bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying biomarkers of the gut bacteria, bacteriophages and serum metabolites associated with three weaning periods in piglets
Authors: Xiong Xinwei , Liu Xianxian , Wang Zhangfeng , Xu Qiao , Xu Jiguo , Rao Yousheng
Published: March 2022

Background

The establishment of the piglet gut microbiome has a prolonged influence on host health, as it sets the stage for establishment of the adult swine microbiome. Substantial changes in host metabolism and immunity around the time of weaning may be accompanied by alterations in the gut microbiome. In this study, we systematically evaluated differences in the gut microbiome and host metabolites among three weaning periods using shotgun metagenomic sequencing and untargeted metabolomic profiling in piglets.

Results

We identified that P. copri was the most significantly different species among three weaning periods, and was the key bacterial species for mitigating piglet adaptation during the weaning transition, while Bacillus_phage_BCD7, the only differential bacteriophages, was significantly and positively correlated with P. copri enriched in day 28 group. Additionally, P. copri and Bacillus_phage_BCD7 was significantly correlated with the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, the altered metabolites we observed were enriched in pathways matched to the functional capacity of the gut microbiome e.g., aminoacyl-tRNA biosynthesis.

Conclusion

The results from this study indicate that the bacteria-phage interactions and host-microbial interactions during the weaning transition impact host metabolism, leading to beneficial host changes among three weaning periods.
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients
Authors: Cui Jiaxing , Hou Siyu , Liu Bing , Yang Mingran , Wei Lai , Du Shiyu , Li Shao
Published: March 2022

Background

In traditional Chinese medicine, it is believed that the “tongue coating is produced by fumigation of stomach gas”, and that tongue coating can reflect the health status of humans, especially stomach health. Therefore, studying the relationship between the microbiome of the tongue coating and the gastric fluid is of great significance for understanding the biological basis of tongue diagnosis.

Methods

This paper detected the microbiomes of the tongue coating and the gastric fluid in 35 gastritis patients using metagenomic sequencing technology, systematically constructed the microbial atlas of tongue coating and gastric juice, and first described the similar characteristics between the two sites.

Results

There was a significant correlation between tongue coating and gastric juice in terms of microbial species composition and overall diversity. In terms of species composition, it was found that the two sites were dominated by five phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, and that most of the gastric microbial species could be detected from the patient's own tongue coating. In terms of overall diversity, a significant correlation was found between the alpha diversity of the tongue coating microbiome and the gastric juice microbiome. Furthermore, in terms of abundance, 4 classes, 2 orders, 4 families, 18 genera and 46 species were found to significantly correlate between the tongue coating and the gastric fluid.

Conclusions

The results provide microbiome-based scientific evidence for tongue diagnosis, and offer a new perspective for understanding the biological basis of tongue diagnosis.
Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures
Authors: Leong Alyssa Zi-Xin , Lee Pey Yee , Mohtar M. Aiman , Syafruddin Saiful Effendi , Pung Yuh-Fen , Low Teck Yew
Published: March 2022

A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), which unveiled sORF-based transcripts at various genome locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated by experimental evidence initially. With recent advancements in multi-omics, the identification, validation, and functional characterisation of sORFs and microproteins have become feasible. In this review, we discuss the history and development of an emerging research field of sORFs and microproteins. In particular, we focus on an array of bioinformatics and OMICS approaches used for predicting, sequencing, validating, and characterizing these recently discovered entities. These strategies include RIBO-Seq which detects sORF transcripts via ribosome footprints, and mass spectrometry (MS)-based proteomics for sequencing the resultant microproteins. Subsequently, our discussion extends to the functional characterisation of microproteins by incorporating CRISPR/Cas9 screen and protein–protein interaction (PPI) studies. Our review discusses not only detection methodologies, but we also highlight on the challenges and potential solutions in identifying and validating sORFs and their microproteins. The novelty of this review lies within its validation for the functional role of microproteins, which could contribute towards the future landscape of microproteomics.
Analysis of factors affecting medical personnel seeking employment at primary health care institutions: developing human resources for primary health care
Authors: Jia Huanhuan , Yu Xihe , Jiang Hairui , Yu Jianxing , Cao Peng , Gao Shang , Shang Panpan , Qiang Bayuzhen
Published: March 2022

Background

The serious shortage of human resources for primary health care (PHC) is a common issue in health reforms worldwide. China has proposed that it is an effective way to encourage and guide qualified medical personnel to work in primary health care institutions (PHCIs). However, few studies have been conducted on the willingness and influencing factors of medical personnel to seek employment at PHCIs.

Methods

Based on implicit theory and lexical approach, pre-investigation was conducted to collect the items that influence the medical personnel to seek employment at PHCIs from the perspective of guided objects. Through a three-phase investigation of 1160 doctors in 29 public hospitals in 9 cities, the items were categorized, and a structural equation model was established and verified to explore the interrelationship of influencing factors.

Results

A total of 6 factors were rotated, including Sense of Gain (SG), Internal Organization Development (IOD), Remuneration and Development (RD), Condition of the City Where the PHCI Is Located (CCPL), Job Responsibilities (JR) and Family Support (FS). The results of the model showed that IOD, RD, JR and FS had a significantly positive effect on the SG. In addition, the FS, RD and JR significantly mediated the relationship between the internal and external environment of PHCIs and SG. The values of the fit index indicated an acceptable-fitting model.

