bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of in-service training plus the collaborative improvement strategy on the quality of routine malaria surveillance data: results of a pilot study in Kayunga District, Uganda
Authors: Westercamp Nelli , Staedke Sarah G. , Maiteki-Sebuguzi Catherine , Ndyabakira Alex , Okiring John Michael , Kigozi Simon P. , Dorsey Grant , Broughton Edward , Hutchinson Eleanor , Massoud M. Rashad , Rowe Alexander K. 
Published: June 2021

Abstract
Background
Surveillance data are essential for malaria control, but quality is often poor. The aim of the study was to evaluate the effectiveness of the novel combination of training plus an innovative quality improvement method—collaborative improvement (CI)—on the quality of malaria surveillance data in Uganda.

Methods
The intervention (training plus CI, or TCI), including brief in-service training and CI, was delivered in 5 health facilities (HFs) in Kayunga District from November 2015 to August 2016. HF teams monitored data quality, conducted plan-do-study-act cycles to test changes, attended periodic learning sessions, and received CI coaching. An independent evaluation was conducted to assess data completeness, accuracy, and timeliness. Using an interrupted time series design without a separate control group, data were abstracted from 156,707 outpatient department (OPD) records, laboratory registers, and aggregated monthly reports (MR) for 4 time periods: baseline—12 months, TCI scale-up—5 months; CI implementation—9 months; post-intervention—4 months. Monthly OPD register completeness was measured as the proportion of patient records with a malaria diagnosis with: (1) all data fields completed, and (2) all clinically-relevant fields completed. Accuracy was the relative difference between: (1) number of monthly malaria patients reported in OPD register versus MR, and (2) proportion of positive malaria tests reported in the laboratory register versus MR. Data were analysed with segmented linear regression modelling.

Results
Data completeness increased substantially following TCI. Compared to baseline, all-field completeness increased by 60.1%-points (95% confidence interval [CI]: 46.9–73.2%) at mid-point, and clinically-relevant completeness increased by 61.6%-points (95% CI: 56.6–66.7%). A relative − 57.4%-point (95% confidence interval: − 105.5, − 9.3%) change, indicating an improvement in accuracy of malaria test positivity reporting, but no effect on data accuracy for monthly malaria patients, were observed. Cost per additional malaria patient, for whom complete clinically-relevant data were recorded in the OPD register, was $3.53 (95% confidence interval: $3.03, $4.15).

Conclusions
TCI improved malaria surveillance completeness considerably, with limited impact on accuracy. Although these results are promising, the intervention’s effectiveness should be evaluated in more HFs, with longer follow-up, ideally in a randomized trial, before recommending CI for wide-scale use.
Dietary and lifestyle behavior in adults with epilepsy needs improvement: a case-control study from northeastern Poland
Authors: Szałwińska Kamila , Cyuńczyk Monika , Kochanowicz Jan , Witkowska Anna M. 
Published: June 2021

Abstract
Background
Several factors predispose individuals with epilepsy to chronic diseases. Among them, nutrition and lifestyle factors have not been sufficiently studied. Therefore, the aim of this study was to evaluate patients with epilepsy in terms of diet, body composition and physical activity compared to healthy sex- and age-matched subjects to investigate whether there are risk factors for nutritional deficiencies and risk factors for the development of metabolic diseases.

Methods
The case-control study involved 60 epileptic male and female volunteers and 70 healthy controls matched according to age and sex. Medical information was collected during the study, and a detailed questionnaire regarding eating and lifestyle habits was conducted. Physical activity was evaluated using the International Physical Activity Questionnaire (IPAQ). Nutritional status was assessed by bioelectric impedance. Venous blood samples were taken for lipid and 25-hydroxyvitamin D3 (25(OH)D3) analyses.

