bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cough associated with the detection of Mycoplasma hyopneumoniae DNA in clinical and environmental specimens under controlled conditions
Authors: Silva Ana Paula S. Poeta , Storino Gabriel Y. , Ferreyra Franco S. Matias , Zhang Min , Fano Eduardo , Polson Dale , Wang Chong , Derscheid Rachel J. , Zimmerman Jeffrey J. , Clavijo Maria J. , Arruda Bailey L. 
Published: January 2022

Abstract
Background
The association of cough with Mycoplasma hyopneumoniae (MHP) DNA detection in specimens was evaluated under conditions in which the MHP status of inoculated and contact-infected pen mates was closely monitored for 59 days post-inoculation (DPI).

Methods
Seven-week-old pigs (n = 39) were allocated to five rooms (with one pen). Rooms contained 9 pigs each, with 1, 3, 6, or 9 MHP-inoculated pigs, respectively, except Room 5 (three sham-inoculated pigs). Cough data (2 × week) and specimens, tracheal swabs (2 × week), oral fluids (daily), drinker wipes (~ 1 × week), and air samples (3 × week) were collected. At 59 DPI, pigs were euthanized, and lung and trachea were evaluated for gross and microscopic lesions. Predictive cough value to MHP DNA detection in drinker and oral fluid samples were estimated using mixed logistic regression.

Results
Following inoculation, MHP DNA was first detected in tracheal swabs from inoculated pigs (DPI 3), then oral fluids (DPI 8), air samples (DPI 10), and drinker wipes (21 DPI). MHP DNA was detected in oral fluids in 17 of 59 (Room 1) to 43 of 59 (Room 3) samples, drinker wipes in 4 of 8 (Rooms 2 and 3) to 5 of 8 (Rooms 1 and 4) samples, and air samples in 5 of 26 (Room 2) or 3 of 26 (Room 4) samples. Logistic regression showed that the frequency of coughing pigs in a pen was associated with the probability of MHP DNA detection in oral fluids (P < 0.01) and nearly associated with drinker wipes (P = 0.08). Pathology data revealed an association between the period when infection was first detected and the severity of gross lung lesions.

Conclusions
Dry, non-productive coughs suggest the presence of MHP, but laboratory testing and MHP DNA detection is required for confirmation. Based on the data from this study, oral fluids and drinker wipes may provide a convenient alternative for MHP DNA detection at the pen level when cough is present. This information may help practitioners in specimen selection for MHP surveillance.
Gene expression alterations from reversible to irreversible stages during coral metamorphosis
Authors: Ishii Yuu , Hatta Masayuki , Deguchi Ryusaku , Kawata Masakado , Maruyama Shinichiro 
Published: January 2022

AbstractFor corals, metamorphosis from planktonic larvae to sedentary polyps is an important life event, as it determines the environment in which they live for a lifetime. Although previous studies on the reef-building coral Acropora have clarified a critical time point during metamorphosis when cells are committed to their fates, as defined by an inability to revert back to their previous states as swimming larvae (here referred to as the “point of no return”), the molecular mechanisms of this commitment to a fate remain unclear. To address this issue, we analyzed the transcriptomic changes before and after the point of no return by inducing metamorphosis of Acropora tenuis with Hym-248, a metamorphosis-inducing neuropeptide. Gene Ontology and pathway enrichment analysis of the 5893 differentially expressed genes revealed that G protein-coupled receptors (GPCRs) were enriched, including GABA receptor and Frizzled gene subfamilies, which showed characteristic temporal expression patterns. The GPCRs were then classified by comparison with those of Homo sapiens, Nematostella vectensis and Platynereis dumerilii. Classification of the differentially expressed genes into modules based on expression patterns showed that some modules with large fluctuations after the point of no return were biased toward functions such as protein metabolism and transport. This result suggests that in precommitted larvae, different types of GPCR genes function to ensure a proper environment, whereas in committed larvae, intracellular protein transport and proteolysis may cause a loss of the reversibility of metamorphosis as a result of cell differentiation.
Reproducibility of radiomic features in CT images of NSCLC patients: an integrative analysis on the impact of acquisition and reconstruction parameters
Authors: Rinaldi Lisa , De Angelis Simone P. , Raimondi Sara , Rizzo Stefania , Fanciullo Cristiana , Rampinelli Cristiano , Mariani Manuel , Lascialfari Alessandro , Cremonesi Marta , Orecchia Roberto , Origgi Daniela , Botta Francesca 
Published: January 2022

Abstract
Background
We investigated to what extent tube voltage, scanner model, and reconstruction algorithm affect radiomic feature reproducibility in a single-institution retrospective database of computed tomography images of non-small-cell lung cancer patients.

Methods
This study was approved by the Institutional Review Board (UID 2412). Images of 103 patients were considered, being acquired on either among two scanners, at 100 or 120 kVp. For each patient, images were reconstructed with six iterative blending levels, and 1414 features were extracted from each reconstruction. At univariate analysis, Wilcoxon-Mann-Whitney test was applied to evaluate feature differences within scanners and voltages, whereas the impact of the reconstruction was established with the overall concordance correlation coefficient (OCCC). A multivariable mixed model was also applied to investigate the independent contribution of each acquisition/reconstruction parameter. Univariate and multivariable analyses were combined to analyse feature behaviour.

Results
Scanner model and voltage did not affect features significantly. The reconstruction blending level showed a significant impact at both univariate analysis (154/1414 features yielding an OCCC < 0.85) and multivariable analysis, with most features (1042/1414) revealing a systematic trend with the blending level (multiple comparisons adjusted p < 0.05). Reproducibility increased in association to image processing with smooth filters, nonetheless specific investigation in relation to clinical endpoints should be performed to ensure that textural information is not removed.

Conclusions
Combining univariate and multivariable models is allowed to identify features for which corrections may be applied to reduce the trend with the algorithm and increase reproducibility. Subsequent clustering may be applied to eliminate residual redundancy.
Comparison between various DNA sterilization procedures applied in forensic analysis
Authors: Al-Snan Noora R. , Alraimi Najib M. 
Published: January 2022

Abstract
Background
The advanced sensitive STR kits applied in forensic DNA typing techniques can cause challenging issues when evidence samples are contaminated with minute quantities of DNA from another source such as forensic analysts or crime scene examiners.

Results
In this study, laboratory air and surfaces, gloves, tools, and equipment were evaluated as potential sources of contaminating DNA. Different sterilization methods were tested for their ability to efficiently eliminate DNA in a sample. Inactivation methods included 10% bleach, ethanol, UV light, and DNA-ExitusPlus IF. Exposure to the different inactivation protocols for varying periods of time was performed in two lab settings: low template DNA and DNA database labs. Surfaces were swabbed and any adhering DNA was quantified using HID real-time PCR. Results were detected using HID Real-Time PCR Analysis Software v1.2 and GeneMapper ID-X Software v1.4.

Conclusions
It was concluded that most of the DNA decontamination methods are not suitable for highly sensitive and precision STR kits such as GlobalFiler PCR Amplification Kit. The most suitable tested method was using DNA-ExitusPlus IF with the incubation time increased from 10 to 15 min.
Quality of care and respect of human rights in mental health services in four West African countries: collaboration between the mental health leadership and advocacy programme and the World Health Organization QualityRights initiative
Authors: Moro Maria Francesca , Kola Lola , Fadahunsi Olawoye , Jah Edward Munda , Kofie Humphrey , Samba Dawda , Thomas Sametta , Drew Natalie , Nwefoh Emeka , Pathare Soumitra , Eaton Julian , Funk Michelle , Gureje Oye 
Published: January 2022

Background
Although recent reports suggest that service users in West African psychiatric facilities are exposed to poor quality of care and human rights violations, evidence is lacking on the extent and profile of specific deficits in the services provided to persons with mental health conditions.

Aims
To evaluate the quality of care and respect of human rights in psychiatric facilities in four West African countries, The Gambia, Ghana, Liberia and Sierra Leone, using the World Health Organization QualityRights Toolkit.

Method
Trained research workers collected information through observation, review of records and interviews with service users, caregivers and staff. Independent panels of assessors used the information to assign scores to the criteria, standards and themes of the QualityRights Toolkit.

Results
The study revealed significant gaps in these facilities. The rights to an adequate standard of living and to enjoyment of the highest attainable standard of health were poorly promoted. Adherence to the right to exercise legal capacity and the right to personal liberty and security was almost absent. Severe shortcomings in the promotion of the right to live independently and be included in the community were reported.

Conclusions
Inadequate appreciation of service users’ rights, lack of basic approaches to protect them and the non-promotion of rights-based services in these facilities are major problems that need to be addressed. Although it recognises the resource constraints and need for more human and financial resources, the study also identifies critical areas and challenges that require significant changes at the facility level.
Human Papillomavirus Infection Determines Prognosis in Cervical Cancer
Authors: Lei Jiayao , Arroyo-Mühr Laila Sara , Lagheden Camilla , Eklund Carina , Nordqvist Kleppe Sara , Elfström Miriam , Andrae Bengt , Sparén Pär , Dillner Joakim , Sundström Karin 
Published: January 2022

PURPOSE Detection of human papillomavirus (HPV) by polymerase chain reaction in invasive cervical cancer is strongly associated with prognosis but previous studies have not considered sequencing efforts. We aimed to assess the association when also including comprehensive analysis of HPV infection by deep sequencing and a longer follow-up period. MATERIALS AND METHODS We subjected all 392 of 2,845 invasive cervical cancer cases that were polymerase chain reaction–negative for HPV to RNA sequencing on the NovaSeq 6000 platform (Illumina) and identified an additional 169 cases as HPV-positive. We followed all women from date of diagnosis to December 31, 2016, emigration, or death, whichever occurred first. The main outcome was all-cause mortality by December 31, 2016. We calculated 5-year cumulative relative survival ratios compared with the female general population and used Poisson regression to estimate excess hazard ratios of all-cause mortality by infection with any of the 13 most oncogenic (high-risk [hr]) HPV types in the tumor. All models were adjusted for age, time since diagnosis, stage, histology, and education level. RESULTS The 5-year cumulative relative survival ratio was 0.45 (95% CI, 0.39 to 0.51) in the hrHPV-negative group, and 0.74 (95% CI, 0.72 to 0.75) in the hrHPV-positive group. This translated to a statistically significantly 43% lower excess mortality in the hrHPV-positive group compared with the hrHPV-negative (corresponding to an excess hazard ratio 0.57; 95% CI, 0.48 to 0.69). There was no association between HPV risk group, clade, or number of HPV infections and prognosis. CONCLUSION hrHPV status is a strong determinant of cervical cancer prognosis over 15 years after diagnosis, above and beyond other established factors.
Obesity correlated to a higher risk of acquiring periodontitis: a cross-sectional study
Authors: Maulani Chaerita , Auerkari Elza Ibrahim , C. Masulili Sri Lelyati , Kusdhany Lindawati S. , Prahasanti Chiquita , Soedarsono Nurtami 
Published: January 2022

Background: The present study aimed to investigate the correlation between obesity and periodontitis, among other risk factors for periodontitis. Methods: In total, 262 Indonesian male and female subjects were analysed for body mass index (BMI), oral hygiene, plaque index, and clinically evaluated periodontitis. Statistical analysis was performed using Spearman tests and Pearson chi-square tests to estimate the correlation between BMI and periodontitis. Multivariate binary logistic analysis was conducted between covariate and periodontitis. P<0.05 was considered as statistically significant. Results: The prevalence of obesity was 48.47%. There were positive correlations between BMI and periodontal status for healthy-mild periodontitis, moderate, and severe periodontitis respectively. BMI and periodontitis crude odds ratio (OR) = 2.31 (95% CI 1.41-3.78); p < 0.05, adjusted OR of BMI among other variables, was 1.88 (95%CI 1.05-3.37); p < 0.05. Exploration of the ROC curve found a BMI cut off point of 24.785 kg/m2. Conclusion: Obesity by BMI measurement of ≥ 25kg/m2 correlated to a higher risk of acquiring periodontitis compared to normal-weight individuals.
The fragmented COVID-19 therapeutics research landscape: a living systematic review of clinical trial registrations evaluating priority pharmacological interventions.
Authors: McLean Alistair R.D. , Rashan Sumayyah , Tran Lien , Arena Lorenzo , Lawal AbdulAzeez , Maguire Brittany J. , Adele Sandra , Antonio Emilia Sitsofe , Brack Matthew , Caldwell Fiona , Carrara Verena Ilona , Charles Reema , Citarella Barbara Wanjiru , Epie Terrence B. , Feteh Vitalis Fambombi , Kennon Kalynn , Makuka Gerald Jamberi , Ngu Roland , Nwosu Amen-Patrick , Obiesie Sopuruchukwu , Ogbonnaa-Njoku Chinwe , Paul Parvesh , Richmond Caitlin , Singh-Phulgenda Sauman , Strudwick Samantha , Tyrrell Carina S.B. , Stepniewska Kasia , Strub-Wourgaft Nathalie , White Nicholas J. , Guérin Philippe J. 
Published: January 2022

Background: Many available medicines have been evaluated as potential repurposed treatments for coronavirus disease 2019 (COVID-19). We summarise the registered study landscape for 32 priority pharmacological treatments identified following consultation with external experts of the COVID-19 Clinical Research Coalition. Methods: All eligible trial registry records identified by systematic searches of the World Health Organisation International Clinical Trials Registry Platform as of 26th May 2021 were reviewed and extracted. A descriptive summary of study characteristics was performed. Results: We identified 1,314 registered studies that included at least one of the 32 priority pharmacological interventions. The majority (1,043, 79%) were randomised controlled trials (RCTs). The sample size of the RCTs identified was typically small (median (25th, 75th percentile) sample size = 140 patients (70, 383)), i.e. individually powered only to show very large effects. The most extensively evaluated medicine was hydroxychloroquine (418 registered studies). Other widely studied interventions were convalescent plasma (n=208), ritonavir (n=189) usually combined with lopinavir (n=181), and azithromycin (n=147). Very few RCTs planned to recruit participants in low-income countries (n=14; 1.3%). A minority of studies (348, 26%) indicated a willingness to share individual participant data. The living systematic review data are available at https://iddo.cognitive.city Conclusions: There are many registered studies planning to evaluate available medicines as potential repurposed treatments of COVID-19. Most of these planned studies are small, and therefore substantially underpowered for most relevant endpoints. Very few are large enough to have any chance of providing enough convincing evidence to change policies and practices. The sharing of individual participant data (IPD) from these studies would allow pooled IPD meta-analyses which could generate definitive conclusions, but most registered studies did not indicate that they were willing to share their data.
Information Salience and Mispricing in Housing
Authors: Agarwal Sumit , Karapetyan Artashes 
Published: January 2022

Making the purchase price fully salient to consumers has been shown to affect demand and equilibrium prices in various markets. Using a setting where part of the home acquisition price is in the form of nonsalient debt, we show this can happen in housing—a market where a typical household makes its largest acquisition. A regulation that made the debt and the total price salient for homebuyers eliminated a large mispricing caused by consumers’ inattention to the debt before the regulation. An average homebuyer would lose about $13,300 by acquiring a dwelling with one-standard deviation ($51,000)-higher debt, but this is nearly eliminated after the regulation. To shed light on the underlying channels, we use administrative data and show that young, financially inexperienced, and first-time homebuyers used to overpay the most. The results are not driven by rational channels based on liquidity constraints and adverse selection. Our findings imply that making all-inclusive house price and mortgage features salient at the time of advertising the sale can help avoid unintentional borrowing. This paper was accepted by David Simchi-Levi, finance. Supplemental Material: The online appendix is available at https://doi.org/10.1287/mnsc.2021.4253 .
Antimicrobial stewardship in wound care implementation and measuring outcomes: results of an e-survey
Authors: Ousey Karen , Rippon Mark , Rogers Alan , Stephenson John 
Published: January 2022

Objective: Antimicrobial resistance (AMR) occurs (as a result of misuse, such as over-prescribing) when certain pathogens fail to respond to treatment with antimicrobials. Consequently, patients can become severely ill and possibly die. A strategy referred to as antimicrobial stewardship (AMS) has been introduced which reduces the impact of this antimicrobial misuse. To explore health professionals' (working in wound care, treating both acute and hard-to-heal wounds) position in terms of the following: awareness of AMS; if they are aware of AMS, if they implement procedures to support its practice; and if they implement AMS, do they measure its impact by and compare pre- and post-implementation? Method: An e-survey designed to explore health professionals' awareness of AMS and its implications for wound care. Results: There were 987 respondents to the survey. The majority were specialist wound care nurses, mainly based in the UK or the US and Canada. A high proportion of those surveyed were completely/partially aware (35.1/57.9%, respectively) of AMS, and almost all implemented strategies to reduce antimicrobial prescribing. Of those surveyed, 36% took steps to measure the impact of AMS, and as a result 35.2% reported positive impacts (for example, cost reductions, a reduction in the systemic use of antimicrobials, a reduction in the topical use of antimicrobials and a reduced level of antimicrobial-resistant microorganisms). Challenging aspects of AMS implementation were reported by 33.2% of respondents (for example, poorer clinical outcomes in terms of healing and increased costs). The data highlighted that 40.49% felt that AMS would be ‘easy’ or ‘very easy’ to implement while 21.73% felt that AMS would be ‘difficult’ or ‘very difficult’ to implement. Conclusion: Education strategies need to be devised to raise awareness and support health professionals, including wound care practitioners, to understand and implement effective AMS programmes. Development of clear metrics is required to evaluate the effect of AMS programmes in clinical practice.
Low-vacuum negative pressure wound therapy protocol for complex wounds with exposed vessels
Authors: Paolini Guido , Sorotos Michail , Firmani Guido , Gravili Gianluca , Ceci Diego , Santanelli di Pompeo Fabio 
Published: January 2022

Objective:Treating high-risk surgical patients with complex wounds over exposed blood vessels is a challenge. Guided wound healing may be the only treatment possible. Negative pressure wound therapy (NPWT) is not recommended in these cases. The authors challenged these current recommendations and share their preliminary experience.Method:The authors adapted a NPWT protocol that uses low-vacuum continuous pressure (−80mmHg) with a silicone sheath and gauze/foam dressing between the wound bed and the device. They monitored the clinical features of patients' wounds to detect bleeding/ischaemia early on. Dressings were changed every 72–96 hours.Results:This protocol was followed in five male patients (aged 23–68 years) with complex wounds over exposed vessels. Two cases were foot crush injuries, one midfoot amputation, one hand self-subamputation and one vascular bypass infection. Comorbidities included monoarterial limbs/stump, severe arteriopathy and psychiatric disorder. The exposed vessels were femoral, radial and ulnar, anterior and posterior tibial arteries and veins. Mean treatment lasted 37 days (range 20–61 days). No episodes of severe bleeding/ischaemia of the extremities were observed. Treatment was discontinued once debridement was complete and granulation tissue allowed spontaneous closure/grafting. All wounds appeared stable at 1-year follow-up.Conclusion:The low-vacuum NPWT protocol was successful in solving five difficult cases. This regimen reduces risks associated with NPWT use on wounds with exposed vessels. The authors believe further validation is required to strengthen the evidence. However, preliminary data are encouraging and might help to change future NPWT recommendations by extending the indications for its use to exposed vessels.
Single-sideband microwave-to-optical conversion in high-Q ferrimagnetic microspheres
Authors: Chai Cheng-Zhe , Shen Zhen , Zhang Yan-Lei , Zhao Hao-Qi , Guo Guang-Can , Zou Chang-Ling , Dong Chun-Hua 
Published: January 2022

Coherent conversion of microwave and optical photons can significantly expand the capabilities of information processing and communications systems. Here, we experimentally demonstrate the microwave-to-optical frequency conversion in a magneto-optical whispering gallery mode microcavity. By applying a magnetic field parallel to the microsphere equator, the intracavity optical field will be modulated when the magnon is excited by the microwave drive, leading to a microwave-to-optical conversion via the magnetic Stokes and anti-Stokes scattering processes. The observed single-sideband conversion phenomenon indicates a nontrivial optical photon–magnon interaction mechanism derived from the magnon that induced both the frequency shift and modulated coupling rate of optical modes. In addition, we demonstrate the single-sideband frequency conversion with an ultrawide tuning range up to 2.5 GHz, showing its great potential in microwave-to-optical conversion.