bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute Toxic Effects of the New Psychoactive Substance “Voodoo” among Patients presented to the Poison Control Center of Ain Shams University Hospitals (PCC-ASUH), Egypt, during 2017
Authors: Hussien Rania , El-Setouhy Maged , Shinawi Mohamed El , El-Hariri Hazem Mohamed , Hirshon Jon Mark 
Published: September 2021

Abstract
Background
Voodoo is a heterogeneous mixture of psychoactive substances that has recently grown in popularity among youth in Egypt. Patients can present with a variety of manifestations that may lead to death in some cases. This study assessed the acute toxic effects of voodoo among patients presented to the Poison Control Center of Ain Shams University Hospitals (PCC-ASUH) during a one year period.

Methods
This is a retrospective study of all patients presented with voodoo intoxication at the PCC-ASUH from 1 January 2017 to 31 December 2017. Clinical data, routine laboratory findings, and ECG results as well as duration of hospitalization and outcome were compiled from hospital records.

Results
Seventy-one voodoo intoxication cases meeting the inclusion criteria were analyzed (mean age: 25.19 ± 9.54 years, range: 15–50 years, 97.2 % male). Pulse, blood pressure, and respiratory rate were normal in more than half of all patients. Neurological abnormalities including agitation, hallucinations, disturbance of consciousness were the most frequent manifestations. Respiratory acidosis was the most common laboratory finding (54.9 %), followed by increased serum urea (43.6 %), hypokalemia (33.8 %), hyperglycemia (28.1 %), and leukocytosis (26.7 %). The most common ECG finding was sinus tachycardia (31 %), followed by QT prolongation (15.4 %). More than half of the studied patients (53.5 %) co-administered other illicit substances, most frequently cannabis and tramadol. Most patients recovered fully and were discharged, but death occurred in two cases.

Conclusions
Voodoo toxicity can manifest with many presentations, hampering timely diagnosis. Clinicians should consider possible voodoo poisoning in patients presenting with a history of drug use with neurological symptoms, and they should conduct follow-up arterial blood gases, electrolytes and ECG as voodoo may contain potentially fatal psychoactive substances.
Patient positioning and immobilization procedures for hybrid MR-Linac systems
Authors: Cuccia Francesco , Alongi Filippo , Belka Claus , Boldrini Luca , Hörner-Rieber Juliane , McNair Helen , Rigo Michele , Schoenmakers Maartje , Niyazi Maximilian , Slagter Judith , Votta Claudio , Corradini Stefanie 
Published: September 2021

AbstractHybrid magnetic resonance (MR)-guided linear accelerators represent a new horizon in the field of radiation oncology. By harnessing the favorable combination of on-board MR-imaging with the possibility to daily recalculate the treatment plan based on real-time anatomy, the accuracy in target and organs-at-risk identification is expected to be improved, with the aim to provide the best tailored treatment. To date, two main MR-linac hybrid machines are available, Elekta Unity and Viewray MRIdian. Of note, compared to conventional linacs, these devices raise practical issues due to the positioning phase for the need to include the coil in the immobilization procedure and in order to perform the best reproducible positioning, also in light of the potentially longer treatment time. Given the relative novelty of this technology, there are few literature data regarding the procedures and the workflows for patient positioning and immobilization for MR-guided daily adaptive radiotherapy. In the present narrative review, we resume the currently available literature and provide an overview of the positioning and setup procedures for all the anatomical districts for hybrid MR-linac systems.
Effects of postoperative radiotherapy on cardiovascular-pulmonary disease mortality in patients with stage IIIA-N2 resected NSCLC: analysis of the SEER database
Authors: Wang Xia , Song Jiaqi , Long Jie , Zeng Zhimin , Liu Anwen 
Published: September 2021

Abstract
Background
The role of postoperative radiotherapy (PORT) in cardiovascular-pulmonary disease mortality in patients with stage IIIA-N2 resected non-small cell lung cancer (NSCLC) remains uncertain. The purpose of this population-based analysis was to explore the effect of PORT on cardiovascular-pulmonary disease mortality in these patients.

Methods
Patients aged ≥ 18 years with stage IIIA-N2 resected NSCLC were identified in the Surveillance, Epidemiology, and End Results (SEER) database from 2004 to 2015 and were grouped according to the use of PORT. Propensity score matching (PSM) was used to account for differences in baseline characteristics between the Non-PORT and PORT groups. The cumulative risk for cardiovascular-pulmonary disease death was estimated using the cumulative incidence curve. Competing risk regression was used to run univariate and multivariate analyses to evaluate risk factors.

