bluuebunny/crossref_metadata_2025 huggingface dataset:
The perils of penile enhancement: case report of a fulminant penile infection
Authors: Khor Nicole Wen Mun , Dhar Ankur , Cameron-Strange Alistair
Published: August 2021

Background

Penile enhancement with injectable agents is a rising trend and yet has received little scientific attention despite the potential for serious complications. These include cosmetic, functional and systemic complications that may require complex penile reconstructive surgery. We report a case of delayed severe infection following penile filler insertion leading to multi-organ failure and intensive care support.

Case presentation

A 31-year-old man presented with fevers and progressive pain and swelling of the penile shaft, 3 days after unprotected sexual intercourse. The patient received subcutaneous hyaluronic filler injections at a cosmetic clinic for penile enlargement two months prior to presentation. Relevant social history include polysubstance abuse and multiple sexual partners. Physical examination revealed gross penile oedema and erythema, with a ventral curvature of the penile shaft and a superficial abrasion on the distal ventral penile shaft. Within 24 h the patient developed septic shock with anuria, hypotension and fevers to 40 °C, requiring transfer to the Intensive Care Unit (ICU) for vasopressor and inotropic support. Intraoperative penile exploration revealed multiple pus stained fillers which were drained and grew Streptococcus Pyogenes on cultures. There was no abscess or evidence of necrotising fasciitis intraoperatively. The patient improved with intravenous antibiotics and was stepped down from the ICU after four days and discharged on day eight. One month post admission there was significant superficial skin loss to both ventral and lateral aspect of the penis, with healthy granulation tissue at the base. The patient opted for conservative management with regular dressings. He reported normal sexual and urinary function three months post admission.

Conclusion

This is the first published case of sepsis from a penile infection in the context of hyaluronic acid penile fillers. In an era of escalating demand for penile cosmetic procedures, there is an increasing need for early recognition and appropriate management of penile filler infections. We report an unusual case of a localised penile infection rapidly progressing to sepsis with multi-organ failure requiring intensive care support. The case demonstrates early surgical intervention with targeted antimicrobials can result in successful eradication of infection, with satisfactory cosmetic and functional outcomes for patients.
Effects of resveratrol supplementation on bone quality: a systematic review and meta-analysis of randomized controlled trials
Authors: Li Qiangqiang , Yang Guangpu , Xu Hongtao , Tang Shaowen , Lee Wayne Yuk-wai
Published: August 2021

Background

The results from clinical trials have revealed that the effects of resveratrol supplementation on bone mineral density (BMD) and bone biomarkers are inconsistent. Our objective was to determine the effects of resveratrol supplementation on BMD and serum bone biomarkers.

Methods

PubMed, Cochrane library, EMBASE, Web of science and Scopus were searched up to August 24, 2020. Two reviewers independently performed the articles search and screen according to defined selection criteria. The study quality of the randomized controlled trials (RCTs) was evaluated with the Cochrane scoring system. Heterogeneity among studies was examined by Cochrane Q test. Retrieved data were pooled after mean differences (MD) were computed between two groups for BMD and serum biomarkers. Subgroup analyses were performed to evaluate a potential difference in terms of dose of resveratrol and intervention duration. Sensitivity analysis was executed by omitting studies with imputed values in order to evaluate the influence of these studies on the overall results.

Results

Ten eligible studies involving 698 subjects were included in this meta-analysis with 401 participants receiving resveratrol and 297 receiving placebo. Supplementation of resveratrol had no statistically significant effects on areal bone mineral density (aBMD) at lumbar spine (MD: -0.02, 95% CI: − 0.05, 0.01, p = 0.26, I2 = 6%), total hip BMD (MD: -0.01, 95% CI: − 0.04, 0.02, p = 0.65, I2 = 0%), and whole body BMD (MD: 0.00, 95% CI: − 0.02, 0.02, p = 0.74, I2 = 0%). Supplementation of resveratrol also did not result in significant change in bone serum markers, including serum alkaline phosphatase (ALP), bone alkaline phosphatase (BAP), osteocalcin (OCN), procollagen I N-terminal propeptide (PINP), C-terminal telopeptide of type I collagen (CTX) and parathyroid hormone (PTH). Subgroup analysis showed the effect of resveratrol supplementation on BMD and serum bone markers were similar in trails of different doses, intervention duration, and pathological conditions of the participants.

Conclusion

Resveratrol supplementation did not show any significant effect on BMD or serum bone markers with the current evidence. Further investigation with more well-organized multicentre randomized trial is warranted.
Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Authors: Gruenheit Nicole , Baldwin Amy , Stewart Balint , Jaques Sarah , Keller Thomas , Parkinson Katie , Salvidge William , Baines Robert , Brimson Chris , Wolf Jason B. , Chisholm Rex , Harwood Adrian J. , Thompson Christopher R. L.
Published: August 2021

Background

Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoebaDictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in the cell, developmental and evolutionary biology.

