bluuebunny/crossref_metadata_2025 huggingface dataset:
Upper Extremity Infection Related to Intravenous Drug Use: Considering the True Cost of the COVID-19 Pandemic and Lockdown
Authors: Sardiwalla Yaeesh , Nachmani Omri , Price Emma , Huynh Minh , Coroneos Christopher , McRae Matthew
Published: February 2022

Background:

The COVID-19 pandemic caused significant morbidity and mortality in people who inject drugs (PWID). Upper extremity soft tissue infections are frequently associated with intravenous drug use (IVDU) due to poor compliance with aseptic technique. In Canada, multiple safe injection sites providing clean injection supplies closed, leaving many PWID with no alternatives to inject safely. It was hypothesized that these closures will correspond with increased morbidity and mortality among PWID. The main objective of this study was to determine the effect of the COVID-19 pandemic on the incidence of upper extremity infections in PWID.

Methods:

This was a retrospective chart review study. The primary outcome of interest was the frequency of upper extremity infections in PWID. Data were filtered to include only those patients presenting to the emergency department between March to June of 2019 and 2020. Chi-squared analysis was used to compare the number of IVDU patients among patients with upper extremity skin infections between these time periods.

Results:

The number of IVDU patients treated for upper extremity infections in Hamilton significantly increased during the pandemic, relative risk = 2.0 (95% confidence interval [CI]: 1.3-2.9, P = .0012,) while total upper extremity infections numbers have decreased overall. During the pandemic, PWID made up a larger proportion of upper extremity infections ( χ2 = 10.444, P = .00123). Demographic data such as age and sex of IVDU patients presenting with upper extremity infection was not significantly affected by the pandemic.

Conclusions:

The effect of the pandemic on accessing harm reduction services has led to evident increases in morbidity as described by this study. Further research on the impact of closures in PWID is needed to quantify these harms and work toward mitigation strategies.
Collaborative Zoom Coding—A Novel Approach to Qualitative Analysis
Authors: Naganathan Gayathri , Srikanthan Sinthu , Balachandran Abhirami , Gladdy Angel , Shanmuganathan Vasuki
Published: February 2022

During the current coronavirus (COVID-19) pandemic, web conferencing became a staple in professional communication, with new and evolving applications amidst unique social distancing measures mandated across the globe. In this article, we describe Collaborative Zoom Coding (CZC) as an adaptive approach to qualitative data analysis that our research team developed in light of social distancing measures imposed due to the COVID-19 pandemic. CZC uses the web conferencing platform Zoom, to help analyze data. Our team used CZC to develop a code book for the community-based research (CBR) project, Sexual Health and Diasporic Experiences of Shadeism (SHADES). CZC enabled all team members to participate in data analysis by providing opportunities for group training and real-time collaborative data analysis, irrespective of team members’ location and level of experience with research. This article describes our specific processes for CZC and outlines its advantages as well as challenges. We conclude with a discussion of how researchers can conduct collaborative coding using Zoom and other conferencing technologies to further democratize the research process, particularly for community-based research endeavors.
Chemical Structures of Phenylbutanoids From Rhizomes of Zingiber cassumunar
Authors: Nakamura Seikou , Iwami Junko , Pongpiriyadacha Yutana , Nakashima Souichi , Matsuda Hisashi , Yoshikawa Masayuki
Published: February 2022

Zingiber cassumunar is widely distributed in Asia, and its rhizomes are used for asthma treatment in traditional medicine and as a spice. Five new phenylbutanoids, cassumunols I–M (1-5), were isolated from Z cassumunar rhizomes collected in Thailand, and their structures were characterized on the basis of physiochemical and chemical evidence.
Systematic Review of Laryngeal Fractures and Trends in Operative Management
Authors: Moroco Annie E. , Patel Vijay A. , Saadi Robert A. , Gniady John P. , Lighthall Jessyka G.
Published: February 2022

Study Design

Systematic review of the literature.

Objective

The goal of this study is to review the current literature on the trends in management of laryngeal fractures following trauma.