Results
A total of 3981 patients were included in the study population. Among them, 1446 patients received PORT, and 2535 did not. A total of 1380 patients remained in each group after PSM, and the baseline characteristics were not significantly different between the two groups. The cumulative incidence of cardiovascular-pulmonary mortality was 10.93% in the Non-PORT group compared with 9.85% in the PORT group. There was no significant difference in the cumulative risk between the two groups (HR 1.07, 95% CI 0.77–1.48, p = 0.703). Multivariate analysis indicated that PORT had no significant impact on increased risk, with an HR of 1.18 (p = 0.377).

Conclusions
No significant differences between the PORT and Non-PORT groups were found in cardiovascular-pulmonary-specific modalities in this study. Further studies are required to validate these results. This study highlights the importance of long-term surveillance for NSCLC patients.
Scaling up care for perinatal depression for improved maternal and infant health (SPECTRA): protocol of a hybrid implementation study of the impact of a cascade training of primary maternal care providers in Nigeria
Authors: Gureje Oye , Oladeji Bibilola , Ayinde Olatunde Olayinka , Kola Lola , Abdulmalik Jibril , Abass Waheed Akinola Lanre , Faregh Neda , Zelkowitz Phyllis 
Published: September 2021

Abstract
Background
The large treatment gap for mental disorders in low- and middle-income countries (LMIC) necessitates task-sharing approaches in scaling up care for mental disorders. Previous work have shown that primary health care workers (PHCW) can be trained to recognize and respond to common mental disorders but there are lingering questions around sustainable implementation and scale-up in real world settings.

Method
This project is a hybrid implementation-effectiveness study guided by the Replicating Effective Programmes Framework. It will be conducted in four overlapping phases in maternal care clinics (MCC) in 11 local government areas in and around Ibadan metropolis, Nigeria. In Phase I, engagement meetings with relevant stake holders will be held. In phase II, the organizational and clinical profiles of MCC to deliver chronic depression care will be assessed, using interviews and a standardized assessment tool administered to staff and managers of the clinics. To ascertain the current level of care, 167 consecutive women presenting for antenatal care for the first time and who screened positive for depression will be recruited and followed up till 12 months post-partum. In phase III, we will design and implement a cascade training programme for PHCW, to equip them to identify and treat perinatal depression. In phase IV, a second cohort of 334 antenatal women will be recruited and followed up as in Phase I, to ascertain post-training level of care. The primary implementation outcome is change in the identification and treatment of perinatal depression by the PHCW while the primary effectiveness outcome is recovery from depression among the women at 6 months post-partum. A range of mixed-method approaches will be used to explore secondary implementation outcomes, including fidelity and acceptability. Secondary effectiveness outcomes are measures of disability and of infant outcomes.

Discussion
This study represents an attempt to systematically assess and document an implementation strategy that could inform the scaling up of evidence based interventions for perinatal depression using the WHO mhGAP-IG in LMIC.
Trial registration This study was registered on 03 December, 2019. https://doi.org/10.1186/ISRCTN94230307.
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions
Authors: Katz Kenneth S. , Shutov Oleg , Lapoint Richard , Kimelman Michael , Brister J. Rodney , O’Sullivan Christopher 
Published: September 2021

AbstractSequence Read Archive submissions to the National Center for Biotechnology Information often lack useful metadata, which limits the utility of these submissions. We describe the Sequence Taxonomic Analysis Tool (STAT), a scalable k-mer-based tool for fast assessment of taxonomic diversity intrinsic to submissions, independent of metadata. We show that our MinHash-based k-mer tool is accurate and scalable, offering reliable criteria for efficient selection of data for further analysis by the scientific community, at once validating submissions while also augmenting sample metadata with reliable, searchable, taxonomic terms.
Aspirin as secondary prevention in colorectal cancer liver metastasis (ASAC trial): study protocol for a multicentre randomized placebo-controlled trial
Authors: Yaqub Sheraz , Bjørnbeth Bjørn Atle , Angelsen Jon-Helge , Fristrup Claus Wilki , Grønbech Jon Erik , Hemmingsson Oskar , Isaksson Bengt , Juel Ingebjørg Soterud , Larsen Peter Nørgaard , Lindell Gert , Mortensen Frank Viborg , Mortensen Kim Erlend , Rizell Magnus , Sandström Per , Sandvik Oddvar Mathias , Sparrelid Ernesto , Taflin Helena , Taskén Kjetil ,   The ASAC study group, Brudvik Kristoffer W. , Fretland Åsmund A. , Horn Arild , Kleive Dyre , Labori Knut J. , Lassen Kristoffer , Røsok Bård I. , Søreide Jon A. , Tholfsen Tore , Villanger Olaug , Waage Anne 
Published: September 2021

Abstract
Background
Colorectal cancer is one the most common cancers in the western world with increasing incidence. Approximately 50% of the patients develop liver metastases. Resection of liver metastases is the treatment of choice although almost half of the resected patients get recurrence in the liver.