Results

We describe REMI-seq, an adaptation of Tn-seq, which allows high throughput,en masse, and quantitative identification of the genomic site of insertion of a drug resistance marker after restriction enzyme-mediated integration. We use REMI-seq to develop tools which greatly enhance the efficiency with which the sequence, transcriptome or proteome variation can be linked to phenotype inD. discoideum. These comprise (1) a near genome-wide resource of individual mutants and (2) a defined pool of ‘barcoded’ mutants to allow large-scale parallel phenotypic analyses. These resources are freely available and easily accessible through the REMI-seq website that also provides comprehensive guidance and pipelines for data analysis. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified.

Conclusions

We present methods and resources, generated using REMI-seq, for high throughput gene function analysis in a key model system.
Association of VEGF haplotypes with breast cancer risk in North-West Indians
Authors: Sambyal Vasudha , Guleria Kamlesh , Kapahi Ruhi , Manjari Mridu , Sudan Meena , Uppal Manjit Singh , Singh Neeti Rajan
Published: August 2021

Background

Angiogenesis is a complex and coordinated process regulated by different growth factors and is one of the hallmark features of cancer. VEGF is one of the most important endothelial cell mitogen and has a critical role in normal physiological and tumor angiogenesis. The objective of this study was to investigate the potential association of haplotypes of six VEGF polymorphisms with breast cancer risk in North-West Indians.

Methods

Samples of 250 breast cancer patients and 250 age and sex matched controls were genotyped for VEGF −2578C/A, −2549I/D, −460T/C, +405C/G, −7C/T and +936C/T polymorphisms. Haplotypes were generated to determine the better contribution of VEGF polymorphisms to breast cancer risk.

Results

Haplotypes CDTCCC (OR = 0.56, 95%CI, 0.38–0.81; p = 0.003) and CDTGCC (OR = 0.63, 95%CI, 0.44–0.92; p = 0.018) of VEGF −2578C/A, −2549I/D, −460T/C, +405C/G, −7C/T and +936C/T polymorphisms were significantly associated with decreased risk of breast cancer. CDTCCC haplotype was also significantly associated with reduced risk of breast cancer in pre and post menopausal as well as both obese and non obese patients. Haplotype CDTGCC was marginally associated (p = 0.07) with reduced risk of breast cancer in non-obese patients as compared with non-obese controls where as haplotype AICGTC was marginally associated (p = 0.09) with reduced risk of breast cancer in obese patients when compared with non-obese patients. The CDTGCC haplotype was significantly associated with increased risk of breast cancer in premenopausal obese patients (OR = 1.98, 95%CI, 1.10–3.56; p = 0.02).

Conclusions

Our data indicated that CDTCCC and CDTGCC haplotypes of VEGF −2578C/A, −2549I/D, −460T/C, +405C/G, −7C/T and +936C/T polymorphisms were significantly associated with breast cancer risk in North-West Indians. Further studies on multiethnic groups with larger sample size are required to confirm our results.
Development of the Pulmonary Hypertension Functional Classification Self-Report: a patient version adapted from the World Health Organization Functional Classification measure
Authors: Highland Kristin B. , Crawford Rebecca , Classi Peter , Morrison Ross , Doward Lynda , Nelsen Andrew C. , Castillo Howard , Mathai Stephen C. , DuBrock Hilary M.
Published: August 2021

Background

Pulmonary arterial hypertension (PAH) is characterized by progressive limitations on physical activity, right heart failure, and premature death. The World Health Organization functional classification (WHO-FC) is a clinician-rated assessment used widely to assess PAH severity and functioning, but no equivalent patient-reported version of PAH symptoms and activity limitations exists. We developed a version of the WHO-FC for self-completion by patients: the Pulmonary Hypertension Functional Classification Self-Report (PH-FC-SR).

Methods

Semistructured interviews were conducted with three health care providers (HCPs) via telephone to inform development of the draft PH-FC-SR. Two rounds of semi-structured interviews were conducted with 14 US patients with a self-reported PAH diagnosis via telephone/online to elicit concepts and iteratively refine the PH-FC-SR.

Results

HCPs reported that the WHO-FC was a useful tool for evaluating patients’ PAH severity over time and for making treatment decisions but acknowledged that use of the measure is subjective. Patients in round 1 interviews (n = 6) reported PAH symptoms, including shortness of breath (n = 6), fatigue (n = 5), syncope (n = 5), chest pains (n = 3), and dizziness (n = 3). Round 1 patients identified challenges with the original WHO-FC, including comprehensibility of clinical terms and overlapping descriptions of class II and III, and preferred the Draft 1 PH-FC-SR over the original WHO-FC. After minor changes were made to Draft 2, round 2 interviews (n = 8) confirmed patients understood the PH-FC-SR class descriptions, interpreting them consistently.

Conclusions

The HCP and patient interviews identified and confirmed certain limitations inherent within the clinician-rated WHO-FC, including subjective assessment and overlapping definitions for class II and III. The PH-FC-SR includes patient-appropriate language, symptoms, and physical activity impacts relevant to patients with PAH. Future research is recommended to validate the PH-FC-SR and explore its correlation with the physician-assessed WHO-FC and other outcomes.
Misdiagnosis in occupational and environmental medicine: a scoping review
Authors: Moon Jinyoung , Yoo HyeKyoung
Published: August 2021

Introduction

There has been no comprehensive review for misdiagnosis in Occupational and Environmental Medicine (OEM). The possible ramifications of an occupational disease (OD) or an environmental disease (ED) misdiagnosis are not just confined to the individual case but may extend to others exposed to the occupational or environmental hazard. Therefore, a comprehensive scoping review of published literature is imperative for understanding the nature of misdiagnoses in OEM.

Methods

A medical librarian searched MEDLINE (PubMed), EMBASE, and the Cochrane Library (on 06 November 2020). All collected OEM misdiagnoses were classified based on 2 conceptual frameworks, the typical framework, and the causation model. The distribution of misdiagnosis across each medical specialty, each diagnostic step of the typical framework and the causation model, and false-negative and false-positive were summarized.

Results

A total of 79 articles were included in the scoping review. For clinical specialty, pulmonology (30 articles) and dermatology or allergy (13 articles) was most frequent and second-most frequent, respectively. For each disease, occupational and environmental interstitial lung diseases, misdiagnosed as sarcoidosis (8 articles), and other lung diseases (8 articles) were most frequent. For the typical framework, the most vulnerable step was the first step, evidence of a disease (38 articles). For the causation model, the first step, knowledge base, was the most vulnerable step (42 articles). For reported articles, the frequency of false-negative (55 articles) outnumbered the frequency of false-positive (15 articles).

Discussion

In OEM, compared to general medicine, causal misdiagnosis associated with the probability of causation is also important. For making a diagnosis in OEM, a knowledge base about possible ODs and EDs is essential. Because of this reason, the education and training of treating physicians for common ODs and EDs are important. For ODs and EDs, various intentional behaviors of stakeholders should be considered. This scoping review might contribute to the improvement of understanding for misdiagnosis in OEM.
Balanced forced-diuresis compared to control as a reno-protective approach in cardiac surgery: secondary outcome of a randomized controlled trial, assessment of neutrophil gelatinase-associated lipocalin levels
Authors: Luckraz Heyman , Giri Ramesh , Wrigley Benjamin , Nagarajan Kumaresan , Senanayake Eshan , Sharman Emma , Beare Lawrence , Nevill Alan
Published: August 2021

Background

Neutrophil gelatinase-associated lipocalin (NGAL) is a recognised biomarker for acute kidney injury (AKI).This study investigated the impact of balanced forced-diuresis using RenalGuard® system (RG), in reducing acute kidney injury (AKI) rates and the associated NGAL levels (6-h post-CPB plasma level) post adult cardiac surgery with cardiopulmonary bypass (CPB).

Methods

Patients included in the study were at high-risk for AKI post cardiac surgery, namely history of diabetes and/or anaemia, e-GFR 20–60 ml/min/1.73 m2, Logistic EuroScore > 5, anticipated CPB time > 120 min. Patients were randomized to either RG (n = 110) or managed as per current practice (control = 110). RIFLE-defined AKI rate (based on serum creatinine level increase) within first 3 days of surgery and 6-h post CPB NGAL levels were the primary and secondary end-points.

Results

Pre and intra-operative characteristics between the two groups were similar (p > 0.05) including the pre-op NGAL levels, the oxygen delivery (ecDO2i) and the carbon dioxide production (ecVCO2i) during CPB. Patients in the RG group had a significantly lower post-operative RIFLE-defined AKI rate compared to control (10% (11/110) v/s 20.9% (23/110), p = 0.03). Overall, median 6-h post CPB NGAL levels in patients with AKI were significantly higher than those who did not develop AKI (211 vs 150 ng/ml, p < 0.001). Patients managed by balanced forced-diuresis had lower post-operative NGAL levels (146 vs 178 ng/ml, p = 0.09). Using previously reported NGAL cut-off level for AKI (142 ng/ml), binary logistic regression analysis confirmed a beneficial effect of the RG system, with an increased risk of AKI of 2.2 times in the control group (OR 2.2, 95% CI 1.14–4.27, p = 0.02).

Conclusions

Overall, the 6-h post-CPB plasma NGAL levels were significantly higher in patients who developed AKI. Patients managed with the novel approach of balanced forced-diuresis, provided by the RenalGuard® system, had a lower AKI rate and lower NGAL levels indicating a lesser degree of renal tissue injury.

Trial registrationClinicalTrials.gov website, NCT02974946,https://clinicaltrials.gov/ct2/show/NCT02974946.
Preoperative incentive spirometry for preventing postoperative pulmonary complications in patients undergoing coronary artery bypass graft surgery: a prospective, randomized controlled trial
Authors: Sweity Essa M. , Alkaissi Aidah A. , Othman Wafiq , Salahat Ahmad
Published: August 2021

Background

Postoperative pulmonary complications (PPCs) often occur after cardiac operations and are a leading cause of morbidity, inhibit oxygenation, and increase hospital length of stay and mortality. Although clinical evidence for PPCs prevention is often unclear and crucial, measures occur to reduce PPCs. One device usually used for this reason is incentive spirometry (IS). The aim of the study is to evaluate the effect of preoperative incentive spirometry to prevent postoperative pulmonary complications, improve postoperative oxygenation, and decrease hospital stay following coronary artery bypass graft (CABG) surgery patients.