Methods

Independent searches of the PubMed and MEDLINE databases were performed. Articles from the period of 1963 to 2020 were collected. All studies which described laryngeal fractures using the Boolean method and relevant search term combinations, including “Laryngeal”, “Fracture”, “Operative”, and “Management” were collected.

Results

A total of 588 relevant unique articles were identified for analysis. Of these, 24 articles were deemed appropriate for inclusion in the literature review. Due to variability in study design and outcome measures, formal synthesis of data in the form of a meta-analysis was not possible.

Conclusions

Laryngeal fractures are rare traumatic injuries that require early identification and evaluation with complex management options. This comprehensive review aims to highlight the breadth of the topic with regard to presentation and clinical management. Though there remains no clear best practice for laryngeal fracture management, we review trends in clinical practice throughout the literature.
Crenotherapy as a Complementary and Integrative Treatment for Chronic Rhinosinusitis: A Systematic Review and Discussion of Current Evidence Limitations
Authors: Nimmagadda Sai V. , Schmale Isaac L. , Man Li-Xing
Published: February 2022

Background

Chronic rhinosinusitis (CRS) is a common condition that affects patients’ quality of life. Standard treatments for CRS have known side effects and variable efficacy rates. Thus, complementary and integrative (CIM) treatments for CRS such as crenotherapy, which utilizes high mineral content water or vapor as an inhalation therapy, are of continued interest.

Objectives

To summarize and evaluate the current research investigating crenotherapy's therapeutic potential and clinical outcomes for the treatment of CRS.

Study Design

Systematic review and qualitative analysis.

Methods

A systematic review was performed, with a comprehensive search strategy applied to 6 databases from inception to March 2021: CINAHL, Cochrane, Embase, PubMed, Scopus, and Web of Science. Studies with at least 10 patients, which investigated crenotherapy as the sole or adjunctive treatment for CRS in humans were included.

Results

In total, 10 articles out of 756 were included. Of these, 6 were randomized controlled trials. The remaining four articles were non-randomized prospective cohort studies. Six studies assessed clinical symptoms in response to crenotherapy, and there were unanimous improvements in Visual Analog Scale (VAS), Sino-Nasal Outcome Test-20 (SNOT-20), and other quality of life metrics. The studies that assessed inflammatory markers, cytology, or other measures showed significant improvement in neutrophil count, spores, ciliary motility, IgE, and manometry. Minimal to no adverse events were reported across all 10 studies.

Conclusion

There is limited data to support crenotherapy's effectiveness in treating patients with CRS. However, published studies suggest that for certain patients crenotherapy can both improve CRS symptoms and objective measures of nasociliary function with minimal side effects. Findings must be interpreted with caution due to study heterogeneity, inconsistent use of standard CRS definitions and outcomes measures, as well as other study design flaws. Given these results, as well as a growing interest in CIM, crenotherapy treatments for CRS deserve further investigation.
Nicotinamide supplementation in diabetic nonalcoholic fatty liver disease patients: randomized controlled trial
Authors: El-Kady Rasha R. , Ali Amani K. , El Wakeel Lamia M. , Sabri Nagwa A. , Shawki May A.
Published: February 2022

Background:

Nicotinamide has been reported to protect against liver steatosis and metabolic imbalances in nonalcoholic fatty liver disease (NAFLD) in animal models.

Objectives:

The objective was to investigate the efficacy and safety of nicotinamide supplementation in diabetic NAFLD patients.

Design:

This is a prospective randomized controlled open label study.

Methods:

Seventy diabetic NAFLD patients were randomly assigned either to the nicotinamide group ( n = 35) who received nicotinamide 1000 mg once daily for 12 weeks in addition to their antidiabetic therapy or the control group ( n = 35) who received their antidiabetic therapy only. The primary outcome was improvement in steatosis score, while secondary outcomes included assessment of liver stiffness, liver enzymes, lipid profile, insulin resistance, serum malondialdehyde, serum adiponectin, and patients’ quality of life (QOL).