Methods
The ASAC trial is a Scandinavian, multicentre, double-blinded, randomized, placebo-controlled study to determine whether adjuvant treatment with low-dose aspirin (acetylsalicylic acid (ASA)) can improve disease-free survival in patients treated for colorectal cancer liver metastases (CRCLM). Up to 800 patients operated for CRCLM will be randomized to Arm#1 ASA 160 mg once daily or Arm#2 Placebo, for a period of 3 years or until disease recurrence. The patients will be recruited at all major hepatobiliary surgical units in Norway, Sweden and Denmark and have follow-up according to standard of care and the National Guidelines.

Discussion
The ASAC trial will be the first clinical interventional trial to assess the potential beneficial role of ASA in recurrence of CRCLM and survival. ASA is an inexpensive, well-tolerated and easily accessible drug that will be highly potential as adjuvant drug in secondary prevention of CRCLM if the study shows a beneficial effect. We will also determine the effect of ASA as adjuvant treatment on Health-Related Quality of Life and the cost-effectiveness.

Trial registration
ClinicalTrials.gov NCT03326791. Registered on 31 October 2017.
Safety and preliminary efficacy of sequential multiple ascending doses of solnatide to treat pulmonary permeability edema in patients with moderate-to-severe ARDS—a randomized, placebo-controlled, double-blind trial
Authors: Schmid Benedikt , Kredel Markus , Ullrich Roman , Krenn Katharina , Lucas Rudolf , Markstaller Klaus , Fischer Bernhard , Kranke Peter , Meybohm Patrick , Zwißler Bernhard , Frank Sandra ,   and the Solnatide Collaborators Group
Published: September 2021

Abstract
Background
Acute respiratory distress syndrome (ARDS) is a complex clinical diagnosis with various possible etiologies. One common feature, however, is pulmonary permeability edema, which leads to an increased alveolar diffusion pathway and, subsequently, impaired oxygenation and decarboxylation. A novel inhaled peptide agent (AP301, solnatide) was shown to markedly reduce pulmonary edema in animal models of ARDS and to be safe to administer to healthy humans in a Phase I clinical trial. Here, we present the protocol for a Phase IIB clinical trial investigating the safety and possible future efficacy endpoints in ARDS patients.

Methods
This is a randomized, placebo-controlled, double-blind intervention study. Patients with moderate to severe ARDS in need of mechanical ventilation will be randomized to parallel groups receiving escalating doses of solnatide or placebo, respectively. Before advancing to a higher dose, a data safety monitoring board will investigate the data from previous patients for any indication of patient safety violations. The intervention (application of the investigational drug) takes places twice daily over the course of 7 days, ensued by a follow-up period of another 21 days.

Discussion
The patients to be included in this trial will be severely sick and in need of mechanical ventilation. The amount of data to be collected upon screening and during the course of the intervention phase is substantial and the potential timeframe for inclusion of any given patient is short. However, when prepared properly, adherence to this protocol will make for the acquisition of reliable data. Particular diligence needs to be exercised with respect to informed consent, because eligible patients will most likely be comatose and/or deeply sedated at the time of inclusion.

Trial registration
This trial was prospectively registered with the EU Clinical trials register (clinicaltrialsregister.eu). EudraCT Number: 2017-003855-47.
Assessing the fidelity of a peer-led chronic pain management program (PAP)
Authors: Tse Mimi M. Y. , Tang Shuk Kwan , Ng Shamay , Li Yajie , Cheung Daphne Sze Ki , Kwan Rick Yiu Cho 
Published: September 2021

Abstract
Background
Intervention fidelity is the core component of a well-designed clinical trial and processes that are used to ensure that the study intervention is delivered as planned. It affects the design and implementation of a study as well as the analysis of the results and interpretation of the findings. The objectives of this study are (a) to describe the methods of assessing the intervention fidelity used in the peer-led chronic pain management program (PAP) and (b) to report the findings on the PAP’s intervention fidelity.

Methods
To optimize fidelity to the intervention, we used various strategies and measured them in a continuous process using several different approaches: (a) peer volunteer (PV) training workshop, (b) biweekly meetings with the research team, (c) a detailed teaching manual, (d) a fidelity checklist, (e) on-site visits and direct observations, and (f) semi-structured interview.

Results
The PVs’ attendance was high, and most of them achieved a high level of implementation in following the fidelity checklist. As part of a large clustered RCT, the fidelity assessment was carried out to help determine the effectiveness of the intervention.

