five-year study period. The number of Precivia® devices distributed across the UK similarly increased including 42,150 devices sold in 2015; 68,125 in 2016; 72,575 in 2017; 88,325 in 2018; 112,850 in 2019 and 115,125 in 2020 observing a 173.31% increase in five years. Conclusion An increasing trend in the use of the Precivia® intravitreal injection assist device was observed across the UK.
Does matching glenosphere size to patient height improve outcomes following reverse total shoulder arthroplasty?
Authors: Levitt William , Roche Christopher , Elwell Josie , Donaldson Oliver 
Published: February 2024

Introduction Optimal biomechanics in reverse total shoulder arthroplasty (rTSA) are still a topic of debate. Although larger glenospheres have been linked with a theoretical improvement in the range of movement, results from clinical studies are mixed. We hypothesised that matching glenosphere diameter to patient height would result in greater improvements in post-operative range of motion (ROM) and patient-reported outcomes (PROMs). Methods An international database of rTSAs was analysed. After exclusions, 3318 rTSA patients were classified as short (<158 cm), average (158–173 cm) or tall(>173 cm). Outcomes were stratified for glenosphere size (small≤38 mm, large≥40 mm). Results were compared preoperatively and at 2 years. Results In short patients glenosphere diameter had no statistically significant impact on the degree of post-operative improvement for any ROM or PROM. Average height patients treated with small glenospheres had significantly more improvement in internal rotation (1.3 vs 1.0, p = 0.01), VAS pain (5.3 vs 4.8, p = 0.002), American Shoulder and Elbow Surgeons (47.8 vs 45.2, p = 0.03) and Shoulder Arthroplasty Smart (30.9 vs 28.2, p = 0.01) but significantly less improvement in constant score (31.7 vs 35.3, p = 0.009). Tall patients treated with small glenospheres had significantly more improvement in external rotation (21.2 vs 16.4, p = 0.01) and VAS pain scores (4.7 vs 4.3, p = 0.04). Conclusions While most significant differences favoured small glenospheres, the magnitude of these differences was small. Overall, patients of all heights can expect similar clinical improvements irrespective of glenosphere size.
A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest
Authors: Kuang Haiyue , Zhang Zhen , Zeng Bin , Liu Xin , Zuo Hao , Xu Xingye , Wang Lei 
Published: February 2024

Abstract
Background
In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditional biological experiments are very expensive and time-consuming. Therefore, it is meaningful to develop efficient computational models to forecast potential microbe-drug associations.

Results
In this manuscript, we proposed a novel prediction model called GARFMDA by combining graph attention networks and bilayer random forest to infer probable microbe-drug correlations. In GARFMDA, through integrating different microbe-drug-disease correlation indices, we constructed two different microbe-drug networks first. And then, based on multiple measures of similarity, we constructed a unique feature matrix for drugs and microbes respectively. Next, we fed these newly-obtained microbe-drug networks together with feature matrices into the graph attention network to extract the low-dimensional feature representations for drugs and microbes separately. Thereafter, these low-dimensional feature representations, along with the feature matrices, would be further inputted into the first layer of the Bilayer random forest model to obtain the contribution values of all features. And then, after removing features with low contribution values, these contribution values would be fed into the second layer of the Bilayer random forest to detect potential links between microbes and drugs.

Conclusions
Experimental results and case studies show that GARFMDA can achieve better prediction performance than state-of-the-art approaches, which means that GARFMDA may be a useful tool in the field of microbe-drug association prediction in the future. Besides, the source code of GARFMDA is available at https://github.com/KuangHaiYue/GARFMDA.git