bluuebunny/crossref_metadata_2025_split huggingface dataset:
Charakterisierung von mikrobiellen Biofilmen aus Tunnelwässern
Authors: Koraimann Günther , Bischof Karin 
Published: August 2022

AbstractMicroorganisms mainly from the domain of bacteria dominate life in the terrestrial subsurface up to a depth of several kilometers. Microbial life in that habitat is dependent on the availability of water and nutrients of biotic or abiotic origin. To produce biomass, bacterial primary producers are capable to use simple building blocks such as CO2, H2, CH4, reduced iron and sulfur, nitrate, phosphate as well as other salts and trace elements. Here, we describe the microbial content of several biofilm samples taken during the construction phase of a railway tunnel between the provinces of Styria and Carinthia (Koralm Tunnel). We could identify bacterial cells using light microscopy and used 16S rDNA based microbial profiling to characterize the bacterial community structure. Our results clearly show that the massive biofilms in tunnel drainage water were produced by a bacterial consortium typical for the deep continental subsurface biosphere. In many cases the majority of the consortium could be assigned to autotrophs, methanotrophs and methylotrophs.
The unintended consequences of hospital strikes on patient outcomes evidence from multiple strikes in the Portuguese National Health Service
Authors: Costa Eduardo 
Published: August 2022

AbstractHospital strikes in the Portuguese National Health Service (NHS) are becoming increasingly frequent. This paper analyses the effect of different health professionals' strikes (physicians, nurses, and diagnostic and therapeutic technicians (DTT) ‐ DTT) on patient outcomes and hospital activity. Patient‐level data, comprising all NHS hospital admissions in mainland Portugal from 2012 to 2018, is used together with a comprehensive strike dataset with almost 130 protests. Data suggests that hospital operations are partially disrupted during strikes, with sharp reductions in surgical admissions (up to 54%) and a decline on both inpatient and outpatient care admissions. The model controls for hospital characteristics, time and regional fixed effects, and case‐mix changes. Results suggest a modest increase in hospital mortality limited for patients admitted during physicians' strikes, and a slight reduction in mortality for patients already at the hospital when a strike takes place. Increases in readmission rates and length of stay are also found. Results suggest that hospitals and legal minimum staffing levels defined during strikes are not flexible enough to accommodate sudden disruptions in staffing, regardless of hospital quality in periods without strikes.
Evaluation of nitrogen mineralization under various irrigation water qualities and nitrogen application rates for mulched drip irrigation in an arid region
Authors: Ma Chao , Wang Jun , Li Jiusheng 
Published: August 2022

AbstractUnderstanding the interactive effects of irrigation water quality and fertilization on nitrogen mineralization (Nmin) and accurately predicting Nmin are of great importance for the secure and efficient utilization of brackish water in arid regions. A pot experiment was conducted to determine the Nmin under different drip irrigation water salinities and nitrogen application rates and to modify the nitrogen mineralization potential (N0) and mineralization rate constants (k) of the first‐order kinetic equation of Nmin. An in situ field experiment was conducted to validate the modified equation. The results showed that the amounts of Nmin for water salinities of 1.27, 3.03, and 4.90 g L−1 were 58.9, 76.1, and 45.4 kg ha−1, respectively. Nmin was stimulated when the soil salinities were lower than 6.6, 6.1 and 3.9 g kg−1 for nitrogen application rates of 255, 315 and 375 kg ha−1, respectively. Nitrogen application significantly reduced Nmin. When the nitrogen application rate increased to 375 kg ha−1, the net Nmin rate remained lower, and the effects of salinity on Nmin were attenuated. The Nmin model with modified N0 and k values was developed considering the impacts of soil organic nitrogen, nitrogen application rate, and soil salinity. Model testing indicated that the modified model provided an acceptable estimation of Nmin under field conditions. It will be helpful for developing rational fertilization strategies of drip irrigation with brackish water in arid regions.
Characterization of microparticles derived from waste plastics and their bio‐interaction with human lung A549 cells
Authors: Bengalli Rossella , Zerboni Alessandra , Bonfanti Patrizia , Saibene Melissa , Mehn Dora , Cella Claudia , Ponti Jessica , La Spina Rita , Mantecca Paride 
Published: August 2022

AbstractMicroplastics (MPs) represent a worldwide emerging relevant concern toward human and environmental health due to their intentional or unintentional release. Human exposure to MPs by inhalation is predicted to be among the most hazardous. MPs include both engineered, or primary MPs, and secondary MPs, materials obtained by fragmentation from any plastic good. The major part of the environmental MPs is constituted by the second ones that are irregular in size, shape and composition. These features make the study of the biological impact of heterogenous MPs of extremely high relevance to better estimate the real toxicological hazards of these materials on human and environmental organisms. The smallest fractions of plastic granules, relying on the micron‐sized scale, can be considered as the most abundant component of the environmental MPs, and for this reason, they are typically used to perform toxicity tests using in vitro systems representative of an inhalation exposure scenario. In the present work, MPs obtained from industrial treatment of waste plastics (wMPs < 50 μm) were investigated, and after the physico‐chemical characterization, the cytotoxic, inflammatory and genotoxic responses, as well as the modality of wMPs interactions with alveolar lung cells, were determined. Obtained results indicated that, at high concentrations (100 μg/ml) and prolonged exposure time (48 h), wMPs affect biological responses by inducing inflammation and genotoxicity, as a result of the cell–wMP interactions, also including the uptake of the smaller particles.
Monitoring stimulus‐evoked hemodynamic response during deep brain stimulation with single fiber spectroscopy
Authors: Yu Linhui , Noor M. Sohail , Kiss Zelma H. T. , Murari Kartikeya 
Published: August 2022

AbstractDeep brain stimulation (DBS) is a revolutionary treatment for movement disorders. Measuring DBS‐induced hemodynamic responses may be useful for surgical guidance of DBS electrode implantation as well as to study the mechanism and assess therapeutic effects of DBS. In this study, we evaluated the performance of a single fiber spectroscopic (SFS) system for measuring hemodynamic response in different cortical layers in a DBS animal model. We showed that SFS is capable of measuring minute relative changes in oxygen saturation and blood volume fraction in‐vivo at a sampling rate of 22–33 Hz. During stimulation, blood volume fraction increased, while oxygen saturation showed both increases and decreases at different cortical depths across animals. In addition, we showed the potential of using SFS for measuring other physiological parameters, for example, heart rate, and respiratory rate.
ppdx: Automated modeling of protein–protein interaction descriptors for use with machine learning
Authors: Conti Simone , Ovchinnikov Victor , Karplus Martin 
Published: August 2022

AbstractThis paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein–protein interactions. The descriptors can be used to predict various properties of interest, such as protein–protein binding affinities, or inhibitory concentrations (IC50), using approaches that range from simple regression to more complex machine learning models. The software is highly modular. It supports different protocols for generating structures, and 95 descriptors can be currently computed. More protocols and descriptors can be easily added. The implementation is highly parallel and can fully exploit the available cores in a single workstation, or multiple nodes on a supercomputer, allowing many systems to be analyzed simultaneously. As an illustrative application, ppdx is used to parametrize a model that predicts the IC50 of a set of antigens and a class of antibodies directed to the influenza hemagglutinin stalk.
Silencing LINC00665 inhibits cutaneous melanoma in vitro progression and induces apoptosis via the miR‐339‐3p/TUBB
Authors: Liu Yi , Ma Shanshan , Ma Qichao , Zhu Haigang 
Published: August 2022

AbstractBackgroundLncRNAs are closely related to cutaneous melanoma (CM) tumorigenesis and metastasis, and it can affect the progression of CM by regulating cell proliferation, migration, invasion, apoptosis, and other cellular mechanisms. This study investigated the role of LINC00665 in CM.MethodsExpressions of LINC00665, miR‐339‐3p, and tubulin beta chain (TUBB) in CM cells were analyzed by qRT‐PCR and/or Western blot. The LINC00665/miR‐339‐3p/TUBB targeting network was predicted by bioinformatics tools, screened out by Venn diagrams and analyzed by Pearson's correlation coefficients, followed by validation via dual‐luciferase reporter assay and/or pull‐down assay. Transfection of siLINC00665 or miR‐339‐3p inhibitor/mimic was conducted with CM cells whose viability, proliferation, migration, invasion, cell cycle progression, and apoptosis were measured by CCK‐8 assay, colony formation assay, wound healing assay, Transwell assay, and flow cytometry. The associations of TUBB with tumor biological characteristics and other proteins were analyzed by CanserSEA and String, respectively.ResultsHigh‐expressed LINC00665 was detected in CM cells. Silencing LINC00665 decreased CM cell viability; inhibited colony formation, cell cycle progression, migration and invasion; enhanced apoptosis; and upregulated miR‐339‐3p. LINC00665 targeted miR‐339‐3p which targeted TUBB. MiR‐339‐3p upregulation induced effects similar to the LINC00665‐silencing‐induced effects and could downregulate TUBB, which was associated with malignant behaviors and related to other five proteins. MiR‐339‐3p downregulation induced the opposite effects of what miR‐339‐3p upregulation induced, and the miR‐339‐3p downregulation‐induced effects could be reversed by LINC00665 silencing.ConclusionSilencing LINC00665 inhibits in vitro CM progression and induces apoptosis via the miR‐339‐3p/TUBB axis.
The postpartum uterine ultrasonographic scale in assessment of uterine involution after cesarean section in treated thrombophilia pregnant patients at term
Authors: Filip Catalina , Covali Roxana , Socolov Demetra , Carauleanu Alexandru , Tanasa Ingrid Andrada , Scripcariu Ioana Sadyie , Ciuhodaru Madalina , Butureanu Tudor , Pavaleanu Ioana , Akad Mona , Boiculese Lucian Vasile , Socolov Razvan 
Published: August 2022

AbstractBackgroundPregnancy is a prothrombotic condition which can be abnormally exaggerated in women with thrombophilia.MethodsIn a prospective study, patients who delivered at term, by cesarean section, between 1 October 2017 and 1 December 2021, who already had a diagnosis of thrombophilia before coming to our hospital, were included in the study group (n = 80). A similar number of nonthrombophilia patients (n = 80) without any history of thrombotic events, age‐ and para‐matched with the study group, were included in the control group. The postpartum uterine ultrasonographic scale (PUUS) values, in the first 24–48 h, were correlated with the patients' data.ResultsThe P‐LCR (platelet large cell ratio), was significantly higher in the treated thrombophilia group (p = 0.042). There was no correlation between PUUS and complete blood count values, coagulation factors, maternal characteristics, or fetal outcomes, except for postpartum neutrophils (p = 0.047) and postpartum platelet count (p = 0.046).ConclusionsPostpartum uterine involution was not significantly different, after cesarean section, between treated thrombophilia patients and nonthrombophilia patients. Involution correlated only with postpartum neutrophils and postpartum platelet count.
Neoantigen‐based cancer vaccination using chimeric RNA‐loaded dendritic cell‐derived extracellular vesicles
Authors: Xiong Xiao , Ke Xiurong , Wang Lu , Lin Yusheng , Wang Shuhong , Yao Zhimeng , Li Kai , Luo Yichen , Liu Fan , Pan Yunlong , Yeung Sai‐Ching J. , Helfrich Wijnand , Zhang Hao 
Published: August 2022

AbstractCancer vaccines critically rely on the availability of targetable immunogenic cancer‐specific neoepitopes. However, mutation‐based immunogenic neoantigens are rare or even non‐existent in subgroups of cancer types. To address this issue, we exploited a cancer‐specific aberrant transcription‐induced chimeric RNA, designated A‐PaschiRNA, as a possible source of clinically relevant and targetable neoantigens. A‐PaschiRNA encodes a recently discovered cancer‐specific chimeric protein that comprises full‐length astrotactin‐2 (ASTN2) C‐terminally fused in‐frame to the antisense sequence of the 18th intron of pregnancy‐associated plasma protein‐A (PAPPA). We used extracellular vesicles (EVs) from A‐PaschiRNA‐transfected dendritic cells (DCs) to produce the cell‐free anticancer vaccine DEXA‐P. Treatment of immunocompetent cancer‐bearing mice with DEXA‐P inhibited tumour growth and prolonged animal survival. In summary, we demonstrate for the first time that cancer‐specific transcription‐induced chimeric RNAs can be exploited to produce a cell‐free cancer vaccine that induces potent CD8+ T cell‐mediated anticancer immunity. Our novel approach may be particularly useful for developing cancer vaccines to treat malignancies with low mutational burden or without mutation‐based antigens. Moreover, this cell‐free anticancer vaccine approach may offer several practical advantages over cell‐based vaccines, such as ease of scalability and genetic modifiability as well as enhanced shelf life.
The goldilocks conundrum: Disclosing discrimination risks in informed consent
Authors: Prince Anya E. R. , Suter Sonia M. , Uhlmann Wendy R. , Scherer Aaron M. 
Published: August 2022