Results
A tendency toward an increase in LDL cholesterol was found in the individuals with epilepsy. Significantly higher body fat and insignificantly higher visceral fat were found in epileptic men than in healthy men. In epileptic women, a tendency toward a lower lean body mass was found. Patients with epilepsy were more sedentary, consumed less cottage cheese, fruit, pulses, nuts and seeds, vitamin C and potassium, and consumed more sugar-sweetened soda, fat and sodium than healthy people. On a positive note, individuals with epilepsy consumed less coffee and alcoholic beverages. More than 80% of the epileptic volunteers had diets that were low in folic acid, vitamin D and calcium, but a similar tendency was observed in the healthy volunteers. A higher percentage of the patients with epilepsy had diets that were low in niacin, vitamin C and potassium than the control group (25% vs. 7, 50% vs. 31% and 73 vs. 56%, respectively). A significantly lower serum concentration of 25(OH)D3 was observed in epileptic individuals and was found to be positively modulated by physical activity.

Conclusions
The results indicate that several behavior-related habits, which may predispose epileptic people to cardiovascular disease, need to be improved. For this reason, patients with epilepsy should be provided with more comprehensive medical care, including advice on nutrition and physical activity.
Biogeography of Italy revisited: genetic lineages confirm major phylogeographic patterns and a pre-Pleistocene origin of its biota
Authors: Schmitt Thomas , Fritz Uwe , Delfino Massimo , Ulrich Werner , Habel Jan Christian 
Published: June 2021

AbstractWarm-adapted species survived the cold stages of the past glacial-interglacial cycles in southern European peninsulas and recolonized major parts of Central and Northern Europe in the wake of postglacial warming. However, many of the genetic lineages which differentiated within these refugia predate even the Pleistocene. One of these refugia is the Italian Peninsula with its surrounding islands. In this meta-analysis, we compiled phylogeographic patterns of multiple species across this region. We transformed existing geographic information on 78 animal and plant species (with a total of 471 genetic lineages) within 17 predefined areas into presence/absence matrices. We elaborated three matrices: (i) only old lineages exclusively distinguished by deep splits, (ii) only young lineages distinguished by shallow (i.e. recent) splits, and (iii) presence/absence of the respective species. To infer biogeographic relationships between the predefined areas, we performed bootstrapped neighbour joining cluster analyses on these three matrices. In addition, we reviewed the geological history of Italy to identify causes of the observed biogeographic patterns. We found Sardinia and Corsica to be biogeographically closely linked with each other, and that they diverge strongly from all other regions. Sicily also diverges strongly from all other regions, while the intra-island differentiation was comparatively low. On the Italian mainland, Calabria exhibited the most pronounced biogeographic differentiation, often with several lineages present, resulting from old vicariance events within the region. Furthermore, southern Apulia and the Po Plain with adjoining areas of northern peninsular Italy displayed considerable distinctiveness. Admixture prevailed in the areas between these three regions. The ancient isolation of Sicily, as well as Sardinia plus Corsica, resulted in endemic lineages with only moderate recent exchange with adjacent mainland regions. Pronounced diversification occurs within the Italian Peninsula. The complex tectonic activities, such as shifting (micro)plates, submergence of major parts of peninsular Italy with the genesis of numerous Pliocene islands, in combination with the climatic cycles during the Pleistocene have most likely generated the current biogeographic pattern of species. Immigrations from the Balkan Peninsula into northern Italy partly accounted for the distinctiveness of this region.
One-step real-time multiplex reverse transcription-polymerase chain reaction assay with melt curve analysis for detection of potato leafroll virus, potato virus S, potato virus X, and potato virus Y
Authors: Onozuka Nobuya , Ohki Takehiro , Oka Norikuni , Maoka Tetsuo 
Published: June 2021

Abstract
Background
Certification of seed potato as free of viruses is essential for stable potato production. Among more than 30 virus species infecting potato, potato leafroll virus (PLRV), potato virus S (PVS), potato virus X (PVX), and potato virus Y (PVY) predominate worldwide and should be the targets of a high-throughput detection protocol for seed potato quarantine.

Results
We developed an assay based on one-step real-time multiplex reverse transcription-polymerase chain reaction (mRT-PCR) with melt curve analysis for the four viruses and one internal control, potato elongation factor 1 alpha gene (EF1α). Virus-specific primers were derived from conserved regions among randomly selected representatives considering viral genomic diversity. Our assay simultaneously detected representative Japanese isolates of PLRV, O lineage of PVS, PVX, and NTN strain of PVY. The variability of melting temperature (Tm) values for each virus was confirmed using Japanese isolates, and virus species could be identified by the values of 87.6 for PLRV, 85.9 for PVX, 82.2 (Ordinary lineage) to 83.1 (Andean lineage) for PVS, and 79.4 (NA-N strain) to 80.5 (O strain and NTN strain) for PVY on average. The reliability of calculation was validated by comparing the calculated Tm values and measured Tm values and the values had a strong linear correlation (correlation of determination: R2 = 0.9875). Based on the calculated Tm values, representative non-Japanese isolates could also be identified by our assay. For removing false positives, two criteria were set for the evaluation of result; successful amplification was considered as 30.0 ≥ threshold cycle value, and the virus-specific peak higher than the EF1α-specific peak was considered as positive. According to these criteria, our assay could detect PLRV and PVS from 100-fold dilution of potato leaf homogenate and PVX and PVY from 1000-fold in a model assay.

Conclusion
This new high-throughput detection protocol using one-step real-time mRT-PCR was sensitive enough to detect viruses in a 100-fold dilution of singly-virus contaminated homogenate in a model assay. This protocol can detect the four viruses in one assay and yield faster results for a vast number of samples, and greatly save the labor for seed potato quarantine and field surveys.
An analysis of policy and funding priorities of global actors regarding noncommunicable disease in low- and middle-income countries
Authors: Jailobaeva Kanykey , Falconer Jennifer , Loffreda Giulia , Arakelyan Stella , Witter Sophie , Ager Alastair 
Published: June 2021

Abstract
Background
Noncommunicable diseases (NCDs), including mental health, have become a major concern in low- and middle-income countries. Despite increased attention to them over the past decade, progress toward addressing NCDs has been slow. A lack of bold policy commitments has been suggested as one of the contributors to limited progress in NCD prevention and management. However, the policies of key global actors (bilateral, multilateral, and not-for-profit organisations) have been understudied.

Methods
This study aimed to map the key global actors investing in action regarding NCDs and review their policies to examine the articulation of priorities regarding NCDs. Narrative synthesis of 70 documents and 31 policy papers was completed, and related to data collated from the Global Health Data Visualisation Tool.

Results
In 2019 41% of development assistance for health committed to NCDs came from private philanthropies, while that for other global health priorities from this source was just 20%. Through a range of channels, bilateral donors were the other major source of NCD funding (contributing 41% of NCD funding). The UK and the US were the largest bilateral investors in NCDs, each contributing 8%. However, NCDs are still under-prioritised within bilateral portfolios – receiving just 0.48% of US funding and 1.66% of the UK. NGOs were the key channels of funding for NCDs, spending 48% of the funds from donors in 2019. The reviewed literature generally focused on NCD policies of WHO, with policies of multilateral and bilateral donors given limited attention. The analysis of policies indicated a limited prioritisation of NCDs in policy documents. NCDs are framed in the policies as a barrier to economic growth, poverty reduction, and health system sustainability. Bilateral donors prioritise prevention, while multilateral actors offer policy options for NCD prevention and care. Even where stated as a priority, however, funding allocations are not aligned.

Conclusion
The growing threat of NCDs and their drivers are increasingly recognised. However, global actors’ policy priorities and funding allocations need to align better to address these NCD threats. Given the level of their investment and engagement, more research is needed into the role of private philanthropies and NGOs in this area.
Ichthyological ethnoknowledge of the “piabeiros” from the Amazon region, Brazil
Authors: da Silva Ladislau Daniel , Ribeiro Maiko Willas Soares , da Silva Castro Philip Dalbert , Pantoja-Lima Jackson , Aride Paulo Henrique Rocha , de Oliveira Adriano Teixeira 
Published: June 2021

Abstract
Background
The capture of ornamental fish is one of the main economic activities of riverine families in the Amazon. However, studies regarding the local ecological knowledge of workers in this activity are still incipient. In view of this, we have studied and explored the local ecological knowledge of artisanal fishers who specialize in the capture of fish for the aquarium trade in the middle part of the Negro River basin and investigated issues related to the ecological aspects of the fish species that are targeted by this trade in the region.

Methods
Therefore, we conducted semi-structured interviews and applied questionnaires to artisanal fishers of ornamental fish (N = 89), from the municipality of Barcelos, from January to April 2016.

Results
In total, 41 popular names were cited, which correspond to four ethnocategories and 10 families. The main species were Paracheirodon axelrodi (12.5%), Hemigrammus bleheri (8.3%), Ancistrus dolichopterus (6.4%), Symphysodon discus (5.3%), and Potamotrygon motoro (3.8%). According to the fishers, the species of fish known in the region as “piabas” have a preference for living in clusters (28.9%) and carry out migratory movements (26.1%). The diet of local fish species reported by fisheries is diverse, though mainly based on periphyton (42.2%), and the reproductive cycle directly influenced by the period of flooding of rivers in the region (37.6%)

Conclusion
Our study revealed that the fishers possess information on the ecological aspects of local ornamental fish species, many of which are consistent with scientific literature. The information presented may assist in the decision-making process for the management of local fishery resources and contribute to the resumption of growth and sustainability in the capture of ornamental fish.
Dose escalation in advanced floor of the mouth cancer: a pilot study using a combination of IMRT and stereotactic boost
Authors: Blažek Tomáš , Zděblová Čermáková Zuzana , Knybel Lukáš , Hurník Pavel , Štembírek Jan , Resová Kamila , Paračková Tereza , Formánek Martin , Cvek Jakub , Soumarová Renata 
Published: June 2021

Abstract
Purpose
We evaluated the efficiency and toxicity of stereotactic hypofractionated boost in combination with conventionally fractionated radiotherapy in the treatment of advanced floor of the mouth cancer.

Methods
Thirty-seven patients with advanced stage of the floor of the mouth cancer, histologically confirmed squamous cell carcinoma (p16 negative) ineligible for surgical treatment, were indicated for radiochemotherapy or hyperfractionated accelerated radiotherapy (HART). The radiotherapy protocol combined external beam radiotherapy (EBRT) and a stereotactic hypofractionated boost to the primary tumor. The dose delivered from EBRT was 70–72.5 Gy in 35/50 fractions. The hypofractionated boost followed with 10 Gy in two fractions. For the variables—tumor volume, stage and grade a multivariate analysis was performed to find the relationship between overall survival, local progression and metastasis. Toxicity was evaluated according to CTCAE scale version 4.

Results
After a median follow-up of 16 months, 23 patients (62%) achieved complete remission. The median time to local progression and metastasis was 7 months. Local control (LC) at 2 and 5-years was 70% and 62%, respectively. Progression-free survival (PFS) and overall survival (OS) were 57% and 49% at 2 years and 41% and 27% at 5 years, respectively. Statistical analysis revealed that larger tumors had worse overall survival and a greater chance of metastasis. Log-Rank GTV > 44 ccm (HR = 1.96; [95% CI (0.87; 4.38)]; p = 0.11). No boost-related severe acute toxicity was observed. Late osteonecrosis was observed in 3 patients (8%).

Conclusion
The combination of EBRT and stereotactic hypofractionated boost is safe and seems to be an effective option for dose escalation in patients with advanced floor of the mouth tumors who are ineligible for surgical treatment and require a non-invasive approach.
DeepBeam: a machine learning framework for tuning the primary electron beam of the PRIMO Monte Carlo software
Authors: Tabor Zbisław , Kabat Damian , Waligórski Michael P. R. 
Published: June 2021

Abstract
Background
Any Monte Carlo simulation of dose delivery using medical accelerator-generated megavolt photon beams begins by simulating electrons of the primary electron beam interacting with a target. Because the electron beam characteristics of any single accelerator are unique and generally unknown, an appropriate model of an electron beam must be assumed before MC simulations can be run. The purpose of the present study is to develop a flexible framework with suitable regression models for estimating parameters of the model of primary electron beam in simulators of medical linear accelerators using real reference dose profiles measured in a water phantom.