Conclusion

Family, remuneration, individual development, and job responsibility are closely related to the willingness of medical personnel to seek employment at PHCIs, and the internal and external environment of PHCIs is also an important factor. Therefore, the development of PHC providers can be promoted by paying attention to the family members of medical personnel, establishing a reasonable remuneration system, providing suitable development opportunities, arranging work rationally and improving the internal construction of PHCIs.
Dual effect of TAT functionalized DHAH lipid nanoparticles with neurotrophic factors in human BBB and microglia cultures
Authors: Hernando Sara , Nikolakopoulou Polyxeni , Voulgaris Dimitrios , Hernandez Rosa Maria , Igartua Manoli , Herland Anna
Published: March 2022

Background

Neurodegenerative diseases (NDs) are an accelerating global health problem. Nevertheless, the stronghold of the brain- the blood–brain barrier (BBB) prevents drug penetrance and dwindles effective treatments. Therefore, it is crucial to identify Trojan horse-like drug carriers that can effectively cross the blood–brain barrier and reach the brain tissue. We have previously developed polyunsaturated fatty acids (PUFA)-based nanostructured lipid carriers (NLC), namely DHAH-NLC. These carriers are modulated with BBB-permeating compounds such as chitosan (CS) and trans-activating transcriptional activator (TAT) from HIV-1 that can entrap neurotrophic factors (NTF) serving as nanocarriers for NDs treatment. Moreover, microglia are suggested as a key causative factor of the undergoing neuroinflammation of NDs. In this work, we used in vitro models to investigate whether DHAH-NLCs can enter the brain via the BBB and investigate the therapeutic effect of NTF-containing DHAH-NLC and DHAH-NLC itself on lipopolysaccharide-challenged microglia.

Methods

We employed human induced pluripotent stem cell-derived brain microvascular endothelial cells (BMECs) to capitalize on the in vivo-like TEER of this BBB model and quantitatively assessed the permeability of DHAH-NLCs. We also used the HMC3 microglia cell line to assess the therapeutic effect of NTF-containing DHAH-NLC upon LPS challenge.

Results

TAT-functionalized DHAH-NLCs successfully crossed the in vitro BBB model, which exhibited high transendothelial electrical resistance (TEER) values (≈3000 Ω*cm2). Specifically, the TAT-functionalized DHAH-NLCs showed a permeability of up to 0.4% of the dose. Furthermore, using human microglia (HMC3), we demonstrate that DHAH-NLCs successfully counteracted the inflammatory response in our cultures after LPS challenge. Moreover, the encapsulation of glial cell-derived neurotrophic factor (GNDF)-containing DHAH-NLCs (DHAH-NLC-GNDF) activated the Nrf2/HO-1 pathway, suggesting the triggering of the endogenous anti-oxidative system present in microglia.

Conclusions

Overall, this work shows that the TAT-functionalized DHAH-NLCs can cross the BBB, modulate immune responses, and serve as cargo carriers for growth factors; thus, constituting an attractive and promising novel drug delivery approach for the transport of therapeutics through the BBB into the brain.
The necessity of abdominal drainage for patients with complicated appendicitis undergoing laparoscopic appendectomy: a retrospective cohort study
Authors: Liao Yu-Tso , Huang John , Wu Chia-Tung , Chen Pei-Chen , Hsieh Tsung-Ting , Lai Feipei , Chen Tzu-Chun , Liang Jin-Tung
Published: March 2022

Background

This study aimed to evaluate the necessity of abdominal drainage after laparoscopic appendectomy in patients with complicated appendicitis.

Methods

Patients with acute appendicitis undergoing laparoscopic appendectomy at two hospitals between January 2014 and December 2018 were retrospectively included. Complicated appendicitis was defined as the American Association for the Surgery of Trauma (AAST) grade ≥ II. The patients were classified according to the AAST grade and the indwelling of abdominal drainage. The postoperative surgical outcomes and recovery were compared among patient groups to evaluate the impact of abdominal drainage for patients with complicated appendicitis undergoing laparoscopic appendectomy.

Results

A total of 1241 patients was retrospectively included. Among them, there were 820 patients with simple appendicitis (AAST grade I) and 421 patients with complicated appendicitis (AAST grade ≥ II). For complicated appendicitis, the drainage group (N = 192) tended to harbor more overall complications, intra-abdominal abscess formation, time to resume a soft diet, and the postoperative length of hospitalization (P = 0.0000 for all). Multivariate logistic regression confirmed that abdominal drainage increased the risk of overall complications [Odds ratio (OR) 2.439; 95% confidence interval (CI) 1.597–3.726; P ≤ 0.0001] and failed to decrease the risk of intra-abdominal abscess formation (OR 1.655; 95% CI 0.487–5.616; P = 0.4193). Multivariate linear regression analysis also showed that the drainage group harbored longer postoperative length of hospitalization (Coefficients: 20.697; 95% CI 15.251–26.143; P < 0.0001) and time to resume a soft diet (Coefficients: 45.899; 95% CI 34.502–57.297; P < 0.0001).