Conclusions
Overall, the PVs successfully delivered the intervention, and the results of the study indicate the effectiveness of the PAP.

Trial registration
ClinicalTrials.govNCT03823495. Registered on 30 January 2019.
ssvQC: an integrated CUT&RUN quality control workflow for histone modifications and transcription factors
Authors: Boyd Joseph , Rodriguez Princess , Schjerven Hilde , Frietze Seth 
Published: September 2021

Abstract
Objective
Among the different methods to profile the genome-wide patterns of transcription factor binding and histone modifications in cells and tissues, CUT&RUN has emerged as a more efficient approach that allows for a higher signal-to-noise ratio using fewer number of cells compared to ChIP-seq. The results from CUT&RUN and other related sequence enrichment assays requires comprehensive quality control (QC) and comparative analysis of data quality across replicates. While several computational tools currently exist for read mapping and analysis, a systematic reporting of data quality is lacking. Our aims were to (1) compare methods for using frozen versus fresh cells for CUT&RUN and (2) to develop an easy-to-use pipeline for assessing data quality.

Results
We compared a workflow for CUT&RUN with fresh and frozen samples, and present an R package called ssvQC for quality control and comparison of data quality derived from CUT&RUN and other enrichment-based sequence data. Using ssvQC, we evaluate results from different CUT&RUN protocols for transcription factors and histone modifications from fresh and frozen tissue samples. Overall, this process facilitates evaluation of data quality across datasets and permits inspection of peak calling analysis, replicate analysis of different data types. The package ssvQC is readily available at https://github.com/FrietzeLabUVM/ssvQC.
A hybrid framework for improving uncertainty quantification in deep learning-based QSAR regression modeling
Authors: Wang Dingyan , Yu Jie , Chen Lifan , Li Xutong , Jiang Hualiang , Chen Kaixian , Zheng Mingyue , Luo Xiaomin 
Published: September 2021

AbstractReliable uncertainty quantification for statistical models is crucial in various downstream applications, especially for drug design and discovery where mistakes may incur a large amount of cost. This topic has therefore absorbed much attention and a plethora of methods have been proposed over the past years. The approaches that have been reported so far can be mainly categorized into two classes: distance-based approaches and Bayesian approaches. Although these methods have been widely used in many scenarios and shown promising performance with their distinct superiorities, being overconfident on out-of-distribution examples still poses challenges for the deployment of these techniques in real-world applications. In this study we investigated a number of consensus strategies in order to combine both distance-based and Bayesian approaches together with post-hoc calibration for improved uncertainty quantification in QSAR (Quantitative Structure–Activity Relationship) regression modeling. We employed a set of criteria to quantitatively assess the ranking and calibration ability of these models. Experiments based on 24 bioactivity datasets were designed to make critical comparison between the model we proposed and other well-studied baseline models. Our findings indicate that the hybrid framework proposed by us can robustly enhance the model ability of ranking absolute errors. Together with post-hoc calibration on the validation set, we show that well-calibrated uncertainty quantification results can be obtained in domain shift settings. The complementarity between different methods is also conceptually analyzed.
A visual fingerprint update algorithm based on crowdsourced localization and deep learning for smart IoV
Authors: Yin Xiliang , Ma Lin , Sun Ping , Tan Xuezhi 
Published: September 2021

AbstractRecently, deep learning and vision-based technologies have shown their great significance for the prospective development of smart Internet of Vehicle (IoV). When the smart vehicle enters the indoor parking of a shopping mall, the vision-based localization technology can provide reliable parking service. As known, the vision-based technique relies on a visual map without a change in the position of the reference object. Although, some researchers have proposed a few automatic visual fingerprinting (AVF) methods, which are aiming at reducing the cost of building the visual map database. However, the AVF method still costs too much under such a situation, since it is impossible to determine the specific location of the displaced object. Given the smart IoV and the development of deep learning approach, we propose an algorithm for solving the problem based on crowdsourcing and deep learning in this paper. Firstly, we propose a Region-based Fully Convolutional Network (R-FCN) based method with the feedback of crowdsourced images to locate the specific displaced object in the visual map database. Secondly, we propose a method based on quadratic programming (QP) for solving the translation vector of the displaced objects, which finally solves the problem of updating the visual map database. The simulation results show that our method can provide a higher detection sensitivity and correction accuracy as well as the relocation results. It means that our proposed algorithm outperforms the compared one, which is verified by both synthetic and real data simulation.
Trophic level drives the host microbiome of soil invertebrates at a continental scale
Authors: Zhu Dong , Delgado-Baquerizo Manuel , Ding Jing , Gillings Michael R. , Zhu Yong-Guan 
Published: September 2021

Abstract
Background
Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.

Results
Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.

Conclusions
Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates.