bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using routinely recorded data in a UK RCT: a comparison to standard prospective data collection methods
Authors: Powell G. A. , Bonnett L. J. , Smith C. T. , Hughes D. A. , Williamson P. R. , Marson A. G. 
Published: July 2021

Abstract
Background
Routinely recorded data held in electronic health records can be used to inform the conduct of randomised controlled trials (RCTs). However, limitations with access and accuracy have been identified. Objective: Using epilepsy as an exemplar condition, we assessed the attributes and agreement of routinely recorded data compared to data collected using case report forms in a UK RCT assessing antiepileptic drug treatments for individuals newly diagnosed with epilepsy.

Methods
The case study RCT is the Standard and New Antiepileptic Drugs II (SANAD II) trial, a pragmatic, UK multicentre RCT assessing the clinical and cost-effectiveness of antiepileptic drugs as treatments for epilepsy. Ninety-eight of 470 eligible participants provided consent for access to routinely recorded secondary care data that were retrieved from NHS Digital Hospital Episode Statistics (N=71) and primary and secondary care data from The Secure Anonymised Information Linkage Databank (N=27). We assessed data items relevant to the identification of individuals eligible for inclusion in SANAD II, baseline and follow-up visits. The attributes of routinely recorded data were assessed including the degree of missing data. The agreement between routinely recorded data and data collected on case report forms in SANAD II was assessed using calculation of Cohen’s kappa for categorical data and construction of Bland-Altman plots for continuous data.

Results
There was a significant degree of missing data in the routine record for 15 of the 20 variables assessed, including all clinical variables. Agreement was poor for the majority of comparisons, including the assessments of seizure occurrence and adverse events. For example, only 23/62 (37%) participants had a date of first-ever seizure identified in routine datasets. Agreement was satisfactory for the date of prescription of antiepileptic drugs and episodes of healthcare resource use.

Conclusions
There are currently significant limitations preventing the use of routinely recorded data for participant identification and assessment of clinical outcomes in epilepsy, and potentially other chronic conditions. Further research is urgently required to assess the attributes, agreement, additional benefits, cost-effectiveness and ‘optimal mix’ of routinely recorded data compared to data collected using standard methods such as case report forms at clinic visits for people with epilepsy.

Trial registration
Standard and New Antiepileptic Drugs II (SANAD II (EudraCT No: 2012-001884-64, registered 05/09/2012; ISRCTN Number: ISRCTN30294119, registered 03/07/2012))
SENSory re-learning of the UPPer limb (SENSUPP) after stroke: development and description of a novel intervention using the TIDieR checklist
Authors: Carlsson Håkan , Rosén Birgitta , Björkman Anders , Pessah-Rasmussen Hélène , Brogårdh Christina 
Published: July 2021

AbstractBackgroundSensorimotor impairments of upper limb (UL) are common after stroke, leading to difficulty to use the UL in daily life. Even though many have sensory impairments in the UL, specific sensory training is often lacking in stroke rehabilitation. Thus, the aim of this paper is to provide a detailed description of the novel intervention “SENSory re-learning of the UPPer limb after stroke (SENSUPP)” that we have developed to improve functioning in the UL in persons with mild to moderate impairments after stroke.MethodsThe SENSUPP protocol was designed using information from literature reviews, clinical experience and through consultation of experts in the field. The protocol integrates learning principles based on current neurobiological knowledge and includes repetitive intensive practice, difficulty graded exercises, attentive exploration of a stimulus with focus on the sensory component, and task-specific training in meaningful activities that includes feedback. For reporting the SENSUPP protocol, the Template for Intervention Description and Replication (TIDieR) checklist was used.ResultsThe essential features of the SENSUPP intervention comprise four components: applying learning principles based on current neurobiological knowledge, sensory re-learning (exercises for touch discrimination, proprioception and tactile object recognition), task-specific training in meaningful activities, and home-training. The training is performed twice a week, in 2.5-h sessions for 5 weeks.ConclusionSince there is close interaction between the sensory and motor systems, the SENSUPP intervention may be a promising method to improve UL functioning after stroke. The TIDieR checklist has been very useful for reporting the procedure and development of the training.Trial registrationClinicalTrials.govNCT03336749. Registered on 8 November 2017.
The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Authors: Steinbrink Julie M. , Myers Rachel A. , Hua Kaiyuan , Johnson Melissa D. , Seidelman Jessica L. , Tsalik Ephraim L. , Henao Ricardo , Ginsburg Geoffrey S. , Woods Christopher W. , Alexander Barbara D. , McClain Micah T. 
Published: July 2021