Conclusions

Abdominal drainage did not prevent overall complications in patients with complicated appendicitis; paradoxically, it delayed the convalescence. Our results discourage the routine use of abdominal drainage and suggest that abdominal drainage should be performed sparingly.
Attitudes about use of preoperative risk assessment tools: a survey of surgeons and surgical residents in an academic health system
Authors: Pradhan Nisha , Dyas Adam R. , Bronsert Michael R. , Lambert-Kerzner Anne , Henderson William G. , Qiu Howe , Colborn Kathryn L. , Mason Nicholas J. , Meguid Robert A.
Published: March 2022

Background

Formal surgical risk assessment tools have been developed to predict risk of adverse postoperative patient outcomes. Such tools accurately predict common postoperative complications, inform patients and providers of likely perioperative outcomes, guide decision making, and improve patient care. However, these are underutilized. We studied the attitudes towards and techniques of how surgeons preoperatively assess risk.

Methods

Surgeons at a large academic tertiary referral hospital and affiliate community hospitals were emailed a 16-question survey via REDCap (Research Electronic Data Capture) between 8/2019-6/2020. Reminder emails were sent once weekly for three weeks. All completed surveys by surgical residents and attendings were included; incomplete surveys were excluded. Surveys were analyzed using descriptive statistics (frequency distributions and percentages for categorical variables, means, and standard deviations for continuous variables), and Fisher’s exact test and unpaired t-tests comparing responses by surgical attendings vs. residents.

Results

A total of 108 surgical faculty, 95 surgical residents, and 58 affiliate surgeons were emailed the survey. Overall response rates were 50.0% for faculty surgeons, 47.4% for residents, and 36.2% for affiliate surgeons. Only 20.8% of surgeons used risk calculators most or all of the time. Attending surgeons were more likely to use prior experience and current literature while residents used risk calculators more frequently. Risk assessment tools were more likely to be used when predicting major complications and death in older patients with significant risk factors. Greatest barriers for use of risk assessment tools included time, inaccessibility, and trust in accuracy.

Conclusions

A small percentage of surgeons use surgical risk calculators as part of their routine practice. Time, inaccessibility, and trust in accuracy were the most significant barriers to use.
Potential of using surface temperature data to benchmark Sentinel-2-based forest phenometrics in boreal Finland
Authors: Majasalmi Titta , Rautiainen Miina
Published: March 2022

Key message

We present a new approach to calibrate timings of phenological events from satellite data (e.g., Sentinel-2 MSI data) with readily available surface temperature data. The new approach improves the estimation of growing season length in boreal forests.

Context

Satellite data is used to calibrate phenology models employed in land surface model components of climate models. However, realistic quantification of forest phenological transitions, such as the greenup and senescence, across large spatial scales remains challenging due to the lack of sufficient ground validation data representative of both forest tree canopy and forest understory species compositions.

Aims

The aim of this study was to develop a new approach to benchmark boreal forest land surface phenology obtained from Sentinel-2 (S2) against surface temperature data.

Methods

We computed S2 phenological transition dates and compared them to ground reference data on temperature from a network of meteorological stations across Finland (60–70N°).

Results

Our results showed that applying standard phenometrics directly to S2 data to estimate the growing season length in boreal forests may lead to clear biases in all species groups.

Conclusion

Our approach to use temperature data to calibrate boreal forest phenometrics allows flexible application across spatial scales (i.e., point or grid) and different satellite sensors. It can be combined with any vegetation land cover product to provide a link between surface temperature data and forest seasonal reflectance properties.
Longitudinal study of the mcr-1 gene prevalence in Spanish food-producing pigs from 1998 to 2021 and its relationship with the use of polymyxins
Authors: Miguela-Villoldo Pedro , Moreno Miguel A. , Rodríguez-Lázaro David , Gallardo Alejandro , Hernández Marta , Serrano Tania , Sáez José L. , de Frutos Cristina , Agüero Montserrat , Quesada Alberto , Domínguez Lucas , Ugarte-Ruiz María
Published: March 2022

Background

Resistance to colistin was an uncommon phenomenon traditionally linked to chromosome point mutations, but since the first description of a plasmid-mediated colistin-resistance in late 2015, transmissible resistance to colistin has become a Public Health concern. Despite colistin is considered as a human last resort antibiotic, it has been commonly used in swine industry to treat post-weaning diarrhoea in piglets. However, the progressively increase of colistin resistance during the last decade led to the Spanish Medicines and Healthcare Products Agency (AEMPS) to launch a strategic and voluntary plan aimed to reduce colistin consumption in pig production. Our longitudinal study (1998–2021) aimed to evaluate the trend of colistin resistance mediated through the mcr-1 mobile gene in Spanish food-producing pig population and compare it with published polymyxin sales data in veterinary medicine to assess their possible relationships.

Results

The first mcr-1 positive sample was observed in 2004, as all samples from 1998 and 2002 were mcr-1 PCR-negative. We observed a progressive increase of positive samples from 2004 to 2015, when mcr-1 detection reached its maximum peak (33/50; 66%). From 2017 (27/50; 54%) to 2021 (14/81; 17%) the trend became downward, reaching percentages significantly lower than the 2015 peak (p < 0.001). The abundance of mcr-1 gene in PCR-positive samples showed a similar trend reaching the highest levels in 2015 (median: 6.6 × 104mcr-1 copies/mg of faeces), but decreased significantly from 2017 to 2019 (median 2.7 × 104, 1.2 × 103, 4.6 × 102mcr-1 copies/mg of faeces for 2017, 2018 and 2019, respectively), and stabilizing in 2021 (1.6 × 102mcr-1 copies/mg of faeces) with similar values than 2019.

Conclusions

Our study showed the decreasing trend of colistin resistance associated to mcr-1 gene, after a previous increase from among 2004–2015, since the European Medicines Agency and AEMPS strategies were applied in 2016 to reduce colistin use in animals, suggesting a connection between polymyxin use and colistin resistance. Thus, these plans could have been effective in mcr-1 reduction, reaching lower levels than those detected in samples collected 17 years ago, when resistance to colistin was not yet a major concern.
Adverse Cardiovascular Complications following prescription of programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors: a propensity-score matched Cohort Study with competing risk analysis
Authors: Zhou Jiandong , Lee Sharen , Lakhani Ishan , Yang Lei , Liu Tong , Zhang Yuhui , Xia Yunlong , Wong Wing Tak , Bao Kelvin King Hei , Wong Ian Chi Kei , Tse Gary , Zhang Qingpeng
Published: March 2022

Background

Programmed death-1 (PD-1) and programmed death- ligand 1 (PD-L1) inhibitors, such as pembrolizumab, nivolumab and atezolizumab, are major classes of immune checkpoint inhibitors that are increasingly used for cancer treatment. However, their use is associated with adverse cardiovascular events. We examined the incidence of new-onset cardiac complications in patients receiving PD-1 or PD-L1 inhibitors.

Methods

Patients receiving PD-1 or PD-L1 inhibitors since their launch up to 31st December 2019 at publicly funded hospitals of Hong Kong, China, without pre-existing cardiac complications were included. The primary outcome was a composite of incident heart failure, acute myocardial infarction, atrial fibrillation, or atrial flutter with the last follow-up date of 31st December 2020. Propensity score matching between PD-L1 inhibitor use and PD-1 inhibitor use with a 1:2 ratio for patient demographics, past comorbidities and non-PD-1/PD-L1 medications was performed with nearest neighbour search strategy (0.1 caliper). Univariable and multivariable Cox regression analysis models were conducted. Competing risks models and multiple propensity matching approaches were considered for sensitivity analysis.

Results

A total of 1959 patients were included. Over a median follow-up of 247 days (interquartile range [IQR]: 72-506), 320 (incidence rate [IR]: 16.31%) patients met the primary outcome after PD-1/PD-L1 treatment: 244 (IR: 12.57%) with heart failure, 38 (IR: 1.93%) with acute myocardial infarction, 54 (IR: 2.75%) with atrial fibrillation, 6 (IR: 0.31%) with atrial flutter. Compared with PD-1 inhibitor treatment, PD-L1 inhibitor treatment was significantly associated with lower risks of the composite outcome both before (hazard ratio [HR]: 0.32, 95% CI: [0.18-0.59], P value=0.0002) and after matching (HR: 0.34, 95% CI: [0.18-0.65], P value=0.001), and lower all-cause mortality risks before matching (HR: 0.77, 95% CI: [0.64-0.93], P value=0.0078) and after matching (HR: 0.80, 95% CI: [0.65-1.00], P value=0.0463). Patients who developed cardiac complications had shorter average readmission intervals and a higher number of hospitalizations after treatment with PD-1/PD-L1 inhibitors in both the unmatched and matched cohorts (P value<0.0001). Multivariable Cox regression models, competing risk analysis with cause-specific and subdistribution hazard models, and multiple propensity approaches confirmed these observations.

Conclusions

Compared with PD-1 treatment, PD-L1 treatment was significantly associated with lower risk of new onset cardiac complications and all-cause mortality both before and after propensity score matching.
Massively parallel sequencing of Cannabis sativa chloroplast hotspots for forensic typing
Authors: Roman Madeline G. , Gutierrez Ryan , Houston Rachel
Published: March 2022

Background

Marijuana (Cannabis sativa) is the most commonly used illicit drug in the USA, and the use of DNA barcodes could assist drug trafficking investigations by indicating the biogeographical origin and crop type of a sample and providing a means for linking cases. Additionally, the legality of marijuana in the USA remains complicated with some states fully legalizing marijuana for recreational use while federally marijuana remains completely illegal. Massively parallel sequencing (MPS) offers distinct advantages over capillary electrophoresis (CE), including more comprehensive coverage of target loci, analysis of hundreds of markers simultaneously, and high throughput capabilities.

Methods

This study reports on the development of a MiSeq FGx® assay targeting seven “hotspot” regions in the Cannabis sativa chloroplast genome that are highly polymorphic and informative in attempts to determine biogeographical origin and distinguishing between marijuana and hemp. Sequencing results were compared to previous studies that used CE-based genotyping methods.

Results

A total of 49 polymorphisms were observed, 16 of which have not been previously reported. Additionally, sequence data revealed isoalleles at one locus, which were able to differentiate two samples that had the same haplotype using CE-based methods. This study reports preliminary results from sequencing 14 hemp and marijuana samples from different countries using the developed MPS assay.

Conclusion

Future studies should genotype a more comprehensive sample set from around the world to build a haplotype database, which could be used to provide investigative leads for law enforcement agencies investigating marijuana trafficking.
Methyltransferase-like 3 gene (METTL3) expression and prognostic impact in acute myeloid leukemia patients
Authors: Nagy Reham Mohamed , Mohamed Amal Abd El Hamid , El-Gamal Rasha Abd El-Rahman , Ibrahim Shereen Abdel Monem , Pessar Shaimaa Abdelmalik
Published: March 2022

Background

DNA methylation is involved in pathogenesis of acute myeloid leukemia (AML). N6-methyladenosine (m6A) modification of mRNA, mediated by methyltransferase-like 3 (METTL3), is one of the well-identified mRNA modifiers associated with the pathogenesis of AML. High level ofMETTL3mRNA is detected in AML cells, thus can be a potential target therapy for AML. This is a preliminary study that aimed at measuringMETTL3mRNA expression level in de novo AML patients and correlating it with clinicopathological, laboratory and prognostic markers.METTL3expression was analyzed by quantitative reverse transcription polymerase chain reaction in 40 newly diagnosed AML adults and was re-measured in the 2nd month of chemotherapy. Patients were followed up for periods up to 6 months post-induction therapy.

Results

METTL3expression was found to be significantly upregulated in AML patients compared to control subjects (p < 0.001).METTL3gene was significantly expressed among non-responders compared to responders (p < 0.001). A cutoff value was assigned for normalizedMETTL3values to categorize AML patients according to response to therapy. Statistically significant association was observed between high pretreatment normalizedMETTL3gene level and failure to attain complete remission at 2nd, 4th and 6th month following therapy (p = 0.01, 0.02 and 0.003, respectively).However, insignificant correlation was found between pretreatment normalizedMETTL3gene level and event free survival or clinicopathological prognostic factors.

Conclusion

METTL3is overexpressed in AML patients and is associated with adverse prognostic effect and failure to attain hematological remission within 6 months post-induction therapy.
Correlation between chest CT severity scoring system with oxygen saturation and laboratory inflammatory markers in adult patients with COVID-19 infection
Authors: Abd El Megid Ahmed Gamil Ibrahim , El Shabrawy Mohamed , Abdalla Ahmed Abd El-Hamid Mohamed
Published: March 2022

Background

COVID-19 pneumonia is responsible for the latest pandemics. Chest computed tomography (CT) scan is known to be an essential tool for diagnosis of COVID-19. In this research, the relationship between on-admission chest CT severity score, capillary blood oxygen saturation level, and laboratory inflammatory markers results in patients with SARS-COV-2 pneumonia was investigated.

Methods

This prospective analytical study was conducted in COVID-19 isolation unit, Zagazig University Hospitals, from 1st to end of April 2021. Adult patients with COVID-19 infection were included. Chest CT scan was performed for all patients, and CT severity score was computed. The initial capillary oxygen saturation was also assessed at the time of admission. The information was gathered and analyzed.

Results

A total number of 305 COVID-19 patients were involved in the study with the following data: age, gender, presence of co morbidities, capillary blood oxygen saturation, laboratory tests including absolute lymphocytic count, CRP, D-dimer and ferritin levels, as well as chest CT severity score. Based on chest CT severity score, we found that 110 cases (36.1%) were mild, 163 cases (53.4%) were moderate, and 32 cases (10.5%) were severe, with significant male predominance among moderate and severe cases. The initial measurements of blood oxygen saturation values revealed that mean blood oxygen saturation was 95.6% among mild to moderate cases and 85.4% among severe cases. Furthermore, there was a high statistically significant negative correlation between chest CT severity score and absolute lymphocytic count of studied cases, while there was a statistically significant positive correlation with D-dimer, CRP and ferritin levels.

Conclusions

CT scans can help clinicians in developing a management strategy and serve as a predictor of illness severity and possible outcomes. In individuals with COVID-19 infection, the severity of a chest CT scan is positively correlated to inflammatory markers and oxygen demand.
Automated fault detection in the Arabian Basin
Authors: Alohali Ruaa , Alzubaidi Fatimah , van Kranendonk Martin , Clark Stuart
Published: March 2022

In recent years, there has been a rapid development of the computer-aided interpretation of seismic data to reduce the otherwise intensive manual labor. A variety of seed detection algorithms for horizon and fault identification are integrated into popular seismic software packages. Recently, there has been an increasing focus on using neural networks for fully automatic fault detection without manually seeding each fault. These networks are usually trained with synthetic fault data sets. These data sets can be used across multiple seismic data sets; however, they are not as accurate as real seismic data, particularly in structurally complex regions associated with several generations of faults. The approach taken here is to combine the accuracy of manual fault identification in certain parts of the data set with a convolutional neural network that can then sweep through the entire data set to identify faults. We have implemented our method using 3D seismic data acquired from the Arabian Basin in Saudi Arabia covering an area of 1051 km2. The network is trained, validated, and tested with samples that included a seismic cube and fault images that are labeled manually corresponding to the seismic cube. The model successfully identifies faults with an accuracy of 96% and an error rate of 0.12 on the training data set. To achieve a robust model, we further enhance the prediction results using postprocessing by linking discontinued segments of the same fault line, thus reducing the number of detected faults. The postprocessing improves the prediction results from the test data set by 77.5%. In addition, we introduce an efficient framework to correlate the predictions and the ground truth by measuring their average distance value. Furthermore, tests using this approach also have been conducted on the F3 Netherlands survey with complex fault geometries and find promising results. As a result, fault detection and diagnosis are achieved efficiently with structures similar to the trained data set.
Evaluating Quality Indicators of Glioblastoma Care: Audit Results From an Indian Tertiary Care Cancer Center
Authors: Basu Achari Rimpa , Chakraborty Santam , Goyal Love , Saha Saheli , Roy Paromita , Zameer Lateef , Mishra Deepak , Parihar Mayur , Das Anirban , Chandra Aditi , Biswas Bivas , Mallick Indranil , Arunsingh Moses A. , Chatterjee Sanjoy , Bhattacharyya Tapesh
Published: March 2022

PURPOSE

There are limited reports of quality metrics in glioblastoma. We audited our adherence to quality indicators as proposed in the PRIME Quality Improvement study.

METHODS

This is a retrospective audit of patients treated between 2017 and 2020. After postsurgical integrated diagnosis, patients received radiotherapy (RT) with concurrent and adjuvant temozolomide (TMZ). Multiparametric magnetic resonance imaging at predefined times guided management. Numbers with proportions for indices were calculated. Survival was estimated using the Kaplan-Meier method.

RESULTS

One hundred six patients were consecutively treated. The median age was 55 years (interquartile range of 47-61 years) with a male preponderance (68%). Ninety-six (90.6%) patients underwent subtotal resection, and 10 (9.4%) biopsy alone. Isocitrate dehydrogenase was wild-type in 96 (91%), and O6-methylguanine-DNA methyltransferase was unmethylated in 70 (66.0%) patients. Telomerase reverse transcriptase promoter was mutated in 64 (60.4%), and TP53 was mutated in 22 (20.8%). Concurrent radiation and TMZ were planned for 104 (98.1%), and radiation alone for 2 (1.9%). The median time to concurrent RT-TMZ was 36 days (interquartile range 30-44 days). All patients planned for RT-TMZ completed treatment, but only 81 (76%) completed adjuvant TMZ. Sixty-three (59%) completed six cycles, 18 (17%) received less than six cycles, and 25 (24%) did not receive adjuvant TMZ. At a median follow-up of 24 months (range 21-31 months), the median (95% CI) progression-free survival and overall survival were 11 (95% CI, 9.4 to 13.0) and 20.0 (95% CI, 15 to 26) months, respectively.

CONCLUSION

Our patients met quality indices in most domains; outcomes are comparable with global results. Metrics will be periodically evaluated to include new standards and assess continuous service appropriateness.
Effect of time-delayed interactions on milling: A minimal model
Authors: Costanzo A. , van Haeringen E. , Hemelrijk C. K.
Published: March 2022

Models of collective motion show a rich variety of patterns. One of these is milling, in which the individuals of a group are circling around a common center. Milling has been generated in a Vicsek-like model of collective motion, i.e., a minimal model where individuals coordinate their headings only via alignment with close neighbors, without being attracted to each other and without avoiding collisions. However, in this Vicsek-like model information propagates instantaneously among neighbors, whereas in nature transfer and processing of information need time. How this delay affects patterns of collective motion, particularly milling, is unknown. Here we investigate the effect of time-delayed interactions on the emergence of milling in a Vicsek-like model. We show that delays may either destroy milling or induce it, depending on the parameters of the system. The range of speeds and fields of view of individuals at which milling occurs is shifted to smaller values if there are time delays in the model. Our findings may help to understand what causes milling in nature.
Epha1 is a cell-surface marker for the neuromesodermal competent population
Authors: de Lemos Luisa , Dias André , Nóvoa Ana , Mallo Moisés
Published: March 2022

The vertebrate body is built during embryonic development by the sequential addition of new tissue as the embryo grows at its caudal end. During this process, progenitor cells within the neuromesodermal competent (NMC) region generate the postcranial neural tube and paraxial mesoderm. Here, we have applied a genetic strategy to recover the NMC cell population from mouse embryonic tissues and have searched their transcriptome for cell-surface markers that would give access to these cells without previous genetic modifications. We found that Epha1 expression is restricted to the axial progenitor-containing areas of the mouse embryo. Epha1-positive cells isolated from the mouse tailbud generate neural and mesodermal derivatives when cultured in vitro. This observation, together with their enrichment in the Sox2+/Tbxt+ molecular phenotype, indicates a direct association between Epha1 and the NMC population. Additional analyses suggest that tailbud cells expressing low Epha1 levels might also contain notochord progenitors, and that high Epha1 expression might be associated with progenitors entering paraxial mesoderm differentiation. Epha1 could thus be a valuable cell-surface marker for labeling and recovering physiologically active axial progenitors from embryonic tissues.
FOXP4 differentially controls cold-induced beige adipocyte differentiation and thermogenesis
Authors: Wang Fuhua , Xu Shuqin , Chen Tienan , Ling Shifeng , Zhang Wei , Wang Shaojiao , Zhou Rujiang , Xia Xuechun , Yao Zhengju , Li Pengxiao , Zhao Xiaodong , Wang Jiqiu , Guo Xizhi
Published: March 2022

Beige adipocytes have a discrete developmental origin and possess notable plasticity in their thermogenic capacity in response to various environmental cues, but the transcriptional machinery controlling beige adipocyte development and thermogenesis remains largely unknown. By analyzing beige adipocyte-specific knockout mice, we identified a transcription factor, forkhead box P4 (FOXP4), that differentially governs beige adipocyte differentiation and activation. Depletion of Foxp4 in progenitor cells impaired beige cell early differentiation. However, we observed that ablation of Foxp4 in differentiated adipocytes profoundly potentiated their thermogenesis capacity upon cold exposure. Of note, the outcome of Foxp4 deficiency on UCP1-mediated thermogenesis was confined to beige adipocytes, rather than to brown adipocytes. Taken together, we suggest that FOXP4 primes beige adipocyte early differentiation, but attenuates their activation by potent transcriptional repression of the thermogenic program.
“We threw away the stones”: a mixed method evaluation of a simple cookstove intervention in Malawi
Authors: Saleh Sepeedeh , Sambakunsi Henry , Makina Debora , Kumwenda Moses , Rylance Jamie , Chinouya Martha , Mortimer Kevin
Published: March 2022

Background: Air pollution exposure is responsible for a substantial burden of respiratory disease globally. Household air pollution from cooking using biomass is a major contributor to overall exposure in rural low-income settings. Previous research in Malawi has revealed how precarity and food insecurity shape individuals’ daily experiences, contributing to perceptions of health. Aiming to avoid a mismatch between research intervention and local context, we introduced a simple cookstove intervention in rural Malawi, analysing change in fine particulate matter (PM2.5) exposures, and community perceptions.

Methods: Following a period of baseline ethnographic research, we distributed ‘chitetezo mbaula’, locally-made cookstoves, to all households (n=300) in a rural Malawian village. Evaluation incorporated village-wide participant observation and concurrent exposure monitoring using portable PM2.5 monitors at baseline and follow-up (three months post-intervention). Qualitative data were thematically analysed. Quantitative analysis of exposure data included pre-post intervention comparisons, with datapoints divided into periods of combustion activity (almost exclusively cooking) and non-combustion periods. Findings were integrated at the interpretation stage, using a convergent design mode of synthesis.

Results: Individual exposure monitoring pre- and post-cookstove intervention involved a sample of 18 participants (15 female; mean age 43). Post-intervention PM2.5 exposures (median 9.9μg/m3 [interquartile range: 2.2–46.5]) were not significantly different to pre-intervention (11.8μg/m3 [3.8–44.4]); p=0.71. On analysis by activity, background exposures were found to be reduced post-intervention (from 8.2μg/m3 [2.5–22.0] to 4.6μg/m3 [1.0–12.6]; p=0.01). Stoves were well-liked and widely used by residents as substitutes for previous cooking methods (mainly three-stone fires). Commonly cited benefits related to fuel saving and shorter cooking times.

Conclusions: The cookstove intervention had no impact on cooking-related PM2.5 exposures. A significant reduction in background exposures may relate to reduced smouldering emissions. Uptake and continued use of the stoves was high amongst community members, who preferred using the stoves to cooking over open fires.
Strengthening capacity for community and public engagement (CPE): a mixed-methods evaluation of the ‘DELTAS Africa CPE seed fund’ pilot
Authors: Mwangi Leah , Mutengu Lillian , Gitau Evelyn , Bates Imelda , Pulford Justin
Published: March 2022

Background: The ‘DELTAS Africa CPE seed fund’ was a pilot scheme designed to strengthen capacity in community and public engagement (CPE) via a ‘learn by doing’ approach.   The scheme supported a total of 25 early career researchers and research support staff belonging to the DELTAS Africa network to design and implement a variety of CPE projects between August 2019 and February 2021.  We examine recipient experiences of the DELTAS Africa CPE seed fund initiative, changes in their CPE attitudes, knowledge and proficiency and their CPE practice and/or practice intentions post-award.

Methods: A mixed-methods process and performance evaluation drawing on three data sources: An anonymous, online knowledge, attitude and practice survey completed by CPE seed fund awardees pre- and post-project implementation (N=23); semi-structured interviews completed with a sub-sample of awardees and programme implementors (N=9); and ‘end-of-project’ reports completed by all seed fund awardees (N=25). 

Results: All awardees described their seed fund experience in positive terms, despite invariably finding it more challenging than originally anticipated.  The combined survey, interview and end of project report data all uniformly revealed improvement in awardees’ self-reported CPE knowledge, attitudes and proficiency by completion of their respective projects.   Commitment to continued CPE activity post-award was evident in the survey data and all interviewees were adamant that they would integrate CPE within their respective research work going forward.

Conclusion: The DELTAS Africa CPE seed fund appeared to work successfully as a CPE capacity strengthening platform and as a vehicle for fostering longer-term interest in CPE activities.
Carbohydrate and Lipid Metabolism Characteristics of Hypoxia Tolerance in Gastrocnemius of the Gansu zokor, Eospalax cansus
Authors:   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, Lin Jinyan , Lin Nannan ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, Yang Qi ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, Hao Zhiqiang ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, Sun Xiaoqi ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, He Jianping ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China, Li Jingang ,   College of Life Science, Shaanxi Normal University, Xi’an 710119, Shaanxi, China
Published: March 2022

Gansu zokor (Eospalax cansus) is a typical subterranean rodent species, and the balance between energy production and consumption has critical function for this creature to adapt to its hypoxia environment. However, little is known about the energy metabolism of gastrocnemius in Gansu zokor. Thus, we exposed Gansu zokors and similar-sized Sprague-Dawley rats (SD rats) to normoxia (21% O2), hypoxia I (6h at 6.5% O2), hypoxia II (44h at 10.5% O2) or hypoxia III ( 10d at 10.5% O2). We fi rst compared the plasma glucose and plasma lipid levels in Gansu zokor with those in SD rats; and we found that Gansu zokor had a higher overall plasma lipid levels than those in SD rats, interestingly, compared with SD rats, the plasma glucose level in Gansu zokor was no higher in all groups and even signifi cantly lower in the normoxia and hypoxia III. Furthermore, transcriptomic analysis of gastrocnemius in Gansu zokor (6.5% O2 VS 21% O2) indicated its carbohydrate and lipid metabolic alterations after exposed to hypoxia, suggesting that the change in metabolism was linked to the hypoxia environment. Hence, we then measured the transcriptional and translational levels of carbohydrate and lipid metabolism-related genes, glucose and fructose levels in gastrocnemius. We found that unlike rat, Gansu zokor gastrocnemius enhanced fructose-driven metabolism through increased the fructose transporter (GLUT5) expression in all hypoxia groups, and Gansu zokor also could enhanced lipid metabolism by increasing the expression of acetyl-Coenzyme A acyltransferase 2 (ACAA2) and stearoyl-CoA desaturase 1 (SCD1) after exposure to long-term hypoxia condition (10d at 10.5% O2). Overall, these fi ndings indicate that Gansu zokor could increase energy supply by enhancing fructose-driven metabolism and lipid metabolism to cope with hypoxia environment, which playing an important role in hypoxia tolerance.
The Osteoporosis Disease Diagnosis and Classification Using U-net Deep Learning Process
Authors: Rao D. Thrivikrama , Ramesh K. S. , Ghali V. S. , Rao M. Venugopala
Published: March 2022

The purpose of this research has been used to detect osteoporosis disease for Knee radiography. It can improve diagnostic performance over using the scan thermal image mode alone. During 2016 and 2021, researchers gathered CT, MRI, CTA, ultra sound images from individuals who had both skeletal bone density assessment and knee radiology at a local medical clinic for subjective labelling. But following models are most complicate to detect diagnosis of osteoporosis. Therefore, five level convolutional neural networks (CNN) models were used to diagnose osteoporosis from knee radiography. They also looked at ensemble models that included clinical variables in each U-Net. Every net was given an efficiency, accuracy, recall, sensitivity, negative predictive value (npv), F1 measure, and area under curve (AUC) rating. Exclusively knee rays were used to test the U-Net model, but GoogleNet, S-transform, ResNet and FCNN had the lowest accuracy, precision, and specificity. Whenever patient’s data were added, Efficient U-Net had the highest accuracy 99.23%, recall 98.76%, npv 0.93%, F1 score 99.23%, and AUC 99.72% scores among five level prediction methods. The U-Net models correctly identified osteoporosis from Knee radiography, and their performance had improved even more when clinical variables from health records were complex. This u-net based osteoporosis diagnosis is most helpful for future generation for better pre-detections.
The Impact of Continuity and Security on Quality of Life
Authors: Friedman Carli
Published: March 2022

Continuity and security includes people with intellectual and developmental disabilities (IDD) not only having resources to meet their basic needs, but also includes the amount of change and disruption people have in their lives and the control they have over that change. We explored the impact of continuity and security on people with IDD's (n = 325) quality of life by analyzing Personal Outcome Measures interviews. Continuity and security not only significantly increased overall quality of life, but it also positively impacted two thirds of the different outcomes, ranging from health to relationships to rights. A stronger community infrastructure is needed to promote the continuity and security, and, by extension, quality of life of people with IDD.
Uplifts, Respite, Stress, and Marital Quality for Parents Raising Children With Down Syndrome or Autism
Authors: Easler Jamie K. , Taylor Tina M. , Roper Susanne Olsen , Yorgason Jeremy B. , Harper James M.
Published: March 2022

Direct, indirect, and partner effects estimated among uplifts, respite care, stress, and marital quality across mothers and fathers of children with autism spectrum disorder (n = 102) and Down syndrome (n = 111) were examined in this cross-sectional study. Parents of children with ASD who reported more uplifts and less stress individually reported better marital quality; these wives reported better marital quality as their husbands reported more uplifts and less stress. Wives with children with DS who reported more uplifts, individually along with their husbands reported less stress and better marital quality. Respite was directly associated with marital quality for parents of children with ASD and indirectly associated with marital quality for parents of children with DS with reduced individual stress. Implications are discussed.