Methods
All simulations were run using PRIMO MC simulator. Two regression models for estimating the parameters of the simulated primary electron beam, both based on machine learning, were developed. The first model applies Principal Component Analysis to measured dose profiles in order to extract principal features of the shapes of the these profiles. The PCA-obtained features are then used by Support Vector Regressors to estimate the parameters of the model of the electron beam. The second model, based on deep learning, consists of a set of encoders processing measured dose profiles, followed by a sequence of fully connected layers acting together, which solve the regression problem of estimating values of the electron beam parameters directly from the measured dose profiles. Results of the regression are then used to reconstruct the dose profiles based on the PCA model. Agreement between the measured and reconstructed profiles can be further improved by an optimization procedure resulting in the final estimates of the parameters of the model of the primary electron beam. These final estimates are then used to determine dose profiles in MC simulations.

Results
Analysed were a set of actually measured (real) dose profiles of 6 MV beams from a real Varian 2300 C/D accelerator, a set of simulated training profiles, and a separate set of simulated testing profiles, both generated for a range of parameters of the primary electron beam of the Varian 2300 C/D PRIMO simulator. Application of the two-stage procedure based on regression followed by reconstruction-based minimization of the difference between measured (real) and reconstructed profiles resulted in achieving consistent estimates of electron beam parameters and in a very good agreement between the measured and simulated photon beam profiles.

Conclusions
The proposed framework is a readily applicable and customizable tool which may be applied in tuning virtual primary electron beams of Monte Carlo simulators of linear accelerators. The codes, training and test data, together with readout procedures, are freely available at the site: https://github.com/taborzbislaw/DeepBeam.
Honeysuckle-derived microRNA2911 inhibits tumor growth by targeting TGF-β1
Authors: Liu Chunyan , Xu Mengzhen , Yan Luocheng , Wang Yulian , Zhou Zhen , Wang Shaocong , Sun Yajie , Zhang Junfeng , Dong Lei 
Published: June 2021

Abstract
Background
Honeysuckle is a time‐honored herb with anticancer activity in traditional Chinese medicine. Recently, accumulating reports are suggesting that the microRNAs in this medicinal plant not only play a physiological role in their original system, but also can be transmitted to another species as potential therapeutic components. In the numerous bioactive investigations, the anti-tumor effects of these microRNAs in the magical herb are rarely studied, especially the special miR2911, a honeysuckle-encoded atypical microRNA, with high stability during the boiling process and unique biological activity to target TGF-β1 mRNA.

Methods
Luciferase assay was conducted to test the ability of miR2911 to target TGF-β1 mRNA. ELISA was performed to determine the expression level of TGF-β1 of mouse colorectal adenocarcinoma CT26 cells when treated with miR2911 and tumor tissue in Sidt1+/+ and Sidt1−/− mice. qRT-PCR was performed to examine the level of expression of miR2911. Tumor-bearing wild and nude mice were employed to evaluate the anti-tumor effect of honeysuckle and miR2911 in vivo. Tumor tissue necrosis was observed by H&E staining. Besides, the infiltration of T lymphocytes across solid tumors was tested by immunostaining staining.

Results
Our results showed that honeysuckle slowed the development of colon cancer down. Further research showed that miR2911 could bind strongly to TGF-β1 mRNA and down-regulate the expression of TGF-β1 and had a high stability under boiling and acid condition. Moreover, SIDT1 mediated dietary miR2911 inter-species absorption. And we found that miR2911 had a similar anticancer effect as honeysuckle. Mechanistically, miR2911 reversed the tumor-promoting effect of TGF-β1 by an increase of T lymphocytes infiltration, resulting in slowing the colon cancer process in immunocompetent mice. Consistent with this inference, the anti-tumor effect of miR2911 was revealed to be abolished in T cell immune deficiency mice.

Conclusion
Taken together, honeysuckle-derived miR2911 showed an anti-tumor effect in colon cancer through targeting TGF-β1 mRNA. The down-regulation of TGF-β1 promoted T lymphocytes infiltration, and accordingly impeded the colon tumor development.