bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence, patterns, and predictors of patient-reported non-motor outcomes at 30 days after acute stroke: Prospective observational hospital cohort study
Authors: Ozkan Hatice , Ambler Gareth , Banerjee Gargi , Browning Simone , Leff Alex P , Ward Nick S , Simister Robert J , Werring David J 
Published: November 2023

Background: Adverse non-motor outcomes are common after acute stroke and likely to substantially affect quality of life, yet few studies have comprehensively assessed their prevalence, patterns, and predictors across multiple health domains. Aims: We aimed to identify the prevalence, patterns, and the factors associated with non-motor outcomes 30 days after stroke. Methods: This prospective observational hospital cohort study—Stroke Investigation in North and Central London (SIGNAL)—identified patients with acute ischemic stroke or intracerebral hemorrhage (ICH) admitted to the Hyperacute Stroke Unit (HASU) at University College Hospital (UCH), London, between August 1, 2018 and August 31, 2019. We assessed non-motor outcomes (anxiety, depression, fatigue, sleep, participation in social roles and activities, pain, bowel function, and bladder function) at 30-day follow-up using the Patient-Reported Outcome Measurement Information System-Version 29 (PROMIS-29) scale and Barthel Index scale. Results: We obtained follow-up data for 605/719 (84.1%) eligible patients (mean age 72.0 years; 48.3% female; 521 with ischemic stroke, 84 with ICH). Anxiety (57.0%), fatigue (52.7%), bladder dysfunction (50.2%), reduced social participation (49.2%), and pain (47.9%) were the commonest adverse non-motor outcomes. The rates of adverse non-motor outcomes in ⩾ 1, ⩾ 2 and ⩾ 3 domains were 89%, 66.3%, and 45.8%, respectively; in adjusted analyses, stroke due to ICH (compared to ischemic stroke) and admission stroke severity were the strongest and most consistent predictors. There were significant correlations between bowel dysfunction and bladder dysfunction (κ = 0.908); reduced social participation and bladder dysfunction (κ = 0.844); and anxiety and fatigue (κ = 0.613). We did not identify correlations for other pairs of non-motor domains. Conclusion: Adverse non-motor outcomes were very common at 30 days after stroke, affecting nearly 90% of evaluated patients in at least one health domain, about two-thirds in two or more domains, and almost 50% in three or more domains. Stroke due to ICH and admission stroke severity were the strongest and most consistent predictors. Adverse outcomes occurred in pairs of domains, such as with anxiety and fatigue. Our findings emphasize the importance of a multi-domain approach to effectively identify adverse non-motor outcomes after stroke to inform the development of more holistic patient care pathways after stroke.
Role of environmental specificity in CASP results
Authors: Roterman Irena , Stapor Katarzyna , Konieczny Leszek 
Published: November 2023

Abstract
Background
Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Prediction) competition. However, the question of the mechanism behind the protein folding process itself remains unanswered. Correctly predicting the structure also does not solve the problem of, for example, amyloid proteins, where a polypeptide chain with an unaltered sequence adopts a different 3D structure.

Results
This work was an attempt at explaining the structural variation by considering the contribution of the environment to protein structuring. The application of the fuzzy oil drop (FOD) model to assess the validity of the selected models provided in the CASP13, CASP14 and CASP15 projects reveals the need for an environmental factor to determine the 3D structure of proteins. Consideration of the external force field in the form of polar water (Fuzzy Oil Drop) and a version modified by the presence of the hydrophobic compounds, FOD-M (FOD-Modified) reveals that the protein folding process is environmentally dependent. An analysis of selected models from the CASP competitions indicates the need for structure prediction as dependent on the consideration of the protein folding environment.

Conclusions
The conditions governed by the environment direct the protein folding process occurring in a certain environment. Therefore, the variation of the external force field should be taken into account in the models used in protein structure prediction.
Development of a robust TaqMan probe-based one-step multiplex RT-qPCR for simultaneous detection of SARS-CoV-2 and Influenza A/B viruses
Authors: Abbasi Hamidreza , Nikoo Hadi Razavi , Fotouhi Fatemeh , Khosravi Ayyoob 
Published: November 2023

Abstract
Background
During the coronavirus disease 2019 (COVID-19) pandemic, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Influenza A, and Influenza B viruses is essential for rapid differential diagnosis in patients with similar symptoms, especially during “flu season” in the post-pandemic era. So far, several multiplex methods have been approved for the simultaneous detection of SARS-CoV-2, Influenza A, and Influenza B. However, due to the rapid mutation rate of the SARS-CoV-2 genome and the emergence of new variants, existing methods must be improved and updated.

Methods
To identify a highly conserved region in the SARS-CoV-2 N-gene, a genomic survey was performed to increase the sensitivity and specificity of primer and probe sets targeting the SARS-CoV-2 genome. The 95% LLOD (95% lower limits of detection) were calculated by probit analysis. A total of 70 predetermined clinical samples using singleplex RT-qPCR assays, were included. The clinical performance of the multiplex RT-qPCR assay was determined and compared with a commercial multiplex kit. The Cohen’s kappa coefficient, P-value (McNemar’s test), Passing-Bablok regression, and Bland Altman agreement analysis were determined to monitor the agreement of the assays.

Results
The novel SARS-CoV-2 primer and probe set designed in this assay was able to detect all variants of concern (VOCs) and variants of interest (VOIs) with high analytical and clinical performance. The 95% LLOD for the multiplex RT-qPCR was 20 copies per reaction for the N gene of SARS-CoV-2, 2 copies per reaction for M1 gene of Influenza A and NS1 gene of Influenza B. The diagnostic sensitivity of the multiplex RT-qPCR was 94.4%, 93.7%, and 100% for the detection of SARS-CoV-2, Influenza A, and Influenza B genomes, respectively. Moreover, the specificity was identical (100%) in both assays. According to the agreement analysis results, there was no statistical difference between our multiplex assay and the commercial kit.

Conclusions
In this study, we developed a novel in-house made multiplex RT-qPCR assay, with high sensitivity, specificity, and reliability for the diagnosis of SARS-CoV-2 infection in clinical samples. This is valuable during Influenza seasons when influenza co-circulates with SARS-CoV-2, as it saves costs, time, and thus specific and timely treatment of patients.
First identification and coinfection detection of Enterocytozoon bieneusi, Encephalitozoon spp., Cryptosporidium spp. and Giardia duodenalis in diarrheic pigs in Southwest China
Authors: Ghebremichael Samson Teweldeberhan , Meng Xianzhi , Yang Yujiao , Andegiorgish Amanuel Kidane , Wu Zongrun , Chen Jie , Wei Junhong , Li Tian , Bao Jialing , Zhou Zeyang , Pan Guoqing 
Published: November 2023

Abstract
Background
Enterocytozoon bieneusi, Encephalitozoon spp., Cryptosporidium spp., and Giardia duodenalis (G. intestinalis) are enteric pathogens that cause diarrhea in pigs. This study aimed to determine the prevalence of these enteric parasites and their coinfection with E. bieneusi in diarrheic pigs in Southwest China (Chongqing and Sichuan) using nested polymerase chain reaction (nPCR) based methods.

Results
A total of 514 fecal samples were collected from diarrheic pigs from 14 pig farms in Chongqing (five farms) and Sichuan (nine farms) Provinces. The prevalence of Encephalitozoon spp., Cryptosporidium spp. and G. duodenalis was 16.14% (83/514), 0% (0/514), and 8.95% (46/514), respectively. Nested PCR revealed 305 mono-infections of E. bieneusi, six of E. cuniculi, two of E. hellem, and nine of G. duodenalis and 106 concurrent infections of E. bieneusi with the other enteric pathogens. No infections of E. intestinalis and Cryptosporidium species were detected. The highest coinfection was detected between E. bieneusi and E. cuniculi (10.5%, 54/514), followed by E. bieneusi and G. duodenalis (5.8%, 30/514) and E. bieneusi and E. hellem (2.9%, 15/514). E. bieneusi was the most frequently detected enteric pathogen, followed by E. cuniculi, G. duodenalis and E. hellem. There was a significant age-related difference in the prevalence of E. cuniculi in fattening pigs (χ2 = 15.266, df = 3, P = 0.002) and G. duodenalis in suckling pigs (χ2 = 11.92, df = 3, P = 0.008) compared with the other age groups. Sequence analysis of the ITS region of Encephalitozoon species showed two genotypes (II and III) for E. cuniculi and one (TURK1B) for E. hellem. Only G. duodenalis assemblage A was identified in all nested PCR-positive samples. E. bieneusi was found more often than other enteric pathogens.

Conclusions
This study showed that E. bieneusi, Encephalitozoon spp. [E. cuniculi and E. hellem] and G. duodenalis were common enteric parasites in diarrheic pigs in Chongqing and Sichuan Provinces. In case of both mono-infection and coinfection, E. bieneusi was the most common enteric pathogen in diarrheic pigs. Thus, it may be a significant cause of diarrhea in pigs. Precautions should be taken to prevent the spread of these enteric parasites.
Expression of OsHARBI1-1 enhances the tolerance of Arabidopsis thaliana to cadmium
Authors: Jiang Nan , Shi Yang , Li Mingyu , Du Zhiye , Chen Ji , Jiang Wenjun , Huang Yanyan , Zhong Min , Yang Ju , Hu Binhua , Huang Jin 
Published: November 2023

Abstract
Background
As one of the major food crops in the world, rice is vulnerable to cadmium (Cd) pollution. Understanding of the molecular mechanisms of Cd uptake, transport and detoxification in rice is essential for the breeding of low-Cd rice. However, the molecular mechanisms underlying the response of rice to Cd stress remains to be further clarified.

Results
In this study, a novel Cd-responsive gene OsHARBI1-1 was identified in the rice genome and its expression pattern and function were characterized. Bioinformatics analysis showed that the promoter region of OsHARBI1-1 had multiple cis-acting elements in response to phytohormones and stress, and the expression of OsHARBI1-1 was induced by phytohormones. OsHARBI1-1 protein was targeted to the nucleus. qRT-PCR analysis results showed that the expression of OsHARBI1-1 in the roots was repressed while the expression in the shoots was increased under Cd stress. Heterologous expression of OsHARBI1-1 in yeast conferred tolerance to Cd and reduced Cd content in the cells. Meanwhile, the expression of OsHARBI1-1 in Arabidopsis thaliana (A. thaliana) enhanced the tolerance of A. thaliana to Cd stress. In addition, compared with the wild type plants, the POD activity of transgenic plants was increased, while the SOD and CAT activities were decreased. Interestingly, the accumulation of Cd in the roots of A. thaliana expressing OsHARBI1-1 was significantly increased, whereas the Cd accumulation in the shoots was slightly decreased. Compared to the WT plants, the expression of genes related to Cd absorption and chelation was upregulated in transgenic A. thaliana under Cd stress, while the expression of genes responsible for the translocation of Cd from the roots to the shoots was downregulated. Moreover, the expression of phytohormone-related genes was significantly influenced by the expression of OsHARBI1-1 with and without Cd treatment.

Conclusions
Findings of this study suggest that OsHARBI1-1 might play a role in the response of plants to Cd response by affecting antioxidant enzyme activities, Cd chelation, absorption and transport, and phytohormone homeostasis and signaling.
Impact of a positive end-expiratory pressure strategy on oxygenation, respiratory compliance, and hemodynamics during laparoscopic surgery in non-obese patients: a systematic review and meta-analysis of randomized controlled trials
Authors: Yessenbayeva Gulfairus A. , Yukhnevich Yekaterina A. , Khamitova Zaukiya K. , Kim Sergey I. , Zhumabayev Murat B. , Berdiyarova Gulbanu S. , Shalekenov Sanzhar B. , Mukatova Irina Y. , Yaroshetskiy Andrey I. 
Published: November 2023

Abstract
Background
Higher positive end-expiratory pressure (PEEP) during laparoscopic surgery may increase oxygenation and respiratory compliance. This meta-analysis aimed to compare the impact of different intraoperative PEEP strategies on arterial oxygenation, compliance, and hemodynamics during laparoscopic surgery in non-obese patients.

Methods
We searched RCTs in PubMed, Cochrane Library, Web of Science, and Google Scholar from January 2012 to April 2022 comparing the different intraoperative PEEP (Low PEEP (LPEEP): 0–4 mbar; Moderate PEEP (MPEEP): 5–8 mbar; high PEEP (HPEEP): >8 mbar; individualized PEEP - iPEEP) on arterial oxygenation, respiratory compliance (Cdyn), mean arterial pressure (MAP), and heart rate (HR). We calculated mean differences (MD) with 95% confidence intervals (CI), and predictive intervals (PI) using random-effects models. The Cochrane Bias Risk Assessment Tool was applied.

Results
21 RCTs (n = 1554) met the inclusion criteria. HPEEP vs. LPEEP increased PaO2 (+ 29.38 [16.20; 42.56] mmHg, p < 0.0001) or PaO2/FiO2 (+ 36.7 [+ 2.23; +71.70] mmHg, p = 0.04). HPEEP vs. MPEEP increased PaO2 (+ 22.00 [+ 1.11; +42.88] mmHg, p = 0.04) or PaO2/FiO2 (+ 42.7 [+ 2.74; +82.67] mmHg, p = 0.04). iPEEP vs. MPEEP increased PaO2/FiO2 (+ 115.2 [+ 87.21; +143.20] mmHg, p < 0.001). MPEEP vs. LPEP, and HPEEP vs. MPEEP increased PaO2 or PaO2/FiO2 significantly with different heterogeneity. HPEEP vs. LPEEP increased Cdyn (+ 7.87 [+ 1.49; +14.25] ml/mbar, p = 0.02). MPEEP vs. LPEEP, and HPEEP vs. MPEEP did not impact Cdyn (p = 0.14 and 0.38, respectively). iPEEP vs. LPEEP decreased driving pressure (-4.13 [-2.63; -5.63] mbar, p < 0.001). No significant differences in MAP or HR were found between any subgroups.

Conclusion
HPEEP and iPEEP during PNP in non-obese patients could promote oxygenation and increase Cdyn without clinically significant changes in MAP and HR. MPEEP could be insufficient to increase respiratory compliance and improve oxygenation. LPEEP may lead to decreased respiratory compliance and worsened oxygenation.

Prospero registration
CRD42022362379; registered October 09, 2022.
Optimal trial design selection: a comparative analysis between two-arm and three-arm trials incorporating network meta-analysis for evaluating a new treatment
Authors: Ye Fangshu , Wang Chong , O’Connor Annette M. 
Published: November 2023

Abstract
Background
Planning the design of a new trial comparing two treatments already in a network of trials with an a-priori plan to estimate the effect size using a network meta-analysis increases power or reduces the sample size requirements. However, when the comparison of interest is between a treatment already in the existing network (old treatment) and a treatment that hasn’t been studied previously (new treatment), the impact of leveraging information from the existing network to inform trial design has not been extensively investigated. We aim to identify the most powerful trial design for a comparison of interest between an old treatment A and a new treatment Z, given a fixed total sample size. We consider three possible designs: a two-arm trial between A and Z (’direct two-arm’), a two-arm trial between another old treatment B and Z (’indirect two-arm’), and a three-arm trial among A, B, and Z.

Methods
We compare the standard error of the estimated effect size between treatments A and Z for each of the three trial designs using formulas. For continuous outcomes, the direct two-arm trial always has the largest power, while for a binary outcome, the minimum variances among the three trial designs are conclusive only when $$p_A(1-p_A) \ge p_B(1-p_B)$$

p
A

(
1
-

p
A

)

≥

p
B

(
1
-

p
B

)

. Simulation studies are conducted to demonstrate the potential for the indirect two-arm and three-arm trials to outperform the direct two-arm trial in terms of power under the condition of $$p_A(1-p_A) < p_B(1-p_B)$$

p
A

(
1
-

p
A

)

<

p
B

(
1
-

p
B

)

.

Results
Based on the simulation results, we observe that the indirect two-arm and three-arm trials have the potential to be more powerful than a direct two-arm trial only when $$p_A(1-p_A) < p_B(1-p_B)$$

p
A

(
1
-

p
A

)

<

p
B

(
1
-

p
B

)

. This power advantage is influenced by various factors, including the risk of the three treatments, the total sample size, and the standard error of the estimated effect size from the existing network meta-analysis.

Conclusions
The standard two-arm trial design between two treatments in the comparison of interest may not always be the most powerful design. Utilizing information from the existing network meta-analysis, incorporating an additional old treatment into the trial design through an indirect two-arm trial or a three-arm trial can increase power.
Multi-disciplinary cooperation for the micro-elimination of hepatitis C in China: a hospital-based experience
Authors: Zheng Lingling , Zhang Xiaoli , Nian Yuxia , Zhou Wenjuan , Li Dan , Wu Yong 
Published: November 2023

Abstract
Background
Hepatitis C virus (HCV) infection is one of the main causes of liver cancer and imposes an enormous social and economic burden. The blood-borne virus screening policy for preventing iatrogenic infections renders hospitals important for identifying individuals infected with hepatitis C. Therefore, we aimed to investigate the establishment of a multi-disciplinary cooperation model in medical institutions to leverage the screening results of patients with hepatitis C. Our objective is to ensure that patients receive timely and effective diagnosis and treatment, thereby enabling the elimination of hepatitis C by 2030.

Method
A multi-disciplinary cooperation model was established in October 2021. This retrospective study was based on the establishment of antibody-positive and HCV RNA-positive patient databases. A Chi-square test was used to compare the HCV RNA confirmation rate in anti-HCV-positive patients, as well as the hepatitis C diagnosis rate and treatment rate in RNA-positive patients before and after the multi-disciplinary cooperation. A multivariable logistic regression was used to analyse the factors affecting the treatment of patients with hepatitis C. In addition, we examined changes in the level of hepatitis C knowledge among medical staff.

Results
After the implementation of the multi-disciplinary cooperation model, the RNA confirmation rate of hepatitis C antibody-positive patients increased from 36.426% to 88.737%, the diagnostic accuracy rate of RNA-positive patients increased from 67.456% to 98.113%, and the treatment rate of patients with hepatitis C increased from 12.426% to 58.491%. Significant improvements were observed among the clinicians regarding their ability to understand the characteristics of hepatitis C (93.711% vs. 58.861%), identify people at high risk (94.340% vs. 53.797%), manage patients with hepatitis C after diagnosis (88.679% vs. 67.089%), and effectively treat hepatitis C (84.277% vs. 51.899%). Multi-disciplinary cooperation in medical institutions was the most important factor for patients to undergo HCV treatment (odds ratio: 0.024, 95% confidence interval: 0.007–0.074).

Conclusions
This study showed that the use of a multi-disciplinary cooperation model to utilise the results of HCV antibody screening fully in patients through further tracking, referral, and treatment may facilitate the detection and treatment of patients with hepatitis C and accelerate the elimination of HCV in China.
Actinomyces meyeri-induced brain abscess in pregnancy: a case report
Authors: Zhang Yaping , Ye Zhinan , Miao Qianqian , Xu Hao , Pang Wenyang 
Published: November 2023

Abstract
Background
Brain abscesses can occur when suppurative, bacterial or protozoan infections spread to the brain. Here, we report a rare case of Actinomyces meyeri-induced brain abscess in a pregnant woman.

Case presentation
We present the case of a 38-years-old primipara admitted to the emergency department at our hospital with a 4-day history of fever and vomiting. The symptoms worsened rapidly during the 8 h prior to admission, and the patient experienced a sudden loss of consciousness 4 h before arrival to the unit. Brain magnetic resonance imaging revealed abnormal signals in the right parietal–temporal lobe, suggesting the possibility of abscess rupture into the ventricle and sulcus. Right lateral ventricle compression and midline structure deviation to the left were noted. A right temporal–occipital mass with midline shift was detected. Emergency procedures were promptly performed, including craniotomy, removal of the right temporal–occipital mass, decompressive craniectomy, implantation of an intracranial pressure monitoring device, and external ventricular drainage. Cerebrospinal fluid culture indicated infection with Actinomyces meyeri. After administration of antibiotics, including linezolid and meropenem injections, along with treatments to decrease intracranial pressure, the patient’s vital signs stabilized. However, the patient developed hydrocephalus, requiring placement of a hydrocephalus shunt several months later. Throughout this period, the patient remained in a coma vigil state, and labor was induced for the fetus.

Conclusions
Although the patient did not present with any apparent predisposing causes for brain abscess, a scout view of CT revealed dental caries. In addition, the occurrence of the brain abscess may have been influenced by the hormonal changes during pregnancy, including increased secretion of estrogen and progesterone, as well as decreased immune function. Early diagnosis and intervention are crucial in such cases. Therefore, it is recommended to seek early medical attention if symptoms such as fever, vomiting, and changes in mental state occur during pregnancy, as the prognosis for both the mother and infant is poor once the abscess ruptures.