Methods

This was a clinical randomized prospective study. A total of 80 patients were selected as candidates for CABG at An-Najah National University Hospital, Nablus-Palestine. Patients had been randomly assigned into two groups: incentive spirometry group (IS), SI performed before surgery (study group) and control group, preoperative spirometry was not performed. The 40 patients in each group received the same protocol of anesthesia and ventilation in the operating room.

Result

The study findings showed a significant difference between the IS and control groups in the incidence of postoperative atelectasis. There were 8 patients (20.0%) in IS group and 17 patients (42.5%) in the control group (p = 0.03). Mechanical ventilation duration was significantly less in IS group. The median was four hours versus six hours in the control group (p < 0.001). Hospital length of stay was significantly less in IS group, and the median was six days versus seven days in the control group (p < 0.001). The median of the amount of arterial blood oxygen and oxygen saturation was significantly improved in the IS group (p < 0.005).

Conclusion

Preoperative incentive spirometry for two days along with the exercise of deep breathing, encouraged coughing, and early ambulation following CABG are in connection with prevention and decreased incidence of atelectasis, hospital stay, mechanical ventilation duration and improved postoperative oxygenation with better pain control. A difference that can be considered both significant and clinically relevant.

Trial registration Thai Clinical Trials Registry: TCTR20201020005. Registered 17 October 2020—retrospectively registered.
Acute depletion of CTCF rewires genome-wide chromatin accessibility
Authors: Xu Beisi , Wang Hong , Wright Shaela , Hyle Judith , Zhang Yang , Shao Ying , Niu Mingming , Fan Yiping , Rosikiewicz Wojciech , Djekidel Mohamed Nadhir , Peng Junmin , Lu Rui , Li Chunliang
Published: August 2021

Background

The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription.

Results

Here, we systematically integrate multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, and CRISPR-Cas9 survival dropout screens, and time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewires genome-wide chromatin accessibility. Increased accessible chromatin regions are frequently located adjacent to CTCF-binding sites at promoter regions and insulator sites associated with enhanced transcription of nearby genes. In addition, we use CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners. We successfully identify 40 candidates, including multiple established partners. Interestingly, many CTCF co-regulators that have alterations of their respective downstream gene expression do not show changes of their own expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription.

Conclusions

This study highlights that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation.
Age-related differences in linear sprint in adolescent female soccer players
Authors: Mainer-Pardos Elena , Gonzalo-Skok Oliver , Nobari Hadi , Lozano Demetrio , Pérez-Gómez Jorge
Published: August 2021

Background

Several studies have observed the contribution of chronological age, biological maturation, and anthropometric characteristics to sprinting performance in young soccer players. Nevertheless, there are no studies that have analysed the contribution of these characteristics to running speed qualities in adolescent female soccer players.

Objective

This study investigated age-related differences in sprint performance in adolescent female soccer players. Also, it examined the possible influence of anthropometry [body mass and body mass index (BMI)] and biological maturation [age at peak height velocity (APHV)] in sprint performance.

Methods

Eighty adolescent female soccer players [under (U) 14, n = 20; U16, n = 37; U18, n = 23] participated in this study. Players were tested for 40 m sprint (each 10 m split times).

Results

Posthoc analysis revealed better performance in all split sprint times of older soccer players (U18 and U16) compared with younger category (F: 3.380 to 6.169; p < 0.05; ES: 0.64 to 1.33). On the contrary in all split sprint times, there were no significant changes between U16 and U18 (p < 0.05; ES: 0.03 to 0.17). ANCOVA revealed differences in all parameters between groups, controlled for APHV (p < 0.05). In contrast, all between-group differences disappeared after body mass and BMI adjustment (p > 0.05). Finally, the results indicate that BMI and body mass were significantly correlated with 40 m sprint (p < 0.05; r: -0.31) and 20 m flying (p < 0.01; r: 0.38), respectively.

Conclusion

In the present players’ sample, body mass and BMI had a significant impact on running speed qualities.
An update on novel approaches for diagnosis and treatment of SARS-CoV-2 infection
Authors: Safarchi Azadeh , Fatima Shadma , Ayati Zahra , Vafaee Fatemeh
Published: August 2021

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has made a serious public health and economic crisis worldwide which united global efforts to develop rapid, precise, and cost-efficient diagnostics, vaccines, and therapeutics. Numerous multi-disciplinary studies and techniques have been designed to investigate and develop various approaches to help frontline health workers, policymakers, and populations to overcome the disease. While these techniques have been reviewed within individual disciplines, it is now timely to provide a cross-disciplinary overview of novel diagnostic and therapeutic approaches summarizing complementary efforts across multiple fields of research and technology. Accordingly, we reviewed and summarized various advanced novel approaches used for diagnosis and treatment of COVID-19 to help researchers across diverse disciplines on their prioritization of resources for research and development and to give them better a picture of the latest techniques. These include artificial intelligence, nano-based, CRISPR-based, and mass spectrometry technologies as well as neutralizing factors and traditional medicines. We also reviewed new approaches for vaccine development and developed a dashboard to provide frequent updates on the current and future approved vaccines.
Outcomes of dental implants in young patients with congenital versus non-congenital missing teeth
Authors: Al Najam Yousef , Tahmaseb Ali , Wiryasaputra Dorothee , Wolvius Eppo , Dhamo Brunilda
Published: August 2021

Objective

This cross-sectional study aims to investigate the effect of the cause of missing teeth on the survival and subjective success of dental implant treatment (DIT) in young patients with missing teeth due to non-congenital causes (tooth loss) in comparison to patients with missing teeth because of congenital causes (hypodontia and oligodontia).

Material and methods

All patients were asked 7 questions to extract information about the survival and subjective success of DIT. Implant survival function was designed using the Kaplan-Meier analysis. Differences in implant success outcomes were studied using binary logistic regression analysis.

Results

One hundred ten patients aged 18 to 40 years old were included, whereof 32 patients with tooth loss, 25 patients with hypodontia and 53 patients with oligodontia. In the tooth loss group, implant survival reached 96.9%; in the hypodontia group 96.0%; and in the oligodontia group 88.7%. Regarding subjective implant success, patient satisfaction was significantly higher (p < 0.040) among patients with congenital missing teeth in comparison to patients with tooth loss. Other implant success components showed no statistically significant difference (p > 0.050) between the groups.

Conclusion

The cause of missing teeth does not influence implant survival. However, the cause of missing teeth does have a significant impact on patient satisfaction (implant success), ascertaining young patients with congenital missing teeth as more satisfied of DIT than young patients with tooth loss.

Clinical relevance

Young patients with tooth agenesis and with an increased number of missing teeth are more content about the treatment with dental implants than patients with tooth loss. Furthermore, a consensus regarding the assessment of implant success is an essential concern for clarification.
Culturally-consistent diet among individuals of Mexican descent at the US-Mexico border is associated with sleep duration and snoring
Authors: Ghani Sadia B. , Taneja Krishna , Wills Chloe C. A. , Tubbs Andrew S. , Delgadillo Marcos E. , Valencia Dora , Halane Mohamed , Killgore William D. S. , Grandner Michael A.
Published: August 2021

Background

Existing studies show that consuming food consistent with one’s culture reduces cardiometabolic risk. However, few studies have assessed whether these dietary choices influence sleep health. Accordingly, this study assessed how Mexican food consumption by individuals of Mexican descent residing at the US-Mexico border, was associated with various measures of sleep, after accounting for acculturation.

Methods

Data were provided by 100 adults between the ages of 18–60, in the city of Nogales, AZ. Questionnaires were provided in either Spanish or English. Acculturation was assessed with the Acculturation Scale for Mexican-Americans (ARSMA-II), with an additional question, asking how often “my family cooks Mexican foods.” Frequency of cooking Mexican food was coded as either “yes” or “no.” Sleep was assessed, using validated measures that include the Insomnia Severity Index (ISI), the Epworth Sleepiness Scale (ESS), the Pittsburgh Sleep Quality Index (PSQI), and sleep duration with the item “how many hours of actual sleep did you get at night?” Regression models estimated the associations between sleep health variables as outcomes and consumption of Mexican food as the independent variable. Covariates included age, sex, and acculturation scores. Parental education level was also included, as an indicator of childhood socioeconomic status and since food culture likely involves parents.

Result

We found that among individuals who identified as Mexican-Americans who consumed culturally-consistent foods, was associated with, on average, 1.41 more hours of sleep (95% CI 0.19, 2.62; p = 0.024) and were less likely to report snoring (OR: 0.25; 95% CI 0.07, 0.93; p = 0.039). Consuming Mexican food was not associated with sleep quality, insomnia severity or sleepiness.

Conclusion

Individuals of Mexican descent residing at the US-Mexico border who regularly consumed Mexican food, reported more sleep and less snoring. Mexican acculturation has been shown previously to improve sleep health. This is likely due to consumption of a culturally- consistent diet. Future studies should examine the role of acculturation in sleep health, dietary choices, and subsequent cardiometabolic risk.
Flipping an on-campus general English course: a focus on technology complexity of instruction and learners’ levels of impulsivity
Authors: Zarrinfard Shakiba , Rahimi Mehrak , Mohseny Ahmad
Published: August 2021

The current study compared the effects of two types of flipped instruction (FI) (low- and mid-tech) with two other class conditions, a blended course and a conventional teaching, on learning outcome of language learners with different levels of impulsivity in an on-campus General English (GE) course. To attain such a goal, four GE classes consisting of 100 freshmen (25 students in each class) were selected and organized into 3 experimental (mid-tech FI, low-tech FI, blended instruction) and 1 control group (conventional teaching). In low-tech flipped class, the students were provided with the vodcasts and podcasts of the instructor’s teaching. For the mid-tech flipped class, the podcasts and vodcasts were integrated into an educational website where all instructional and supplementary materials were available. The blended group accessed the educational website after the instructor’s teaching as the extension of the class activities. The control group received the GE conventional instruction (chalk and talk approach). The participants’ learning outcome was assessed by reading paper of Preliminary English Test and their level of impulsivity was measured by BIS-11. The quantitative data were analysed by a two-way analysis of variance (ANOVA) and the results revealed a statistically significant difference in reading proficiency of the four groups after the study, in favour of the mid-tech FI. Moreover, while the type of instruction had no effect on reading proficiency of students with different levels of impulsivity across groups, within group comparisons revealed that only mid-tech group members with different levels of impulsivity benefited equally from the instruction. The results of the qualitative data analysis revealed that the majority of students in both groups had positive attitudes towards the experience, although they expressed their needs for some modifications in teacher role, their own role, and the way the instructional materials are prepared and presented.
Separation of split S-waves in two nonorthogonal sets of vertical fractures
Authors: Li Mengqi , Lu Jun , Wang Yun , Zhang Xueying , Li Zongjie
Published: August 2021

The phenomenon of S-wave splitting indicates the development of fractures in the shallow crust. Therefore, methods based on S-wave splitting have been established to predict the development of one set of parallel fractures. However, for rocks containing two nonorthogonal sets of vertical fractures, the mechanism of S-wave splitting is more complex, and the available methods cannot be applied. To resolve this inadequacy, we have developed a two-way rotation method to separate split S-waves with the aim of restoring the split S-wave polarizations and predicting the fracture azimuths. First, we calculate the stiffness matrix of fractured media based on the linear slip theory and derive the phase velocities and polarizations of split S-waves induced by fractures using the Christoffel equation. Second, we clarify the S-wave splitting mechanism in this media by using velocity analysis and deconstruct the S-wave polarizations on the horizontal components. Third, we deduce a two-way rotation matrix obtained by the S-wave splitting modes to separate the split S-waves. To solve for the angle parameters related to the fracture azimuths in the two-way rotation matrix, we superpose the subspace polarizations in two dimensions to determine the polarization azimuths of the split S-waves. Numerical model tests demonstrate that our method is stable under noisy conditions. Finally, we apply our method to real near offset and walkaround vertical seismic profiling data, and the predicted fracture results are verified by imaging logs and prior knowledge.
Self-supervised delineation of geologic structures using orthogonal latent space projection
Authors: Aribido Oluwaseun Joseph , AlRegib Ghassan , Alaudah Yazeed
Published: August 2021

We have developed two machine-learning frameworks that could assist in automated lithostratigraphic interpretation of seismic volumes without any manual hand labeling from an experienced seismic interpreter. The first framework is an unsupervised hierarchical clustering model used to divide seismic images from a volume into a certain number of clusters determined by the algorithm. The clustering framework uses a combination of density and hierarchical techniques to determine the size and homogeneity of the clusters. The second framework consists of a self-supervised deep learning framework to label regions of geologic interest in seismic images. It projects the latent space of an encoder-decoder architecture onto two orthogonal subspaces, from which it learns to delineate regions of interest in the seismic images. To demonstrate an application of both frameworks, a seismic volume is clustered into various contiguous clusters, from which four clusters are selected based on distinct seismic patterns: horizons, faults, salt domes, and chaotic structures. Images from the selected clusters are used to train the encoder-decoder network. The output of the encoder-decoder network is a probability map of the possibility that an amplitude reflection event belongs to an interesting geologic structure. The structures are delineated using the probability map. The delineated images are further used to posttrain a segmentation model to extend our results to full vertical sections. The results on vertical sections indicate that we can factorize a seismic volume into its corresponding structural components. Finally, we find that our deep learning framework can be modeled as an attribute extractor and we compare our attribute result with various existing attributes in the literature and determine the competitive performance with them.
Highly efficient density inversion of gravity data using nonlinear density polynomial fitting
Authors: Ma Guoqing , Li Zongrui , Li Lili , Wang Taihan
Published: August 2021

The density inversion of gravity data is commonly achieved by discretizing the subsurface into prismatic cells and calculating the density of each cell. During this process, a weighting function is introduced to the iterative computation to reduce the skin effect during the inversion. Thus, the computation process requires a significant number of matrix operations, which results in low computational efficiency. We have adopted a density inversion method with nonlinear polynomial fitting (NPF) that uses a polynomial to represent the density variation of prismatic cells in a certain space. The computation of each cell is substituted by the computation of the nonlinear polynomial coefficients. Consequently, the efficiency of the inversion is significantly improved because the number of nonlinear polynomial coefficients is less than the number of cells used. Moreover, because representing the density change of all of the cells poses a significant challenge when the cell number is large, we adopt the use of a polynomial to represent the density change of a subregion with fewer cells and multiple nonlinear polynomials to represent the density changes of all prism cells. Using theoretical model tests, we determine that the NPF method more efficiently recovers the density distribution of gravity data compared with conventional density inversion methods. In addition, the density variation of a subregion with 8 × 8 × 8 prismatic cells can be accurately and efficiently obtained using our cubic NPF method, which also can be used for noisy data. Finally, the NPF method is applied to real gravity data in an iron mining area in Shandong Province, China. Convergent results of a 3D perspective view and the distribution of the iron ore bodies are acquired using this method, demonstrating the real-life applicability of this method.
Numerical modeling of multifrequency complex dielectric permittivity dispersion of clay-rich rocks
Authors: Posenato Garcia Artur , Heidari Zoya
Published: August 2021

Dielectric permittivity measurements in sedimentary rocks are dominated by mineralogy, the volumetric concentration and spatial distribution of solids and fluids, and interfacial polarization. Conventional interpretation models oversimplify these factors, leading to uncertainties in estimates of formation properties such as hydrocarbon reserves. Interpretation challenges are magnified in clay-rich rocks, such as shaly sands and organic-rich mudrocks, due to convoluted rock fabric and mineralogical composition. However, the impact of fabric features and mineralogy on broadband permittivity is not well understood. Therefore, the main objective of this work is to develop a numerical framework to quantify the impact of different minerals and corresponding spatial distribution on the multifrequency complex permittivity of clay-rich rocks. We have solved the quasielectrostatic approximation to Maxwell’s equations in the frequency domain through the finite-volume method. We also introduce a workflow to calculate the effective admittance of the clay network. Furthermore, we derive an equation to incorporate the induced polarization effect into the effective admittance of pyrite particles. Finally, we perform a sensitivity analysis of the complex permittivity of clay-rich rocks in the frequency range from 100 Hz to 1 GHz to the volumetric concentration and spatial distribution of clays, cation exchange capacity (CEC), volumetric concentration of pyrite, and the orientation of the electric field. The simulation results confirm that the presence of clay minerals affects the permittivity and conductivity of the rocks. However, clays can enhance or diminish electrical conductivity values at different frequencies depending on their intrinsic properties and spatial distribution. For instance, laminations significantly enhance permittivity in the sub-MHz frequency range, but their effect is imperceptible at 1 GHz. The CEC variation affects conductivity in the entire frequency range from 100 Hz to 1 GHz and the permittivity at sub-MHz frequencies. A volumetric concentration of pyrite of 5% can enhance permittivity and conductivity at 100 Hz by approximately 50% and 30%, respectively.
Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer
Authors: Kerlavage Anthony R. , Kirchhoff Anne C. , Guidry Auvil Jaime M. , Sharpless Norman E. , Davis Kara L. , Reilly Karlyne , Reaman Gregory , Penberthy Lynne , Deapen Dennis , Hwang Amie , Durbin Eric B. , Gallotto Sara L. , Aplenc Richard , Volchenboum Samuel L. , Heath Allison P. , Aronow Bruce J. , Zhang Jinghui , Vaske Olena , Alonzo Todd A. , Nathan Paul C. , Poynter Jenny N. , Armstrong Greg , Hahn Erin E. , Wernli Karen J. , Greene Casey , DiGiovanna Jack , Resnick Adam C. , Shalley Eve R. , Nadaf Sorena , Kibbe Warren A.
Published: August 2021

Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute–funded cancer centers. This consortium has regularly held topic-focused biannual face-to-face symposiums. These meetings are a place to review cancer informatics and data science priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues that we faced at our respective institutions and cancer centers. Here, we provide meeting highlights from the latest CI4CC Symposium, which was delayed from its original April 2020 schedule because of the COVID-19 pandemic and held virtually over three days (September 24, October 1, and October 8) in the fall of 2020. In addition to the content presented, we found that holding this event virtually once a week for 6 hours was a great way to keep the kind of deep engagement that a face-to-face meeting engenders. This is the second such publication of CI4CC Symposium highlights, the first covering the meeting that took place in Napa, California, from October 14-16, 2019. We conclude with some thoughts about using data science to learn from every child with cancer, focusing on emerging activities of the National Cancer Institute's Childhood Cancer Data Initiative.
Magnetic-medium–based metamaterial for broadband microwave absorption and multiband transmission characteristics
Authors: Yang Zhihui , Sun Xin , Zhang Jiulin , Zhao Yilun , He Junzhe , Sun Xianjun , Zhou Yang , Wang Chong , Nie Wenjun
Published: August 2021

To fulfill the antenna system criteria for broadband microwave-absorbing materials, herein, a magnetic medium is introduced into the metamaterial structure design process, which can produce the artificially required transmission properties in the microwave region. The composite meta-structure can effectively provide microwave absorption at low frequency and microwave transmission at high frequency by optimising the design of the metasurface, dielectric and magnetic medium. The magnetic-medium–based metamaterial is fabricated in accordance with the design, and its electromagnetic characteristics are investigated. Experimental results show that the absorptivity of the proposed metamaterial structure is higher than 85% at 2.4–9.8 GHz, and that the transmissivity is higher than 71% at 15.5–18.8 GHz, 19.6–20.5 GHz, and 36–39 GHz. The absorptivity bandwidth exceeding 90% reaches 6.0 GHz, which is significantly higher than the traditional metamaterial without a magnetic medium. Moreover, the electromagnetic characteristics of the composite material are consistent under varying microwave polarisations.
Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence
Authors: Lichtinger Simon M. , Garaizar Adiran , Collepardo-Guevara Rosana , Reinhardt Aleks
Published: August 2021