AbstractInformed consent is a foundational ethical and legal principle in human subjects research and clinical care. Yet, there is extensive debate over how much information must be disclosed to meet ethical goals and legal requirements, especially about non‐medical risks. In this online, survey‐based experiment of a diverse sample of the US general population, we explored one aspect of this debate by testing whether the level of detail included in informed consent regarding genetic anti‐discrimination protections alters individuals' willingness to participate in a hypothetical research study and their concerns regarding genetic discrimination. Participants were randomized to receive sample informed consent language with one of three levels of disclosure regarding the protections and limitations of the Genetic Information Nondiscrimination Act (GINA). Our sample (n = 1,195) had a mean age of 45.9 (SD = 17.9) years and 40% with ≤high school education. Participants were 51.3% female and 36.7% non‐Hispanic White. On average, those who received consent language with none of GINA's limitations highlighted were more willing to participate than those who were warned about various gaps in GINA. They also had significantly lower perceived risk of discrimination than those presented with the most information about limitations. Our study found that providing more comprehensive information about GINA notably lessened willingness to participate in the hypothetical studies, highlighting the need for clinicians and researchers to thoughtfully consider how to disclose anti‐discrimination risks in informed consent.
Foot gangrene following Tagraxofusp treatment for blastic plasmacytoid dendritic cell neoplasm: Case report
Authors: Sibai Jad , Chen RuiQi , Nabhani Ibrahim Al , Perusini Maria Agustina , Sibai Hassan 
Published: August 2022

AbstractBlastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and aggressive hematologic malignancy. It is associated with poor prognosis and heterogenous presentation. The CD123‐directed cytotoxin, Tagraxofusp, is a targeted therapy for BPDCN. Here, we report an 81‐year‐old female diagnosed with BPDCN. The patient was treated with Tagraxofusp and underwent a remarkably long remission (>20 months) without stem‐cell transplantation. She, however, experienced blue toe syndrome and left foot gangrene. We postulate that these previously unreported side effects were caused by microembolization. Characterization of the incidence of thrombo‐ and microembolizations in such a context, as well as prophylactic management options, are warranted.
Trends in all‐cause mortality and inpatient and outpatient visits for ambulatory care sensitive conditions during the first year of the COVID‐19 pandemic: A population‐based study
Authors: Kendzerska Tetyana , Zhu David T. , Pugliese Michael , Manuel Douglas , Sadatsafavi Mohsen , Povitz Marcus , Stukel Therese A. , To Teresa , Aaron Shawn D. , Mulpuru Sunita , Chin Melanie , Kendall Claire E. , Thavorn Kednapa , Robillard Rebecca , Gershon Andrea S. 
Published: August 2022

AbstractBackgroundThe impact of the COVID‐19 pandemic on the management of ambulatory care sensitive conditions (ACSCs) remains unknown.ObjectivesTo compare observed and expected (projected based on previous years) trends in all‐cause mortality and healthcare use for ACSCs in the first year of the pandemic (March 2020 to March 2021).Design, Setting and ParticipantsWe conducted a population‐based study using provincial health administrative data on general adul population (Ontario, Canada).Outcomes and MeasuresMonthly all‐cause mortality, and hospitalizations, emergency department (ED) and outpatient visit rates (per 100,000 people at‐risk) for seven combined ACSCs (asthma, chronic obstructive pulmonary disease, angina, congestive heart failure, hypertension, diabetes, and epilepsy) during the first year were compared with similar periods in previous years (2016–2019) by fitting monthly time series autoregressive integrated moving‐average models.ResultsCompared to previous years, all‐cause mortality rates increased at the beginning of the pandemic (observed rate in March to May 2020 of 79.98 vs. projected of 71.24 [66.35–76.50]) and then returned to expected in June 2020—except among immigrants and people with mental health conditions where they remained elevated. Hospitalization and ED visit rates for ACSCs remained lower than projected throughout the first year: observed hospitalization rate of 37.29 versus projected of 52.07 (47.84–56.68); observed ED visit rate of 92.55 versus projected of 134.72 (124.89–145.33). ACSC outpatient visit rates decreased initially (observed rate of 4299.57 vs. projected of 5060.23 [4712.64–5433.46]) and then returned to expected in June 2020.
Drop‐offs in the isoniazid preventive therapy cascade among children living with HIV in western Kenya, 2015–2019
Authors: Onyango Dickens Otieno , van der Sande Marianne A. B. , Yuen Courtney M. , Mecha Jerphason , Matemo Daniel , Oele Elizabeth , Kinuthia John , John‐Stewart Grace , LaCourse Sylvia M. 
Published: August 2022