AbstractBackgroundCandidemia is one of the most common nosocomial bloodstream infections in the United States, causing significant morbidity and mortality in hospitalized patients, but the breadth of the host response toCandidainfections in human patients remains poorly defined.MethodsIn order to better define the host response toCandidainfection at the transcriptional level, we performed RNA sequencing on serial peripheral blood samples from 48 hospitalized patients with blood cultures positive forCandidaspecies and compared them to patients with other acute viral, bacterial, and non-infectious illnesses. Regularized multinomial regression was utilized to develop pathogen class-specific gene expression classifiers.ResultsCandidemia triggers a unique, robust, and conserved transcriptomic response in human hosts with 1641 genes differentially upregulated compared to healthy controls. Many of these genes corresponded to components of the immune response to fungal infection, heavily weighted toward neutrophil activation, heme biosynthesis, and T cell signaling. We developed pathogen class-specific classifiers from these unique signals capable of identifying and differentiating candidemia, viral, or bacterial infection across a variety of hosts with a high degree of accuracy (auROC 0.98 for candidemia, 0.99 for viral and bacterial infection). This classifier was validated on two separate human cohorts (auROC 0.88 for viral infection and 0.87 for bacterial infection in one cohort; auROC 0.97 in another cohort) and an in vitro model (auROC 0.94 for fungal infection, 0.96 for bacterial, and 0.90 for viral infection).ConclusionsTranscriptional analysis of circulating leukocytes in patients with acuteCandidainfections defines novel aspects of the breadth of the human immune response during candidemia and suggests promising diagnostic approaches for simultaneously differentiating multiple types of clinical illnesses in at-risk, acutely ill patients.
Clinical characteristics and outcomes of patients with pediatric acute lymphoblastic leukemia after induction of chemotherapy: a pilot descriptive correlational study from Palestine
Authors: Shawahna Ramzi , Mosleh Sultan , Odeh Yahya , Halawa Rami , Al-Ghoul Majd 
Published: July 2021

Abstract
Objective
Pediatric acute lymphoblastic leukemia (ALL) is the most prevalent type of cancer among children. This study was conducted to describe and correlate the clinical characteristics and outcomes of treatment of patients with pediatric ALL in the main referral hospital in Palestine.

Results
Complete data of 69 patients were included in this analysis. The majority (79.7%) of the patients had B-ALL phenotype. After induction chemotherapy, remission was experienced by the vast majority of the patients and 5 (7.2%) experienced relapses. Cytogenetics for patients with B-ALL phenotype indicated that 10 (18.2%) patients had t(12, 21) translocation, 5 (9.1%) had hyperdiploidy, 4 (7.3%) had t(1, 19) translocation, and 2 (3.6%) had t(9, 22) translocation. The initial white blood cells (p value < 0.001), absolute neutrophils (p value = 0.011), and hemoglobin (p value < 0.001) were significantly lower in patients with B-cell ALL. Platelet counts were significantly lower (p value = 0.012) in patients with splenomegaly and those with bleeding symptoms (p value = 0.008). Presence of palmar pollar was positively associated (p value = 0.035) with T-cell ALL. Presence of hepatomegaly was positively associated (p value < 0.001) with splenomegaly.
Plasma biomarker profiles and the correlation with cognitive function across the clinical spectrum of Alzheimer’s disease
Authors: Xiao Zhenxu , Wu Xue , Wu Wanqing , Yi Jingwei , Liang Xiaoniu , Ding Saineng , Zheng Li , Luo Jianfeng , Gu Hongchen , Zhao Qianhua , Xu Hong , Ding Ding 
Published: July 2021