Rationally and efficiently modifying the amino-acid sequence of proteins to control their ability to undergo liquid–liquid phase separation (LLPS) on demand is not only highly desirable, but can also help to elucidate which protein features are important for LLPS. Here, we propose a computational method that couples a genetic algorithm to a sequence-dependent coarse-grained protein model to evolve the amino-acid sequences of phase-separating intrinsically disordered protein regions (IDRs), and purposely enhance or inhibit their capacity to phase-separate. We validate the predicted critical solution temperatures of the mutated sequences with ABSINTH, a more accurate all-atom model. We apply the algorithm to the phase-separating IDRs of three naturally occurring proteins, namely FUS, hnRNPA1 and LAF1, as prototypes of regions that exist in cells and undergo homotypic LLPS driven by different types of intermolecular interaction, and we find that the evolution of amino-acid sequences towards enhanced LLPS is driven in these three cases, among other factors, by an increase in the average size of the amino acids. However, the direction of change in the molecular driving forces that enhance LLPS (such as hydrophobicity, aromaticity and charge) depends on the initial amino-acid sequence. Finally, we show that the evolution of amino-acid sequences to modulate LLPS is strongly coupled to the make-up of the medium (e.g. the presence or absence of RNA), which may have significant implications for our understanding of phase separation within the many-component mixtures of biological systems.
Latent class evaluation of the performance of serological tests for exposure to Brucella spp. in cattle, sheep, and goats in Tanzania
Authors: Bodenham Rebecca F. , Mazeri Stella , Cleaveland Sarah , Crump John A. , Fasina Folorunso O. , de Glanville William A. , Haydon Daniel T. , Kazwala Rudovick R. , Kibona Tito J. , Maro Venance P. , Maze Michael J. , Mmbaga Blandina T. , Mtui-Malamsha Niwael J. , Shirima Gabriel M. , Swai Emanuel S. , Thomas Kate M. , Bronsvoort Barend M. deC. , Halliday Jo E. B.
Published: August 2021

Background

Brucellosis is a neglected zoonosis endemic in many countries, including regions of sub-Saharan Africa. Evaluated diagnostic tools for the detection of exposure to Brucella spp. are important for disease surveillance and guiding prevention and control activities.

Methods and findings

Bayesian latent class analysis was used to evaluate performance of the Rose Bengal plate test (RBT) and a competitive ELISA (cELISA) in detecting Brucella spp. exposure at the individual animal-level for cattle, sheep, and goats in Tanzania. Median posterior estimates of RBT sensitivity were: 0.779 (95% Bayesian credibility interval (BCI): 0.570–0.894), 0.893 (0.636–0.989), and 0.807 (0.575–0.966), and for cELISA were: 0.623 (0.443–0.790), 0.409 (0.241–0.644), and 0.561 (0.376–0.713), for cattle, sheep, and goats, respectively. Sensitivity BCIs were wide, with the widest for cELISA in sheep. RBT and cELISA median posterior estimates of specificity were high across species models: RBT ranged between 0.989 (0.980–0.998) and 0.995 (0.985–0.999), and cELISA between 0.984 (0.974–0.995) and 0.996 (0.988–1). Each species model generated seroprevalence estimates for two livestock subpopulations, pastoralist and non-pastoralist. Pastoralist seroprevalence estimates were: 0.063 (0.045–0.090), 0.033 (0.018–0.049), and 0.051 (0.034–0.076), for cattle, sheep, and goats, respectively. Non-pastoralist seroprevalence estimates were below 0.01 for all species models. Series and parallel diagnostic approaches were evaluated. Parallel outperformed a series approach. Median posterior estimates for parallel testing were ≥0.920 (0.760–0.986) for sensitivity and ≥0.973 (0.955–0.992) for specificity, for all species models.

Conclusions

Our findings indicate that Brucella spp. surveillance in Tanzania using RBT and cELISA in parallel at the animal-level would give high test performance. There is a need to evaluate strategies for implementing parallel testing at the herd- and flock-level. Our findings can assist in generating robust Brucella spp. exposure estimates for livestock in Tanzania and wider sub-Saharan Africa. The adoption of locally evaluated robust diagnostic tests in setting-specific surveillance is an important step towards brucellosis prevention and control.
Don’t close the book on tocilizumab for the treatment of severe COVID-19 pneumonia–the jury is still out: The Kuwait experience
Authors: Al-Shamali Yousef , M. Ali Yaser , Al-Shamali Rawan A. , Al-Melahi Maryam , Al-Shammari Farah R. , Alsaber Ahmad , Al-Adsani Wasl
Published: August 2021

Purpose

This cross-sectional observational study aims to report preliminary data from the first experience using tocilizumab for patients with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in three of Kuwait’s largest public hospitals City.

Patients and methods

This chart review study examined the benefits of tocilizumab treatment among 127 patients diagnosed with severe coronavirus disease of 2019 (COVID-19) pneumonia.

Results

90 of 127 patients (71%) survived. Mortality was highest in the elderly with multiple medical conditions.

Conclusion

Despite the small sample size and retrospective nature of the work, our findings are consistent with recent studies suggesting tocilizumab administration in patients presenting with severe COVID pneumonia with associated hyperinflammatory features conferred mortality benefit.