AbstractIntroductionIsoniazid preventive therapy (IPT) can reduce the risk of tuberculosis (TB) in children living with HIV (CLHIV), but data on the outcomes of the IPT cascade in CLHIV are limited.MethodsWe evaluated the IPT cascade among CLHIV aged <15 years and newly enrolled in HIV care in eight HIV clinics in western Kenya. Medical record data were abstracted from September 2015 through July 2019. We assessed the proportion of CLHIV completing TB symptom screening, IPT eligibility assessment, IPT initiation and completion. TB incidence rate was calculated stratified by IPT initiation and completion status. Risk factors for IPT non‐initiation and non‐completion were assessed using Poisson regression with generalized linear models.ResultsOverall, 856 CLHIV were newly enrolled in HIV care, of whom 98% ([95% CI 97–99]; n = 841) underwent screening for TB symptoms and IPT eligibility. Of these, 13 (2%; 95% CI 1–3) were ineligible due to active TB and 828 (98%; 95% CI 97–99) were eligible. Five hundred and fifty‐nine (68%; 95% CI 64–71) of eligible CLHIV initiated IPT; median time to IPT initiation was 3.6 months (interquartile range [IQR] 0.5–10.2). Overall, 434 (78%; 95% CI 74–81) IPT initiators completed. Attending high‐volume HIV clinics (aRR = 2.82; 95% CI 1.20–6.62) was independently associated with IPT non‐initiation. IPT non‐initiation had a trend of being higher among those enrolled in the period 2017–2019 versus 2015–2016 (aRR = 1.91; 0.98–3.73) and those who were HIV virally non‐suppressed (aRR = 1.90; 95% CI 0.98–3.71). Being enrolled in 2017–2019 versus 2015–2016 (aRR = 1.40; 1.01–1.96) was independently associated with IPT non‐completion. By 24 months after IPT screening, TB incidence was four‐fold higher among eligible CLHIV who never initiated (8.1 per 1000 person years [PY]) compared to CLHIV who completed IPT (2.1 per 1000 PY; rate ratio [RR] = 3.85; 95% CI 1.08–17.15), with a similar trend among CLHIV who initiated but did not complete IPT (8.2/1000 PY; RR = 4.39; 95% CI 0.82–23.56).ConclusionsDespite high screening for eligibility, timely IPT initiation and completion were suboptimal among eligible CLHIV in this programmatic cohort. Targeted programmatic interventions are needed to address these drop‐offs from the IPT cascade by ensuring timely IPT initiation after ruling out active TB and enhancing completion of the 6‐month course to reduce TB in CLHIV.
Correcting for selection bias in HIV prevalence estimates: an application of sample selection models using data from population‐based HIV surveys in seven sub‐Saharan African countries
Authors: Palma Anton M. , Marra Giampiero , Bray Rachel , Saito Suzue , Awor Anna Colletar , Jalloh Mohamed F. , Kailembo Alexander , Kirungi Wilford , Mgomella George S. , Njau Prosper , Voetsch Andrew C. , Ward Jennifer A. , Bärnighausen Till , Harling Guy 
Published: August 2022

AbstractIntroductionPopulation‐based biomarker surveys are the gold standard for estimating HIV prevalence but are susceptible to substantial non‐participation (up to 30%). Analytical missing data methods, including inverse‐probability weighting (IPW) and multiple imputation (MI), are biased when data are missing‐not‐at‐random, for example when people living with HIV more frequently decline participation. Heckman‐type selection models can, under certain assumptions, recover unbiased prevalence estimates in such scenarios.MethodsWe pooled data from 142,706 participants aged 15–49 years from nationally representative cross‐sectional Population‐based HIV Impact Assessments in seven countries in sub‐Saharan Africa, conducted between 2015 and 2018 in Tanzania, Uganda, Malawi, Zambia, Zimbabwe, Lesotho and Eswatini. We compared sex‐stratified HIV prevalence estimates from unadjusted, IPW, MI and selection models, controlling for household and individual‐level predictors of non‐participation, and assessed the sensitivity of selection models to the copula function specifying the correlation between study participation and HIV status.ResultsIn total, 84.1% of participants provided a blood sample to determine HIV serostatus (range: 76% in Malawi to 95% in Uganda). HIV prevalence estimates from selection models diverged from IPW and MI models by up to 5% in Lesotho, without substantial precision loss. In Tanzania, the IPW model yielded lower HIV prevalence estimates among males than the best‐fitting copula selection model (3.8% vs. 7.9%).ConclusionsWe demonstrate how HIV prevalence estimates from selection models can differ from those obtained under missing‐at‐random assumptions. Further benefits include exploration of plausible relationships between participation and outcome. While selection models require additional assumptions and careful specification, they are an important tool for triangulating prevalence estimates in surveys with substantial missing data due to non‐participation.