Abstract
Background
Plasma biomarkers showed a promising value in the disease diagnosis and management of Alzheimer’s disease (AD). However, profiles of the biomarkers and the associations with cognition across a spectrum of cognitive stages have seldom been reported.

Methods
We recruited 320 individuals with cognitive impairment and 131 cognitively normal participants from a memory clinic and a community cohort. Participants were classified into 6 groups based on their Clinical Dementia Rating (CDR) scores and clinical diagnosis, including AD, amnestic mild cognitive impairment (aMCI), and normal cognition (NC). A battery of neuropsychological tests was used to assess the global and domain-specific cognition. Plasma Aβ1-40, Aβ1-42, Aβ1-42/Aβ1-40, total tau (t-tau), neurofilament protein light chain (NfL), and phosphorylated tau at threonine 181 (p-tau181) were quantified using the single-molecule array (Simoa) platform.

Results
All the plasma markers (Aβ1-40, Aβ1-42, Aβ1-42/Aβ1-40, t-tau, NfL, p-tau181) showed certain discrepancies among NC, aMCI, and AD groups. The p-tau181 level showed a continuous escalating trend as the CDR scores increased from 0 (NC group) to 3 (severe AD). Compared with other biomarkers, p-tau181 had correlations with broader cognitive domains, covering global cognition (r = −0.536, P < 0.0001), memory (r = −0.481, P < 0.0001), attention (r = −0.437, P < 0.0001), visuospatial function (r = −0.385, P < 0.0001), and language (r = −0.177, P = 0.0003). Among participants with CDR ≥ 1, higher p-tau181 was correlated with worse global cognition (r = −0.301, P < 0.001).

Conclusions
Plasma p-tau181 had correlations with broader cognitive domains, suggesting its potential as a promising clinical-relevant blood-based biomarker.
Fulminant myocarditis induced by immune checkpoint inhibitor nivolumab: a case report and review of the literature
Authors: Wang Feifei , Liu Yang , Xu Wei , Zhang Changjing , Lv Jianhong , Ma Shaolin 
Published: July 2021

Abstract
Background
Nivolumab, an anti-programmed cell death protein 1 antibody, is commonly used as an immune checkpoint inhibitor in various cancers. Various adverse events are associated with these therapies, including hepatitis, dermatitis, and myocarditis. Myocarditis is a relatively rare but potentially fatal immune-mediated adverse reaction.

Case presentation
We report a case of colon cancer in a 56-year-old Chinese patient with lung and liver metastasis who developed fulminant myocarditis by nivolumab and survived with the support of extracorporeal membrane oxygenation. After six cycles (within 3 months) of nivolumab treatment, the patient developed chest tightness and was hospitalized. A diagnosis of fulminant myocarditis associated with immunotherapy was confirmed based on the clinical manifestations and laboratory examinations. He recovered well and was discharged on day 45 after management with extracorporeal membrane oxygenation, intravenous methylprednisolone, and immunoglobulin.

Conclusions
This case illustrates a severe cardiovascular complication of immunotherapy, strongly suggesting the necessity of close monitoring for outpatient usage of nivolumab. Additionally, our experience provided an efficient management strategy of extracorporeal membrane oxygenation in terms of life-threatening conditions.
Advanced treatment of effluent extended aeration process using biological aerated filter (BAF) with natural media: modification in media, design and backwashing process
Authors: Malakootian Mohammad , Toolabi Ali , Hosseini Saeed 
Published: July 2021

AbstractBiological aerated filters (BAFs) have high filtration efficiency due to their tolerance of hydraulic and organic shocks are suitable for the treatment of complex and sanitary wastewater. In this study, for the first time, natural media of date kernel from Bam city was used as the BAF reactor media, with a meshing sand filter separated by a standard metal grid from the natural filter section used at the end of the reactor. This can be considered an innovation in the media and filtration. Aeration in the related reactor with 160 cm height was performed bilaterally as up-flow and continuously by nozzles throughout the reactor media. In this work, the actual effluent of the hospital wastewater treatment plant was employed as the inflow wastewater to the reactor, and its organic and inorganic parameters were measured before and after the treatment by the BAF reactor. The backwashing process was also studied in three ways: bottom backwashing (TB), top backwashing (BB), and top and bottom backwashing (TBBS), to determine the amount of water consumed and to achieve the desired result. According to the results obtained in this study, the removal efficiencies of inorganic and microbial contaminants, amoxicillin and azithromycin were obtained as follows: BOD5: 98.48%, COD: 92.42%, $${\text{NO}}_{3}^{ - }$$

NO

3

-

: 99.4%, P: 93.3%, Coliforms: 97%, Color: 42.8%, Turbidity: 95%, Sulphate: 30%, TSS: 98.9%, Amoxicillin: 20% and azithromycin: 13%. In the backwashing process, the amount of water consumed in these three TB, BB, and TBBS methods were obtained 300, 164, and 118 L, respectively, So, TBBS method was selected as the optimal method. Based on the results obtained in this study, it is concluded that the BAF process with natural date kernel has a high efficiency in removing organic and inorganic contaminants from hospital wastewater, also the concentration of most of the effluent parameters was less or in accordance with EPA standard.
A pilot study on the prevalence of lice in Irish beef cattle and the first Irish report of deltamethrin tolerance in Bovicola bovis
Authors: Mckiernan Fiona , O’Connor Jack , Minchin William , O’Riordan Edward , Dillon Alan , Harrington Martina , Zintl Annetta 
Published: July 2021

Abstract
Background
Pediculosis in cattle causes significant itching, irritation and stress to the animal, often resulting in skin damage and poor coat condition. The control of bovine pediculosis in Ireland is based predominantly on commercial insecticides belonging to one of two chemical classes, the synthetic pyrethroids and the macrocyclic lactones. In recent years, pyrethroid tolerance has been reported in a number of species of livestock lice in the United Kingdom and Australia.

Results
In this pilot survey, lice were detected in 16 (94%) out of 17 herds visited. Two species of lice, Bovicola bovis and Linognathus vituli were identified. In vitro contact bioassays showed evidence of deltamethrin tolerance in Bovicola bovis collected from 4 farms. This was confirmed by repeatedly assessing louse infestations on treated animals on one farm.

Conclusions
To our knowledge this is the first record of insecticide tolerant populations of lice in Irish cattle. The results also provide new data on the species of lice infesting beef cattle in Ireland and the prevalence and control of louse infestations in Irish beef cattle herds.
Levels of physical activity in four domains and affective wellbeing before and during the Covid-19 pandemic
Authors: Engels Eliane S. , Mutz Michael , Demetriou Yolanda , Reimers Anne K. 
Published: July 2021

AbstractBackgroundLatest studies indicated that the general mental health level is low during the pandemic. Probably, this deterioration of the mental health situation is partly due to declines in physical activity. The aim of this study was to investigate differences in and the association between affective wellbeing and levels of different domains of physical activity at three time points before and during the pandemic.MethodWe used a nationwide online panel with a trend data design encompassing a total sample ofN = 3517, representing the German population (> 14 years). Four different activity domains (sport and exercise, light outdoor activity, housework/gardening, active travel) and affective wellbeing (positive and negative affect) were assessed at three time points before and during the Covid-19 pandemic (October 2019, March 2020, October 2020).ResultsMultivariate analyses of variance(MANOVA) indicate differences regarding affective wellbeing over the three time points with the lowest values at the second time point. Levels of activity in the four domains differed significantly over time with the strongest decrease for sport and exercise from the first to the second time point. Partial correlations indicated that the relationships between sport and exercise and positive affect were most consistent over time.ConclusionsOverall, our findings suggest that physical activity plays a particularly important role in the pandemic period as a protective factor against poor mental health. Especially sports and exercise seem to be supportive and should be encouraged, e.g. by providing additional support in finding adequate outdoor, home-based or digital substitutes.
Not too close! impact of roommate status on MRSA and VRE colonization and contamination in Nursing Homes
Authors: Cassone Marco , Linder Meghan , Shin Cheon Jee , Mantey Julia , Gibson Kristen , Lansing Bonnie , Mody Lona 
Published: July 2021

AbstractMultiple room occupancy is common in Nursing Homes (NHs), and its role in transmission of antibiotic-resistant pathogens is unclear. We investigated prevalence of patient colonization and environmental contamination with vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) in NH roommates, compared it with expected prevalence, and determined specific body and environmental sites that may act as sources of roommate colonization. Roommate contamination was associated with index patient’s colonization (relative risk (RR): 2.57 (95% CI 1.04–6.37)) for MRSA, and index patient’s immediate environment contamination for VRE (RR: 3.60 (95% CI 1.59–8.12)). When specific index patient sites associated with roommate colonization were investigated, the side table (Fisher’s p = 0.029 and 0.047 for VRE and MRSA, respectively) and the nurse call button (p = 0.001 and 0.052) stood out, together with patient hands in the case of VRE (p = 0.026). Future studies should be carried out to establish whether these sites should be a specific target of infection prevention campaigns in NHs with multiple occupancy rooms.
The relationship between time to a high COVID-19 response level and timing of peak daily incidence: an analysis of governments’ Stringency Index from 148 countries
Authors: Ma Yan , Mishra Shiva Raj , Han Xi-Kun , Zhu Dong-Shan 
Published: July 2021

Abstract
Background
The transmission dynamics and severity of coronavirus disease 2019 (COVID-19) pandemic is different across countries or regions. Differences in governments’ policy responses may explain some of these differences. We aimed to compare worldwide government responses to the spread of COVID-19, to examine the relationship between response level, response timing and the epidemic trajectory.

Methods
Free publicly-accessible data collected by the Coronavirus Government Response Tracker (OxCGRT) were used. Nine sub-indicators reflecting government response from 148 countries were collected systematically from January 1 to May 1, 2020. The sub-indicators were scored and were aggregated into a common Stringency Index (SI, a value between 0 and 100) that reflects the overall stringency of the government’s response in a daily basis. Group-based trajectory modelling method was used to identify trajectories of SI. Multivariable linear regression models were used to analyse the association between time to reach a high-level SI and time to the peak number of daily new cases.

Results
Our results identified four trajectories of response in the spread of COVID-19 based on when the response was initiated: before January 13, from January 13 to February 12, from February 12 to March 11, and the last stage—from March 11 (the day WHO declared a pandemic of COVID-19) on going. Governments’ responses were upgraded with further spread of COVID-19 but varied substantially across countries. After the adjustment of SI level, geographical region and initiation stages, each day earlier to a high SI level (SI > 80) from the start of response was associated with 0.44 (standard error: 0.08, P < 0.001, R2 = 0.65) days earlier to the peak number of daily new case. Also, each day earlier to a high SI level from the date of first reported case was associated with 0.65 (standard error: 0.08, P < 0.001, R2 = 0.42) days earlier to the peak number of daily new case.

Conclusions
Early start of a high-level response to COVID-19 is associated with early arrival of the peak number of daily new cases. This may help to reduce the delays in flattening the epidemic curve to the low spread level.

Graphic abstract