bluuebunny/crossref_metadata_2025 huggingface dataset:
EGFR Mutations and PD-L1 Expression in Early-Stage Non-Small Cell Lung Cancer: A Real-World Data From a Single Center in Brazil
Authors: Alves Pinto Icaro , de Oliveira Cavagna Rodrigo , Virginio da Silva Aline Larissa , Dias Josiane Mourão , Santana Iara Vidigal , Souza Laísa Caroline , Ferreira da Silva Flávio Augusto , Biazotto Fernandes Maria Fernanda , Junqueira Pinto Gustavo Dix , Negreiros Izabella Santos , Santiago Gonçalves Maria Fernanda , de Paula Flávia Escremim , Berardinelli Gustavo Nóriz , Casagrande Giovanna Maria Stanfoca , Oliveira da Silva Marcela , Albino da Silva Eduardo Caetano , de Oliveira Marco Antonio , Jacinto Alexandre Arthur , Duval da Silva Vinicius , Reis Rui Manuel , De Marchi Pedro , Leal Letícia Ferro
Published: September 2022

Background

Targeted and immunotherapies are currently moving toward early-stage settings for patients with non-small cell lung cancer (NSCLC). Predictive biomarkers data are scarce in this scenario. We aimed to describe the frequency of EGFR mutations and PD-L1 expression levels in early-stage non-squamous patients with NSCLC from a large, single Brazilian oncology center.

Methods

We retrospectively evaluated patients with NSCLC diagnosed at an early-stage (IB to IIIA-AJCC seventh edition) at Barretos Cancer Hospital (n = 302). EGFR mutational status was assessed in FFPE tumor tissues using distinct methodologies (NGS, Cobas, or Sanger sequencing). PD-L1 expression was evaluated by immunohistochemistry (clone 22C3) and reported as Tumor Proportion Score (TPS), categorized as <1%, 1-49%, and ≥50%. We evaluated the association between EGFR mutational status and PD-L1 expression with sociodemographic and clinicopathological parameters by Fisher’s test, qui-square test, and logistic regression. Survival analysis was assessed by the Kaplan-Meier method and Cox regression model.

Results

EGFR mutations were detected in 17.3% (n = 48) of cases and were associated with female sex, never smokers, and longer overall and event-free survival. PD-L1 positivity was observed in 36.7% (n = 69) of cases [TPS 1-49% n = 44(23.4%); TPS ≥50% n = 25(13.3%)]. PD-L1 positivity was associated with smoking, weight loss, and higher disease stages (IIB/IIIA).

Conclusion

The frequencies of EGFR mutations and PD-L1 positivity were described for early-stage non-squamous patients with NSCLC. These results will be essential for guiding treatment strategies with the recent approvals of osimertinib and immunotherapy in the adjuvant setting.
Reductions in All-Cause Mortality Associated with the Use of Methylnaltrexone for Opioid-Induced Bowel Disorders: A Pooled Analysis
Authors: Webster Lynn R , Brenner Darren , Israel Robert J , Stambler Nancy , Slatkin Neal E
Published: September 2022

Objective

Preclinical and clinical studies suggest that activation of the µ-opioid receptor may reduce overall survival and increase the risk for all-cause mortality in patients with cancer and noncancer pain. Methylnaltrexone, a selective, peripherally acting µ-opioid receptor antagonist, has demonstrated efficacy for the treatment of opioid-induced constipation. This retrospective analysis of 12 randomized, double-blind, placebo-controlled studies of methylnaltrexone evaluated the treatment of opioid-induced bowel disorders in patients with advanced illness or noncancer pain.

Methods

The risk of all-cause mortality within 30 days after the last dose of study medication during the double-blind phase was compared between methylnaltrexone and placebo groups. The data were further stratified by cancer vs noncancer, age, gender, and acute vs chronic diagnoses.

Results

Pooled data included 2,526 methylnaltrexone-treated patients of which 33 died, and 1,192 placebo-treated patients of which 35 died. The mortality rate was 17.8 deaths/100 person-years of exposure in the methylnaltrexone group and 49.5 deaths/100 person-years of exposure for the placebo group. The all-cause mortality risk was significantly lower among patients receiving methylnaltrexone compared with placebo (hazard ratio: 0.399, 95% confidence interval: 0.25, 0.64; P = .0002), corresponding to a 60% risk reduction. Significant risk reductions were observed for those receiving methylnaltrexone who had cancer or chronic diagnoses. Methylnaltrexone-treated patients had a significantly reduced mortality risk compared with placebo regardless of age or gender.

Conclusions

Methylnaltrexone reduced all-cause mortality vs placebo treatment across multiple trials, suggesting methylnaltrexone may confer survival benefits in patients with opioid-induced bowel disorders taking opioids for cancer-related or chronic noncancer pain.
Analgesic Electrical Stimulation Combined with Wrist-Ankle Acupuncture Reduces the Cortical Response to Pain in Patients with Myofasciitis: A Randomized Clinical Trial
Authors: Du Jiahao , Shi Ping , Liu Junwen , Yu Hongliu , Fang Fanfu
Published: September 2022

Objective

Transcutaneous electrical nerve stimulation (TENS) based on wrist-ankle acupuncture has been shown to relieve pain levels in patients with myofascial pain syndrome (MPS). However, its efficacy is highly subjective. The purpose of this study was to evaluate the feasibility and effectiveness of TENS based on wrist-ankle acupuncture for pain management in patients with MPS from the perspective of cerebral cortex hemodynamics.

Design, setting, participants and interventions

We designed a double-blind, randomized, controlled clinical trial. Thirty-one male patients with MPS were randomly assigned to two parallel groups. The experimental group (n = 16) received TENS based on wrist-ankle acupuncture for analgesic treatment, while the control group (n = 15) did not. The pain was induced by mechanically pressurized at acupoint Jianjing. The multichannel functional near-infrared spectroscopy (fNIRS) equipment was utilized for measuring oxyhemoglobin (HbO) levels in the cerebral cortex during the tasks.

Results

After the intervention, visual analog scale (VAS), the activation degree and activation area of pain perception cortices were significantly reduced in the experimental group compared to the baseline values (P < .05). Particularly, Frontopolar Area (FPA), and Dorsolateral Prefrontal Cortex (DLPFC) are highly involved in the pain process and pain modulation.

Conclusion

Compared to no intervention, TENS based on wrist-ankle acupuncture can be effective in relieving pain in patients with MPS in terms of cerebral cortical hemodynamics. However, further studies are necessary to quantify the analgesic effect in terms of cerebral hemodynamics and brain activation.
Contribution of the Wolffian duct mesenchyme to the formation of the female reproductive tract
Authors: Zhao Fei , Grimm Sara A , Jia Shua , Yao Humphrey Hung-Chang
Published: September 2022

The female reproductive tract develops from its embryonic precursor, the Müllerian duct. In close proximity to the Müllerian duct lies the precursor for the male reproductive tract, the Wolffian duct, which is eliminated in the female embryo during sexual differentiation. We discovered that a component of the Wolffian duct, its mesenchyme, is not eliminated after sexual differentiation. Instead, the Wolffian duct mesenchyme underwent changes in transcriptome and chromatin accessibility from male tract to female tract identity, and became a unique mesenchymal population in the female reproductive tract with localization and transcriptome distinct from the mesenchyme derived from the Müllerian duct. Partial ablation of the Wolffian duct mesenchyme stunted the growth of the fetal female reproductive tract in ex vivo organ culture. These findings reveal a new fetal origin of mesenchymal tissues for female reproductive tract formation and reshape our understanding of sexual differentiation of reproductive tracts.
Work participation is unaffected in Belgian spondyloarthritis patients: data from the BelGian Inflammatory Arthritis and SpoNdylitis cohorT
Authors: De Craemer Ann-Sophie , Deroo Liselotte , Renson Thomas , Desimpele Ine , Delmez Lauren , Decuman Saskia , Janssens Xavier , Boonen Annelies , Elewaut Dirk , Carron Philippe , Van den Bosch Filip
Published: September 2022

Objectives

This study aimed to (i) investigate actual work participation in Belgian spondyloarthritis (SpA) patients compared with the general population, and (ii) identify determinants of work-related outcomes.

Material and methods

Adult SpA patients from the Ghent University Hospital based Be-GIANT cohort (fulfilling ASAS classification criteria) were cross-sectionally questioned on their socio-economic status and completed a Work Productivity and Activity Impairment questionnaire (May 2018 to May 2019). Results were compared with national and regional data on the general population using indirect standardization. Associations between clinical and job characteristics and work-related outcomes were analysed with logistic regression (having a paid job) and negative binomial hurdle models (sick leave and presenteeism, i.e. restrictions while at work).

Results

A total of 215/262 (82%) patients of working age (<65 y/o) had a paid job, corresponding to an age- and sex-adjusted employment ratio of 1.00 (95% CI 0.88, 1.14). Patients worked 39.6h (10.5h)/week, and 49% (95% CI 42, 56%) reported sick leave in the previous year, similar to the general population (39.7h/week, 42%). In total, 56% reported presenteeism of median (IQR) 10% (0–20%). In multivariate analysis, functional impairment (BASFI) and health-related quality of life (HRQoL, EuroQoL-VAS) were associated with each work-related outcome, while contextual factors (education, physically demanding job) were positively associated with, respectively, having a paid job and presenteeism. Clinical characteristics showed no independent association with any of these outcomes.

Conclusions

Evidence from this academic cohort study does not support a work participation gap between SpA patients and the general population, but confirms the role of physical function, overall HRQoL, and education or job type as risk factors for adverse work outcomes.
Evaluation of Patient Transmission Factor Following the Administration of 177Lu-DOTATATE
Authors: Recca Kimyli , Muneeb Aeman , Helstern Christopher , Lemieux Bryan , Das Satya , Jessop Aaron
Published: September 2022

177Lu-DOTATATE is a radionuclide therapy that is FDA approved for the treatment of somatostatin receptor-positive gastroenteropancreatic neuroendocrine tumors. Treatment facilities are required to determine the maximum radiation dose from such subjects to the maximally exposed member of the public, ensuring that the total effective dose equivalent (TEDE) does not exceed regulatory limits. If the calculated TEDE meets the regulatory limits, the patient is eligible for release and provided instructions with radiation precautions. This study aims to determine a mean transmission factor to the patient to improve accuracy and individualize the estimation of the TEDE.
A Risk Comparison of Non-cancer Mortality between Lifestyle, Socioeconomic Status, and Radiation among Japanese Nuclear Workers (J-EPISODE)
Authors: Kudo Shin’ichi , Miwa Yoshie , Furuta Hiroshige , Saigusa Shin
Published: September 2022

Many epidemiological studies have been conducted to investigate the health effects of low-dose radiation. Most of these investigations have focused on cancer, and fewer studies have examined non-cancer topics than cancer subjects. The purpose of this study is to compare the relative risks of non-cancer mortality from low-dose radiation with lifestyle factors (such as smoking habits) and socioeconomic status (such as years of education). The cohort consisted of 43,692 males who responded to a lifestyle questionnaire survey conducted from 2003 to 2004 among nuclear workers in Japan. Missing questionnaire data were imputed by multiple imputation, each variable was categorized, and the relative risks for the reference group were calculated using Poisson regression. The total number of observed person-years was 300,000, and the mean age and dose were 55.2 y and 24.5 mSv (10-y lagged dose), respectively. For many of the causes of death in this analysis, significantly high risks existed for lifestyle differences, such as smoking, alcohol consumption, frequency of medical examination, breakfast intake, sleep, and BMI, but few for socioeconomic status. Radiation showed no significantly high risks. Taken together, the risk of non-cancer mortality from low-dose radiation is likely smaller than that from lifestyle factors.
The Development of a Comprehensive Physical Function Measure for the Intensive Care Unit Using Rasch Analysis and Item Response Theory
Authors: Peterson Michelle L. , Litwin Bini , Fulk George D.
Published: September 2022

Objective:

This study serves to create a comprehensive, robust functional measurement tool for use with patients in the intensive care unit.

Design:

Two physical therapists conducted outcome measure research at a large hospital in the Northeast United States using item response theory (IRT) Rasch analysis for individual activity task evaluation, ranking of task difficulty, and removal of duplicate tasks. IRT Rasch analysis included item fit, hierarchy, reliability, dimensionality, differential item functioning (DIF), and probability.

Results:

Fifteen items out of a total of 53 met the requirements for an optimal rating scale. The items were ranked according to difficulty and there was no misfit. The reliability indexes were 5.13, α= 0.96, and 21.52, α= 1.00 for person and item scores respectively confirming scale hierarchy. The Cronbach α (KR-20) person raw score “test” reliability was 0.96, with standard error of measurement 2.72. DIF was deemed nonsignificant, and the probability curves were well delineated and ordered.

A robust, reliable, and valid 15-item Comprehensive Physical Function Measure for use in the intensive care unit was developed through Rasch analysis and item response theory.
Mastoid Obliteration Using S53P4 Bioactive Glass in Cholesteatoma Surgery: A 10-Year Single-Center Experience in 173 Adult Patients with Long-Term Magnetic Resonance Imaging Controlled Follow-up
Authors: Kroon Victor J. , Mes Steven W. , Borggreven Pepijn A. , van de Langenberg Rick , Colnot David R. , Quak Jasper J.
Published: September 2022

Objective

To present the long-term outcomes of mastoid obliteration in cholesteatoma surgery using S53P4 bioactive glass (BAG) in an adult population.

Study Design

Retrospective cohort study.

Setting

Single-center study.

Patients

All 173 adult patients who underwent primary or revision surgery for cholesteatoma with mastoid obliteration using S53P4 BAG with at least 1 year of follow-up including nonecho planar diffusion-weighted magnetic resonance imaging (MRI) (non-EP DWI MRI) and/or second-look surgery to evaluate recidivism. Both canal wall up (CWU) and canal wall down (CWD) procedures were included.

Intervention(s)

Patients underwent CWU or CWD mastoidectomy using S53P4 BAG.

Main Outcome and Measures

Cholesteatoma recidivism, postoperative complications, Merchant grade, hearing outcome.

Results

Cholesteatoma recidivism was assessed by MRI in 97% of all cases and second-look surgery look surgery in 3% of cases. After a mean follow-up period of 53 months, cholesteatoma recidivism was seen in 10% of the cases (n = 18). Using the Kaplan-Meier curve to extrapolate, a 5-year recidivism rate of 12% was estimated. Only minor complications occurred, all resolving spontaneously or after minor treatment. Merchant grade of 0 to 1 was achieved 95% of the patients, no persistently wet ears were observed. Closure of the air-bone gap within 20 dB was possible in 32%.

Conclusion

In this long-term (up to 10 yr) follow-up study, we demonstrated the safety of S53P4 BAG. Minimal and only minor postoperative complications were observed. The effectiveness of BAG was indicated by the low rate of recidivism, even when using non-EP DWI MRI, a sensitive and specific noninvasive technique to detect cholesteatoma recidivism.
Patient Preferences for Neoadjuvant Therapy in Pancreatic Ductal Adenocarcinoma
Authors: Hamad Ahmad , Crossnohere Norah , Ejaz Aslam , Tsung Allan , Pawlik Timothy M. , Sarna Angela , Santry Heena , Wills Celia , Cloyd Jordan M.
Published: September 2022

Objectives

Physicians are increasingly recommending neoadjuvant therapy (NT) before surgery for pancreatic ductal adenocarcinoma (PDAC). However, patient preferences for and opinions regarding NT are poorly understood.

Methods

Survivors and caregivers from a national PDAC patient advocacy organization completed an online survey assessing preferences for NT versus surgery first (SF) and factors influencing their decision making.

Results

Among 54 participants, 74.1% had a personal history of PDAC. While most patients preferred SF for resectable disease, NT was the preferred treatment approach for borderline resectable, locally advanced, and resectable cancers with high carbohydrate antigen 19-9. The most important factor influencing patient decision making regarding NT was its impact on overall survival while the least important was published national guidelines. The most preferred rationale for NT was ability to downstage to surgical resection and early treatment of micrometastatic disease.

Conclusions

Among a national cohort of PDAC survivors and caregivers, the majority preferred SF for resectable PDAC, whereas NT was preferred when the resectability of a tumor was in question. The impact of NT on quantity and quality of life, as well as the likelihood of achieving surgical resection, was most highly valued by participants.
A State Health Department and Health Information Exchange Partnership: An Effective Collaboration for a Data-Driven Response for COVID-19 Contact Tracing in Maryland
Authors: Feldman Katherine A. , Hanks Andrew , Williams Thelonious W. , Blouse Brandon , Babcock Carly , Goode Alexandra , Dowling Steve , Thakuria Ayanjyoti , Teichmann Jeremy , Aljalahma Humoud , Pearlowitz Marcia
Published: September 2022

Background

Accurate, complete, timely data were essential to effective contact tracing for COVID-19. Maryland Department of Health partnered with Maryland's designated health information exchange, Chesapeake Regional Information System for Our Patients (CRISP), to establish data enhancement processes that provided the foundation for Maryland's successful contact tracing program.

Methods

Hourly, electronic positive COVID-19 test results were routed through CRISP to the contact tracing data platform. The CRISP matched reports against its master patient index to enhance the record with demographic, locating, fatality, vaccination, and hospitalization data. Records were deduplicated and flagged if associated with a congregate setting, select state universities, or recent international travel. χ2 Tests were used to assess if CRISP-added phone numbers resulted in better contact tracing outcomes.

Results

During June 15, 2020, to September 1, 2021, CRISP pushed 531,094 records to the state's contact tracing data platform within an hour of receipt; of those eligible for investigation, 99% had a phone number. The CRISP matched 521,731 (98%) records to their master patient index, allowing for deduplication and enrichment. The CRISP flagged 15,615 cases in congregate settings and 3304 cases as university students; these records were immediately routed for outbreak investigation. Records with an added phone number were significantly more likely to be successfully reached compared with cases with no added phone number (P = 0.01).

Conclusions

The CRISP enhanced COVID-19 electronic laboratory reports with a near-instant impact on public health actions. The partnership and data processing workflows can serve as a blueprint for data modernization in public health agencies across the United States.
Qualitative exploration of family caregivers' perception and experience caring for pediatric patients with cancer
Authors: Akin-Odanye Elizabeth O. , Peate Michelle , Asuzu Chioma C. , Brown Biobele J. , Henry Melissa
Published: September 2022

Background:

Literature on the experience of those caring for children with cancer from low- and middle-income countries is scant. Gaining insight into their experiences may be important to providing appropriate services for this group. This study sought to identify the concerns and explore the experiences of family caregivers of pediatric patients with cancer in Nigeria.

Method:

This qualitative study used semistructured interviews to collect data from 16 consenting family caregivers of pediatric patients with cancer seen at the University College Hospital, Ibadan. Recorded audio data were transcribed and subjected to content analysis.

Results:

Most family caregivers were unaware of pediatric cancer before getting the diagnosis. They experienced anticipatory grief fearing the possibility of their children dying and feeling helpless regarding funding the treatments. In addition, they expressed powerlessness in controlling the illness/treatment outcome and in managing how they were treated by hospital staff. Siblings were said to experience distress from seeing the deteriorating physical changes in their siblings with cancer. Participants reported disruption in usual domestic and socioeconomic activities in the family. They mostly coped through using religious/spiritual coping strategies and accessing some social support from hospital staff and well-wishers. Family caregivers perceived a need for greater government involvement in pediatric cancer care and prevention efforts and seek more cooperation from hospital staff in the care of their children.

Conclusions:

Family caregivers of pediatric patients with cancer experience challenges worthy of psycho-oncologists’ attention. This population might benefit from interventions to manage anticipatory grief and promote assertive communication and problem-solving skills.
Early Developmental Trends in High-Risk Neonates Later Diagnosed With Autism Spectrum Disorder
Authors: Carey Helen , Tanner Kelly , Ratliff-Schaub Karen , Baldino Maria , Kelly Nicholas , Andridge Rebecca R.
Published: September 2022

Purpose:

We hypothesized that clinical data from a neonatal intensive care unit (NICU) infant developmental follow-up clinic would identify early manifestations of autism spectrum disorder (ASD).

Methods:

One hundred forty-four infants were identified; 72 later diagnosed with ASD and 72 controls. Retrospective chart review provided data from the Test of Infant Motor Performance (TIMP) and the Bayley Scales of Infant and Toddler Development, third edition (Bayley-III), between 8 and 26 months of age.

Results:

Between-group comparisons indicated no significant group difference in TIMP scores; however, Bayley-III scaled scores differed between the groups at 2 administration times. The within-group Bayley-III change scores declined significantly more for the ASD group in cognitive and communication subtests.

Conclusion:

High-risk neonates, due to prematurity or morbidity, later diagnosed with ASD demonstrated statistically significant differences, including a more precipitous drop in Bayley-III scores over time. Early, longitudinal developmental surveillance for neonates at risk of ASD is critical. What this adds to the evidence: Early identification of ASD is critical to optimize developmental outcomes in young children, including infants born prematurely or with neonatal morbidity, who are perceived to have an increased risk for ASD. Despite these findings, minimal research has been conducted to evaluate the utility of commonly administered norm-referenced developmental surveillance instruments to identify possible early signs of ASD in this high-risk population due to prematurity or neonatal morbidity and not familial association. The present study analyzed retrospectively collected clinical data from a NICU developmental follow-up clinic for 144 infants, 72 of which were later diagnosed with ASD and 72 sex- and gestational age-matched controls. Results demonstrated statistically significant poorer Bayley-III outcomes for the ASD group compared with controls at 2 different study time points, including a more precipitous drop in Bayley-III scaled scores over time. This study highlights the importance of early and longitudinal developmental surveillance for high-risk neonates at risk of ASD.
TRAJECTORIES OF COGNITIVE AND MOTOR FUNCTIONAL INDEPENDENCE IN HISPANIC INDIVIDUALS DURING THE 10 YEARS AFTER TRAUMATIC BRAIN INJURY
Authors: Lasprilla Juan Carlos Arango , Watson Jack D. , Merced Kritzia , Mascialino Guido , Lequerica Anthony H. , Perrin Paul B.
Published: September 2022

Objective

This study examined demographic and injury-related predictors of cognitive and motor functional independence in Hispanics with TBI at years 1, 2, 5, and 10 after hospital discharge.

Design

Hispanic participants (n = 1,360) from the TBI Model Systems Study were included in if they had at least one Functional Independence Measure (FIM) Cognitive and Motor score at any time point (years 1, 2, 5, or 10). Hierarchical linear modeling was used to examine baseline predictors of FIM Cognitive and Motor trajectories across this time period.

Results

FIM Cognitive trajectories showed a quadratic movement (initial increase followed by a plateau or slight decrease), whereas FIM Motor trajectories showed a cubic movement (initial increase, followed by a plateau, then another increase). Higher FIM Cognitive trajectories were predicted by younger age, shorter length of posttraumatic amnesia (PTA), higher education, and having experienced a non-violent mechanism of injury. Higher FIM Motor trajectories were predicted by younger age, shorter PTA, and a non-violent mechanism of injury.

Conclusions

The baseline predictors of functional trajectories identified may help create tailored, evidence-based rehabilitation interventions along the continuum of recovery during the first 10 years for Hispanics with TBI at-risk for reduced functional outcomes.
Dissecting the mechanisms of environment sensitivity of smart probes for quantitative assessment of membrane properties
Authors: Ragaller Franziska , Andronico Luca , Sykora Jan , Kulig Waldemar , Rog Tomasz , Urem Yagmur Balim , Abhinav  , Danylchuk Dmytro I. , Hof Martin , Klymchenko Andrey , Amaro Mariana , Vattulainen Ilpo , Sezgin Erdinc
Published: September 2022

The plasma membrane, as a highly complex cell organelle, serves as a crucial platform for a multitude of cellular processes. Its collective biophysical properties are largely determined by the structural diversity of the different lipid species it accommodates. Therefore, a detailed investigation of biophysical properties of the plasma membrane is of utmost importance for a comprehensive understanding of biological processes occurring therein. During the past two decades, several environment-sensitive probes have been developed and become popular tools to investigate membrane properties. Although these probes are assumed to report on membrane order in similar ways, their individual mechanisms remain to be elucidated. In this study, using model membrane systems, we characterized the probes Pro12A, NR12S and NR12A in depth and examined their sensitivity to parameters with potential biological implications, such as the degree of lipid saturation, double bond position and configuration (
cis
versus
trans
), phospholipid headgroup and cholesterol content. Applying spectral imaging together with atomistic molecular dynamics simulations and time-dependent fluorescent shift analyses, we unravelled individual sensitivities of these probes to different biophysical properties, their distinct localizations and specific relaxation processes in membranes. Overall, Pro12A, NR12S and NR12A serve together as a toolbox with a wide range of applications allowing to select the most appropriate probe for each specific research question.
Does peer review improve the statistical content of manuscripts? A study on 27 467 submissions to four journals
Authors: Garcia-Costa Daniel , Forte Anabel , Lòpez-Iñesta Emilia , Squazzoni Flaminio , Grimaldo Francisco
Published: September 2022

Improving the methodological rigour and the quality of data analysis in manuscripts submitted to journals is key to ensure the validity of scientific claims. However, there is scant knowledge of how manuscripts change throughout the review process in academic journals. Here, we examined 27 467 manuscripts submitted to four journals from the Royal Society (2006–2017) and analysed the effect of peer review on the amount of statistical content of manuscripts, i.e. one of the most important aspects to assess the methodological rigour of manuscripts. We found that manuscripts with both initial low or high levels of statistical content increased their statistical content during peer review. The availability of guidelines on statistics in the review forms of journals was associated with an initial similarity of statistical content of manuscripts but did not have any relevant implications on manuscript change during peer review. We found that when reports were more concentrated on statistical content, there was a higher probability that these manuscripts were eventually rejected by editors.
Spatial heterogeneity affects predictions from early-curve fitting of pandemic outbreaks: a case study using population data from Denmark
Authors: Heltberg Mathias L. , Michelsen Christian , Martiny Emil S. , Christensen Lasse Engbo , Jensen Mogens H. , Halasa Tariq , Petersen Troels C.
Published: September 2022

The modelling of pandemics has become a critical aspect in modern society. Even though artificial intelligence can help the forecast, the implementation of ordinary differential equations which estimate the time development in the number of susceptible, (exposed), infected and recovered (SIR/SEIR) individuals is still important in order to understand the stage of the pandemic. These models are based on simplified assumptions which constitute approximations, but to what extent this are erroneous is not understood since many factors can affect the development. In this paper, we introduce an agent-based model including spatial clustering and heterogeneities in connectivity and infection strength. Based on Danish population data, we estimate how this impacts the early prediction of a pandemic and compare this to the long-term development. Our results show that early phase SEIR model predictions overestimate the peak number of infected and the equilibrium level by at least a factor of two. These results are robust to variations of parameters influencing connection distances and independent of the distribution of infection rates.
A mobile application to protect groundwater during unconventional oil and gas extraction
Authors: Worthmann Charissa , Esterhuyse Surina
Published: September 2022

Unconventional oil and gas (UOG) is an important energy source for many countries, but requires large quantities of water for its development, and may pollute water resources. Regulations are one of the main tools to achieve government policy on natural resource protection. South Africa, which is energy-constrained, but also water-scarce, is currently considering UOG extraction as an additional energy resource. UOG development could commence as soon as regulations to protect natural resources such as water have been published. Such regulations are, however, often not effectively enforced, which negatively affects the protection of water resources during UOG extraction. This study addresses these enforcement challenges in South Africa. It focuses on the science–society–policy interface by proposing a civic informatics platform to assist with on-the-ground enforcement of regulations via a mobile application. This mobile application aims to address both groundwater monitoring and management as well as UOG extraction operations in a single platform, to enable regulators to protect groundwater resources more effectively during UOG extraction, while simultaneously enhancing transparency in the UOG industry.
Oxidation of
l
-leucine amino acid initiated by hydroxyl radical: are transition metal ions an enhancement factor?
Authors: Truong Dinh Hieu , Ngo Thi Chinh , Nguyen Thi Huong Lan , Dao Duy Quang
Published: September 2022

Hydroxyl radical (HO·) formation initiated by the Fenton-type reactions of Fe and Cu complexes of
l
-leucine (Leu) amino acid as well as its oxidation reaction by HO· was computationally investigated by using the density functional theory method at the M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the aqueous phase. The results showed that dipole-salt is the main form of Leu in the physiological condition. Leu exhibits high chelating potential towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favourable coordinating positions at two oxygen atoms of the –COO functional group. Furthermore, the Leu-ions complexes show a high risk of HO· formation via Fenton-like reactions, especially when ascorbate anion exists in the environment as a reducing agent. Finally, the oxidation reaction of
l
-leucine by HO· demonstrated a relatively high overall apparent reaction rate,
k
overall
, being 1.18 × 10
9
M
−1
s
−1
, in which formal hydrogen transfer reactions of the dipole-salt form occur as the primary mechanism. Consequently, the Leu oxidation by HO· radical can be promoted by the Fenton reaction enhancement of its transition metal complexes.
Physical simulation of the influence of the original rock strength on the compaction characteristics of caving rock in longwall goaf
Authors: Qin Yan , Xu Nengxiong , Guo Yuxi , Li Jinyang , Han Wenbin
Published: September 2022

The compaction characteristics of broken rock in a caving zone have a significant impact on the movement law of overburden and the prediction of surface subsidence. The mechanical properties of the broken rock were clearly affected by the original rock strength of the roof. Based on the similarity theory, the ‘quartz sand-gypsum-lime-water’ mixed material was used to make similar samples of original rocks with different strengths, and the compaction mechanical behaviour of broken loose rock masses with different original rock strengths was studied. The results show that (i) the greater the original rock strength of broken rock, the shorter the initial compaction stage, the earlier the transition and stable compaction stages and the lower the degree of compaction; (ii) the initial deformation modulus and ultimate axial strain had a linear relationship with the original strength of the broken rock; and (iii) under different axial pressures, the deformation modulus increased with the increasing original rock strength of the broken rock. The tangent modulus and axial stress change approximately linearly, the secant modulus and stress change linearly, and the tangent modulus and secant modulus exhibit an exponential/hyperbolic relationship with the strain. The research results have high engineering application value for using numerical method to predict the mechanical behaviour of roof rock mass with different strength in coal mining and analysing the surface subsidence.
The phenotypic plasticity of an evolving digital organism
Authors: Fortuna Miguel A.
Published: September 2022

Climate change will fundamentally reshape life on Earth in the coming decades. Therefore, understanding the extent to which species will cope with rising temperatures is of paramount importance. Phenotypic plasticity is the ability of an organism to change the morphological and functional traits encoded by its genome in response to the environment. I show here that plasticity pervades not only natural but also artificial systems that mimic the developmental process of biological organisms, such as self-replicating and evolving computer programs—digital organisms. Specifically, the environment can modify the sequence of instructions executed from a digital organism’s genome (i.e. its transcriptome), which results in changes in its phenotype (i.e. the ability of the digital organism to perform Boolean logic operations). This genetic-based pathway for plasticity comes at a fitness cost to an organism’s viability and generation time: the longer the transcriptome (higher fitness cost), the more chances for the environment to modify the genetic execution flow control, and the higher the likelihood for the genome to encode novel phenotypes. By studying to what extent a digital organism’s phenotype is influenced by both its genome and the environment, I make a parallelism between natural and artificial evolving systems on how natural selection might slide trait regulation anywhere along a continuum from total environmental control to total genomic control, which harbours lessons not only for designing evolvable artificial systems, but also for synthetic biology.
Environmental memory gained from exposure to extreme pCO2variability promotes coral cellular acid–base homeostasis
Authors: Brown Kristen T. , Mello-Athayde Matheus A. , Sampayo Eugenia M. , Chai Aaron , Dove Sophie , Barott Katie L.
Published: September 2022

Ocean acidification is a growing threat to coral growth and the accretion of coral reef ecosystems. Corals inhabiting environments that already endure extreme diel pCO2fluctuations, however, may represent acidification-resilient populations capable of persisting on future reefs. Here, we examined the impact of pCO2variability on the reef-building coralPocillopora damicornisoriginating from reefs with contrasting environmental histories (variable reef flat versus stable reef slope) following reciprocal exposure to stable (218 ± 9) or variable (911 ± 31) diel pCO2amplitude (μtam) in aquaria over eight weeks. Endosymbiont density, photosynthesis and net calcification rates differed between origins but not treatment, whereas primary calcification (extension) was affected by both origin and acclimatization to novel pCO2conditions. At the cellular level, corals from the variable reef flat exhibited less intracellular pH (pHi) acidosis and faster pHi recovery rates in response to experimental acidification stress (pH 7.40) than corals originating from the stable reef slope, suggesting environmental memory gained from lifelong exposure to pCO2variability led to an improved ability to regulate acid–base homeostasis. These results highlight the role of cellular processes in maintaining acidification resilience and suggest that prior exposure to pCO2variability may promote more acidification-resilient coral populations in a changing climate.
Assessment of microbial contamination in laser materials processing laboratories used for prototyping of biomedical concepts
Authors: Somorin Yinka M. , O'Connor Gerard M.
Published: September 2022

Microbial contamination of medical devices during pilot production can be a significant barrier as the laboratory environment is a source of contamination. There is limited information on microbial contaminants in laser laboratories and environments involved in the pilot production of medical devices. This study aimed to determine the bioburden and microbial contaminants present in three laser laboratories - an ISO Class 7 clean room, a pilot line facility, and a standard laser laboratory. Microbiological air sampling was by passive air sampling using settle plates and the identity of isolates was confirmed by DNA sequencing. Particulate matter was analysed using a portable optical particle counter. Twenty bacterial and 16 fungal genera were isolated with Staphylococcus and Micrococcus being the predominant genera. Most isolates are associated with skin, mouth, or upper respiratory tract. There was no significant correlation between microbial count and PM 2.5 concentration in the three laboratories. There is low level but diverse microbial population in laser-processing environments. These results provide data that will be useful for developing a contamination control plan for controlling microbial contamination and facilitating advanced manufacturing of laser-based pilot production of medical devices.
Qualities of rice-based home meal replacement products upon
microwave cooking
Authors: Seong Gi-Un , Kim Yu Mi , Cho Jun-Hyeon , Lee Ji-Yoon , Lee Sais-Beul , Shin Dongjin , Park Dong-Soo , Youn Kwang-Sup , Kang Ju-Won
Published: September 2022

The physicochemical characteristics of five types of rice-based home meal
replacement (HMR) products (instant rice, doshirak,
kimbab, frozen fried rice, and freeze-dried rice) were
measured before and after microwave cooking, and principal component analysis
(PCA) was performed. HMR products contained grains from 8.42 to 8.72 mm before
and after the microwave cooking. The amylose content and water absorption index
(WAI) ranged from 20.10-23.15% and 0.50-2.87%, respectively.
Frozen fried rice showed high amylose content but low WAI, and dry rice showed
low amylose content but high WAI. There was a change in the moisture content of
freeze-dried rice: moisture increased from 1.3 to 60.3% after cooking.
The rehydration rate of freeze-dried rice was about twice higher than that of
other HMR products, while instant rice showed a low rehydration rate. The
texture profile's hardness and cohesiveness respectively were 306.1
g/cm2 and 47.9% before cooking, but 209.6 g/cm2
and 66.0% after cooking. The lightness value decreased from 72.5 to 68.9
after the microwave cooking, while there was little change in the lightness
value of instant rice, and that of the frozen fried rice decreased. PCA revealed
that, microwave cooking apparently affected WAI and rehydration rate in the
freeze-dried rice yellowness in the frozen fried rice, and stickiness and
lightness in the instant rice, respectively.
Strategy for reduction of microorganisms during rice cakes
manufacturing process
Authors: Han Sangha , Kim Kyeongjun , Park Jun-Ha , Byun Kye-Hwan , Choi Song-yi , Ha Sang-Do
Published: September 2022

This study was conducted to establish effective reduction strategy during the
manufacturing process of rice cakes. Simple washing (3 times) and ultrasonic
washing (40 kHz, 10 min) were used in the rice washing process, and sodium
hypochlorite (100 ppm, 5 min) and chlorine dioxide (20 ppm, 5 min) were used as
chemical disinfectants. Combination treatment using ultrasonic washing and the
two chemical disinfectants was also performed. The chemical disinfectants were
more effective than the ultrasonic cleaning in a single treatment of each
method, and sodium hypochlorite showed a greater reduction effect than chlorine
dioxide. The combination treatment using both chemical disinfectant and
ultrasonic cleaning was found to be more effective than using a single
treatment, and no significant difference was observed in the results based on
the disinfectant used. During the heating process, which is an important control
point of HACCP system, total aerobic bacteria, coliforms, Bacillus
cereus and Escherichia coli were inactivated. UV
sterilization (30 min, 60 min) was applied as the nonthermal treatment and
compared with the general drying method (5, 12 h) during the cooling process of
rice cakes. No bacteria were not found after the treatment, whereas the total
number of bacteria in the naturally dried rice cakes increased after 12 h,
indicating the potential of UV sterilization as an important control point
during the cooling process of rice cakes.
Identification of growth characteristics and physiological
functionality of useful fungi from nuruk
Authors: Jeong Woo Soo , Lee Su Jeong , Kim So-Young , Yeo Soo-Hwan
Published: September 2022

Fungi were isolated and identified from nuruk produced in six
regions, and the growth characteristics and various physiological functions of
the five selected strains were investigated. These fungi exhibited optimum
growth characteristics at 28-35°C and pH 5, and were acid resistant. The
antibacterial activity of the five fungi against four types of harmful bacteria
was determined using Salmonella typhimurium (57.9-71.4%)
and Staphylococus aureus (57.5-70.0%), respectively. The
antihypertensive activity showed ACE inhibitory activity of 98.9-99.6%
and relatively high thrombolytic activity of 84.7-91.9%, compared to the
positive control. The antidiabetic effect of five strains of the fungus showed
α-amyloglucosidase inhibitory activity ranging from
20.4 to 26.6% of 0.5% acarbose. The fungi (Lichtheimia
ramosa KJ-WF, Aspergillus oryzae SU-Y, and
Lichtheimia panacisoli SU-BF) were confirmed to reduce the
production of two or more types of cytokines by treating Raw 264.7 cells with
LPS. In particular, Lichtheimia panacisoli SU-BF exhibited the
best anti-inflammatory effect. Therefore, the five strains of fungus showed
potential to be used as a functional material in food manufacturing and
pharmaceuticals industries.
Coarse-scale Optoretinography(CoORG) with extended field-of-view for normative characterization
Authors: Jiang Xiaoyun , Liu Teng , Pandiyan Vimal Prabhu , Slezak Emily , Sabesan Ramkumar
Published: September 2022

Optoretinography (ORG) has the potential to be an effective biomarker for light-evoked retinal activity owing to its sensitive, objective, and precise localization of retinal function and dysfunction. Many ORG implementations have used adaptive optics (AO) to localize activity on a cellular scale. However, the use of AO restricts field-of-view (FOV) to the isoplanatic angle, necessitating the montaging of multiple regions-of-interest to cover an extended field. In addition, subjects with lens opacities, increased eye movements and decreased mobility pose challenges for effective AO operation. Here, we developed a coarse-scale ORG (CoORG) system without AO, which accommodates FOVs up to 5.5 deg. in a single acquisition. The system is based on a line-scan spectral domain OCT with volume rates of up to 32 Hz (16,000 B-frames per second). For acquiring ORGs, 5.5 deg. wide OCT volumes were recorded after dark adaptation and two different stimulus bleaches. The stimulus-evoked optical phase change was calculated from the reflections encasing the cone outer segments and its variation was assessed vs. eccentricity in 12 healthy subjects. The general behavior of ΔOPL vs. time mimicked published reports. High trial-to-trial repeatability was observed across subjects and with eccentricity. Comparison of ORG between CoORG and AO-OCT based ORG at 1.5°, 2.5°, and 3.5° eccentricity showed an excellent agreement in the same 2 subjects. The amplitude of the ORG response decreased with increasing eccentricity. The variation of ORG characteristics between subjects and versus eccentricity was well explained by the photon density of the stimulus on the retina and the outer segment length. Overall, the high repeatability and rapid acquisition over an extended field enabled the normative characterization of the cone ORG response in healthy eyes, and provides a promising avenue for translating ORG for widespread clinical application.