Results:

Only 61 patients completed the study; 31 in the nicotinamide group and 30 in the control group. Comparisons between groups and within groups revealed nonsignificant changes in steatosis and fibrosis scores. However, significant reduction was observed in liver enzymes with a median decrease in alanine transaminase of 26.6% versus 0.74% in nicotinamide and control groups, respectively. After 12 weeks of treatment, the nicotinamide group showed significantly lower levels of low-density lipoprotein cholesterol ( p value = 0.004), total cholesterol ( p value = 0.006), and insulin resistance marker ( p value = 0.005) compared with control. Serum triglycerides, malondialdehyde, and adiponectin levels were all comparable between the two groups. Regarding QOL, a significant improvement was detected in the total scores and the activity and fatigue domains scores.

Conclusion:

Nicotinamide at a dose of 1000 mg daily was tolerable, improved metabolic abnormalities and QOL of diabetic NAFLD patients with no effect on liver fibrosis or steatosis.

Trial Registration:

The study was registered at clinicaltrials.gov and given the ID number: ‘NCT03850886’. https://clinicaltrials.gov/ct2/show/NCT03850886 .
Cash-based aid and civil war violence: New evidence from Myanmar (2012–2020)
Authors: Choi Hyun Jin , Park Jiyoun
Published: February 2022

Why do some aid projects in conflict environments improve the welfare of local communities and reduce insurgent violence, whereas other projects place them in greater danger? This study investigates this question by testing the effects of aid projects on the intensity of civil war using subnational data on violence and service provision in Myanmar (2012–2020). We find that small-scale, cash-based aid projects significantly reduce battlefield violence at the township level, and the effects of such projects are larger than those of other projects aimed at reducing violence (e.g., peacebuilding). These results provide support for recent counterinsurgency theories, which argue that smaller projects can reduce violence by motivating civilians to share information about rebels with the government (or pro-government) forces. This analysis offers a unique insight into the way cash-based services, though small and relatively inexpensive, can foster stability in conflict zones and save more lives.
Anti-inflammatory, anti-infectious and anti-cancer potential of marine algae and sponge: A review
Authors: Naqvi Syed Ali Raza , Sherazi Tauqir A , Hassan Sadaf U , Shahzad Sohail A , Faheem Zahra
Published: February 2022

Marine organisms are potentially a pretty good source of highly bioactive secondary metabolites that are best known for their anti-inflammation, anti-infection, and anti-cancer potential. The growing threat of bacterial resistance to synthetic antibiotics, is a potential source to screen terrestrial and marine natural organisms to discover promising anti-inflammatory and antimicrobial agents which can synergistically overcome the inflammatory and infectious disases. Algae and sponge have been studied enormously to evaluate their medicinal potential to fix variety of diseases, especially inflammation, infections, cancers, and diabetes. Cytarabine is the first isolated biomolecule from marine organism which was successfully practiced in clinical setup as chemotherapeutic agent against xylogenous leukemia both in acute and chronic conditions. This discovery opened the horizon for systematic evaluation of broad range of human disorders. This review is designed to look into the literature reported on anti-inflammatory, anti-infectious, and anti-cancerous potential of algae and sponge to refine the isolated compounds for value addition process.
Contested Racial Democracy: The 2014 World Cup, the 2016 Olympics, and the Emergence of Civic Nationalism in Brazil
Authors: Jung Hoyoon
Published: February 2022

The advent of the 2014 FIFA World Cup and 2016 Olympic Games witnessed a widespread upsurge in bending and ignoring the law in Brazil. Consequently, there was a torrent of exasperated public voices questioning the results of these events for ordinary Brazilians. This paper aims to examine how the Brazilian people’s experiences of these mega-events impacted the traditional Brazilian ideology of racial democracy. Using archival data, in-depth interviews with experts, and unstructured and spontaneous interviews with 143 ordinary citizens in five Brazilian state capitals conducted during field research, I explore how constructive opposition spurred the emergence of civic nationalism, based on shared norms and values of justice, democracy, equality, and the rights to become full-fledged citizens. The emergence of such shared “civic” principles among many groups, as a counter-narrative of traditional Brazilian national identity, destabilized the long-standing narrative of “racial democracy” as a Brazilian ethnic national identity.
Safety and Efficacy of Intraoperative Doppler Sonography-Assisted Cervical Pedicle Screw Fixation—A Retrospective Comparison with Conventional Pedicle Screw Implantation
Authors: Lee Sang Hyo , Park Jong-Hyeok , Lee Jong Beom , Lee Ho Jin , Kim Il Sup , Hur Jeong Woo , Hong Jae Taek
Published: February 2022

Study Design

A Retrospective Cohort Study.

Objective

To introduce a new Doppler sonography-assisted pedicle screw fixation technique that enables vertebral artery (VA) monitoring during surgery and compares the accuracies of Doppler sonography-assisted cervical pedicle screw fixation and the conventional technique.

Methods

This retrospective study was performed on 164 consecutive patients that underwent pedicle-based screw fixation from C2 to C6 between January 2013 and August 2020. Surgery was performed without intraoperative Doppler sonography in 84 cases (the Control group) or with intraoperative Doppler sonography in 80 cases (the Doppler group). Proper positioning of pedicle screws was graded, and the incidences of VA injury and screw breach in the Control and Doppler groups were compared.

Results

Three hundred and ninety-nine screws were placed in the 164 patients (Doppler, 186 screws; Control, 213 screws). The percentages of well-positioned screws in the two groups were significantly different (Doppler, 97.8%; Control, 85.0%). There were two cases of VA injury in the Control group, an incidence of 2.4%, but no case in the Doppler group.

Conclusion

Doppler sonography can be used intraoperatively to help guide the trajectory of the cervical pedicle screw insertion. It can detect the VA inside the screw trajectory and may reduce the risk of VA injury during cervical pedicle screw fixation.
Craniocervical Instability in Ehlers-Danlos Syndrome—A Systematic Review of Diagnostic and Surgical Treatment Criteria
Authors: Lohkamp Laura-Nanna , Marathe Nandan , Fehlings Michael G.
Published: February 2022

Study Design

Systematic review.

Objective

Ehlers-Danlos Syndrome (EDS) comprises a spectrum of connective tissue disorders, which may be associated with cranio-cervical instability (CCI). There is a lack of consensus on diagnostic imaging parameters, indications, and outcomes of surgical treatment.

Methods

This systematic review analyses the literature on diagnostic methods and/or criteria for CCI, screening the databases Ovid Medline, Embase, Cochrane Library, and PubMed. Articles were included based on the PRISMA guidelines and assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS) and according to their evidence level.

Results

Sixteen articles, including 78 surgical patients, met the inclusion criteria. The main diagnostic measures for CCI were dynamic x-rays and CT imaging. Ten different radiographic parameters were reported, of which 4 were the most frequently applied for surgical decision-making: the clivo-axial angle (CXA), the Harris measurement, the Grabb–Mapstone–Oakes measurement, and the angular displacement of C1 to C2. The evidence level ranged between III and V and the article quality between 4 and 8 out of 9 stars on the NOS Scale.

Conclusions

There is a lack of high quality, prospective evidence regarding the evaluation of suspected CCI in patients with EDS. Based on our systematic review, we recommend that the CXA, Harris measurement, Grabb–Mapstone–Oakes measurement, and the angular displacement of C1 to C2 be used to evaluate suspected CCI in EDS patients. Surgical fixation of suspected CCI should only be performed in cases with clear radiographic presence of instability and concordant symptoms/signs. Consensus-based guidelines and care pathways are required.
Obesity: An Independent Risk Factor for Complications in Anterior Lumbar Interbody Fusion? A Systematic Review
Authors: Feeley Aoife , McDonnell Jake , Feeley Iain , Butler Joseph
Published: February 2022

Study Design

Systematic Review and Meta-analysis

Objectives

Raised patient BMI is recognised as a relative contraindication to posterior lumbar interbody fusion (PLIF) due to the anaesthetic challenges, difficult positioning and increased intraoperative and postoperative complications, with the relative risk rising in patients with a BMI >25 kg/m2. The impact of obesity defined as a BMI > 30 kg/m2 on Anterior Lumbar Interbody Fusion (ALIF) outcomes is not yet established. The aim of this review was to evaluate if the presence of a raised BMI in patients undergoing ALIF procedures was an independent risk factor for intra- and postoperative complications.

Methods

A systematic review of search databases PubMed; Google Scholar and OVID Medline was made to identify studies related to complications in patients with increased body mass index during anterior lumbar interbody fusion. PRISMA guidelines were utilised for this review. Complication rates in raised BMI patient cohort was compared to normal BMI complication rates with meta-analysis where available.

Results

315 articles returned with search criteria applied. Six articles were included for review, with 2190 patients included for analysis. Vascular complications in obese vs. non-obese patients undergoing the anterior approach demonstrate no significant difference in complication rates ( P = .62; CI = −.03–.02). Obesity is found to result in an increased rate of overall complications ( P = .002; CI = .04–.16).

Conclusions

Obesity was demonstrated to have an impact on overall complication rates in Anterior Lumbar Interbody Fusion procedures, with postoperative complications including wound infections and lower fusion rates more common in patients in increased BMIs. Increased focus on patient positioning and reporting of outcomes in this patient cohort is warranted to further evaluate perioperative complications.
10-Year Survival Rates After High Tibial Osteotomy Using Angular Stable Internal Plate Fixation: Case Series With Subgroup Analysis of Outcomes After Combined Autologous Chondrocyte Implantation and High Tibial Osteotomy
Authors: Bode Lisa , Eberbach Helge , Brenner Anna-Sophie , Kloos Ferdinand , Niemeyer Philipp , Schmal Hagen , Suedkamp Norbert P. , Bode Gerrit
Published: February 2022

Background:

Good-to-excellent midterm results after high tibial osteotomy (HTO) to treat medial compartment cartilage defects or osteoarthritis (OA) have been published, but little is known about long-term survival rates in terms of conversion to total knee arthroplasty (TKA) using angular stable internal plate fixation.

Purpose:

To determine TKA-free survival rates and functional and radiological outcomes at 10 years after HTO. A subgroup analysis of patients who underwent combined HTO and autologous cartilage implantation (ACI) was also performed.

Study Design:

Case series; Level of evidence, 4.

Methods:

Included were 125 patients with a mean follow-up of 9.90 ± 2.25 years; 90 patients underwent HTO for medial OA, and 35 patients underwent ACI and HTO for medial focal cartilage defects. Functional outcome measures included visual analog scale (VAS) for pain, Lysholm, International Knee Documentation Committee (IKDC), and Knee injury and Osteoarthritis Outcome Score (KOOS) subscales and KOOS4 (average of 4 KOOS subscales: Pain, Symptoms, Sport, and Quality of Life). Radiological outcomes included lateral distal femoral angle, medial proximal tibial angle, and joint line convergence angle.

Results:

Overall, 16 patients required conversion to TKA at a mean 86.75 ± 25.73 months (10-year survival rate, 87.2%). Only 2 patients in the HTO+ACI subgroup required a conversion to TKA (10-year survival rate, 94.3%). The complication rate for all patients was 8.8%. In both the HTO and HTO+ACI subgroups, VAS pain levels decreased and Lysholm scores increased significantly from pre- to postoperatively ( P < .001). A higher preoperative Tegner score led to a significantly lower risk for conversion to TKA ( P = .001), and a preoperative body mass index of ≥35 was associated with a significantly higher risk ( P = .019), as was female sex ( P = .046). Radiological parameters remained within physiological ranges. The postoperative joint line conversion angle did correlate with postoperative functional outcome but not with TKA conversion.

Conclusion:

Long-term results of HTO for medial compartment OA or cartilage defects with underlying varus deformity were good to excellent. In particular, patients who underwent HTO+ACI presented excellent long-term survival rates. HTO, therefore, delays or prevents TKA implantation, especially in young, active patients with medial compartment damage.
Neural Sociometrics: Toward Early Screening of Infant Psychosocial and Brain Health to Improve Lifelong Mental Well-Being
Authors: Leong Victoria
Published: February 2022

Infant development depends on warm, responsive social interactions that richly stimulate the senses, acting through multiple pathways to orchestrate healthy maturation of the neonatal brain, mind, and body. Conversely, adverse early experiences seed vulnerabilities for poor cognition and emotional instability. Although we routinely measure many aspects of infant physical health (hearing, weight), no clinical tools currently exist to measure early psychosocial health and brain development. Here, neural sociometrics (real-time multi-sensor imaging of adult–infant social interactive behavior and neurophysiology) is discussed as one possible precision measurement framework. Early psychosocial health screening, paired with precision therapeutics, could fundamentally alter a child's development trajectory toward lifelong mental well-being and productivity. Further, population-level measurements of social brain health could forecast mental capital growth (and deficits) for entire communities and generations. This article calls for the prioritized development of early scalable diagnostic instruments to reveal the status of infant mental wellbeing and brain health.
Discrimination and Health: Fostering Better Health for Black American Youth
Authors: Clendinen Cherita A. , Kertes Darlene A.
Published: February 2022

The Black Lives Matter movement has heightened US cultural awareness of the disproportionate burden of racial discrimination for Black Americans. With a special emphasis on Black youth, this review describes the health consequences of discrimination, including depression, anxiety, suicide, stress biology, immune system dysfunction, and cellular aging. However, as evidence documents, ethnic-racial socialization (ERS) reduces the mental, academic, and physical impacts of racial discrimination. A specific policy recommendation would integrate ERS into intervention efforts to reduce the health burden of discrimination on minority youth.
Preparation of layered double hydroxide films using an electrodeposition and subsequent crystal growth method
Authors: Sonoyama Noriyuki , Yamada Shizuka , Ota Tomoki , Inagaki Haruna , Dedetemo Patrick K. , Yoshida Satoshi
Published: February 2022

The surface coating of a gas reaction electrode with layered double hydroxides (LDHs) featuring various electrode catalyst activities was prepared via electrodeposition and the subsequent crystal growth of LDHs. LDH formation was confirmed by X-ray diffraction and Raman scattering measurements after subsequent crystal growth on respective electrodeposited precursor films in Ni-Fe and Zn-Al LDH systems. However, the crystal growth of LDHs in Ni-Mn and Cu-Mn systems was observed on the Mg-Al LDH-electrodeposited films. LDH films were also deposited on the surface of a carbon paper electrode with a rugged surface via electrodeposition and subsequent crystal growth. Using the prepared LDH-coated carbon paper electrodes, the electrode catalytic activity for the oxygen reduction reaction (ORR) was examined. For Ni-Mn, Ni-Al and Ni-Fe LDH-coated carbon paper electrodes, the threshold voltages of the ORR decreased. Hence, the LDHs electrodeposited on a gas reaction electrode have high electrochemical catalytic activity for the ORR.
Altered subcortical and cortical brain morphology in adult women with 47,XXX: a 7-Tesla magnetic resonance imaging study
Authors: Serrarens Chaira , Otter Maarten , Campforts Bea C. M. , Stumpel Constance T. R. M. , Jansma Henk , van Amelsvoort Thérèse A. M. J. , Vingerhoets Claudia
Published: February 2022

Background

Triple X syndrome (47,XXX) is a relatively common sex chromosomal aneuploidy characterized by the presence of a supernumerary X chromosome in females and has been associated with a variable cognitive, behavioural and psychiatric phenotype. 47,XXX may serve as a suitable model for studying the effect of genetic architecture on brain morphology. Previous studies have shown alterations in brain structure in 47,XXX particularly in childhood and adolescence. In this study, we examined subcortical and cortical brain morphology in adult women with 47,XXX using ultra-high field 7T MRI. Given previous evidence of impaired social functioning and emotion recognition in adults with 47,XXX, we also investigated the relationship of these functions with brain morphology.

Methods

Twenty-one adult women with 47,XXX and 22 age- and sex-matched healthy controls were included. Structural T1-weighted images were acquired using a 7-Tesla magnetic resonance scanner. Measures of subcortical brain volumes, cortical surface area and thickness, and cortical folding were obtained and compared between the groups using general linear models. Additionally, we examined potential relationships between brain outcome measures and social functioning and social cognition in 47,XXX using correlation analyses.

Results

Adults with 47,XXX showed lower volumes of the thalamus, caudate, putamen, hippocampus, nucleus accumbens and pallidum, and larger lateral ventricle volumes. Lower surface area was found in the superior frontal gyrus and superior temporal gyrus in 47,XXX participants compared to healthy controls. Altered cortical thickness and cortical folding were not present in 47,XXX. Cortical thickness was associated with social cognition in 47,XXX.

Conclusions

Results suggest that a supernumerary X chromosome in females affects subcortical and lateral ventricle volumes, and cortical surface area in adulthood. 47,XXX may serve as a suitable model for studying genetic influences on structural brain morphology across developmental stages in order to understand neurobiological mechanisms underlying cognitive and behavioural impairments.
SEAseq: a portable and cloud-based chromatin occupancy analysis suite
Authors: Adetunji Modupeore O. , Abraham Brian J.
Published: February 2022

Background

Genome-wide protein-DNA binding is popularly assessed using specific antibody pulldown in Chromatin Immunoprecipitation Sequencing (ChIP-Seq) or Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing experiments. These technologies generate high-throughput sequencing data that necessitate the use of multiple sophisticated, computationally intensive genomic tools to make discoveries, but these genomic tools often have a high barrier to use because of computational resource constraints.

Results

We present a comprehensive, infrastructure-independent, computational pipeline called SEAseq, which leverages field-standard, open-source tools for processing and analyzing ChIP-Seq/CUT&RUN data. SEAseq performs extensive analyses from the raw output of the experiment, including alignment, peak calling, motif analysis, promoters and metagene coverage profiling, peak annotation distribution, clustered/stitched peaks (e.g. super-enhancer) identification, and multiple relevant quality assessment metrics, as well as automatic interfacing with data in GEO/SRA. SEAseq enables rapid and cost-effective resource for analysis of both new and publicly available datasets as demonstrated in our comparative case studies.

Conclusions

The easy-to-use and versatile design of SEAseq makes it a reliable and efficient resource for ensuring high quality analysis. Its cloud implementation enables a broad suite of analyses in environments with constrained computational resources. SEAseq is platform-independent and is aimed to be usable by everyone with or without programming skills. It is available on the cloud at https://platform.stjude.cloud/workflows/seaseq and can be locally installed from the repository at https://github.com/stjude/seaseq.
Risk stratification for predicting postoperative recurrence/metastasis of colorectal cancer by grade of venous invasion coupled with histological subtype
Authors: Imai Yasuo , Ichinose Masanori
Published: February 2022

Background

Colorectal cancer (CRC) consists of several histological subtypes that greatly affect prognosis. Venous invasion (VI) has been implicated in the postoperative recurrence of CRC, but the relationship between the VI grade and postoperative recurrence in each histological subtype has not been clarified thus far.

Methods

A total of 323 CRCs without distant metastasis at surgery (pathologic stage III or lower), including 152 well-to-moderately differentiated adenocarcinomas (WMDAs), 98 poorly differentiated adenocarcinomas (PDAs), and 64 mucinous adenocarcinomas (MUAs), were analyzed. They were routinely processed pathologically, and VI was graded as follows irrespective of location by elastica van Gieson staining: v0 (none), no venous invasion; v1 (mild), 1–3 invasions per glass slide; v2 (moderate), 4–6 invasions per glass slide; and v3 (severe), ≥ 7 invasions per glass slide. Filling-type invasion in veins with a minor axis of ≥ 1 mm increased the grade by 1. The association of VI grade with prognosis was statistically analyzed.

Results

All recurrences occurred as distant metastases. Recurrence increased with VI grade in WMDA (v0 11.8%, v1 15.8%, v2 73.9%, v3 75.0%) and MUA (v0 15.2%, v1 30.8%, v2 40.0%). The recurrence rate was relatively high in PDA even with v0 and increased with VI grade (v0 27.8%, v1 32.7%, v2 33.3%, v3 60.0%). VI grade was a significant predictor of recurrence in WMDA but not in PDA and MUA by multivariate analysis. In node-negative (stage II or lower) CRC, the recurrence-free survival (RFS) rate exceeded 90% in v0 and v1 WMDA until postoperative day (POD) 2100 and v0 MUA until POD 1600 but fell below 80% in the other settings by POD 1000. In node-positive (stage III) CRC, the RFS rate fell below 80% in all histological subtypes by POD 1000.

Conclusions

VI grade v1 had a similar recurrence rate and RFS as grade v0 and may not warrant adjuvant chemotherapy in node-negative (stage II or lower) WMDA. In addition to node-positive (stage III) CRC, adjuvant chemotherapy may be indicated for node-negative (stage II or lower) CRC when it is WMDA with VI grade v2 or v3, MUA with VI, or PDA.
Impact of age, sex and medical history on adverse reactions to the first and second dose of BNT162b2 mRNA COVID-19 vaccine in Japan: a cross-sectional study
Authors: Urakawa Ryuta , Isomura Emiko Tanaka , Matsunaga Kazuhide , Kubota Kazumi , Ike Miho
Published: February 2022

Background

Vaccines for coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are being promoted worldwide. In this study, we analyzed the relationship between adverse reactions and the profile of vaccinated recipients.

Methods

Vaccinated subjects who received two doses of BNT162b2 between May 17 and June 11, 2021, at Osaka University Dental Hospital were included in this study. Adverse reactions and profiles were collected by questionnaires, and the relationship between the presence of adverse reactions and the profiles of the vaccinated persons was analyzed by logistic regression analysis. The correlation between the severity of adverse reactions and age was analyzed by Spearman’s rank correlation.

Results

Logistic regression analysis showed that, for many kinds of adverse reactions, the incidence was significantly higher in females than in males and in younger than in older people. There was a very weak but significant negative correlation between age and the severity of many kinds of adverse reactions. The relationship between sex and the incidence of each adverse reaction was significant for injection site reactions and fatigue in the first vaccination, whereas significant relationships were found for fatigue, chills, fever, arthralgia, myalgia and headache in the second vaccination, all of which were clearly more likely to occur in females.

Conclusion

Adverse reactions to BNT162b2 were found to be more frequent and more intense in females and younger people in Japan, especially after the second vaccination.
Gamma-glutamyl transferase levels are associated with the occurrence of post-stroke cognitive impairment: a multicenter cohort study
Authors: Li Siqi , Liao Xiaoling , Pan Yuesong , Xiang Xianglong , Zhang Yumei
Published: February 2022

Background

Gamma-glutamyl transferase (GGT) is involved in maintenance of physiological concentrations of glutathione in cells, and protects them from oxidative stress-induced damage. However, its role in post-stroke cognitive impairment (PSCI) remains unknown. Here, we investigated the effects of serum GGT on PSCI.

Methods

We conducted a prospective, multicenter cohort study. A total of 1, 957 participants with a minor ischemic stroke or transient ischemic attack whose baseline GGT levels were measured were enrolled from the Impairment of Cognition and Sleep (ICONS) study of the China National Stroke Registry-3 (CNSR-3). They were categorized into four groups according to quartiles of baseline GGT levels. Cognitive functions were assessed using the Montreal Cognitive Assessment (MoCA) approach. Multiple logistic regression models were performed to evaluate the relationship between GGT and PSCI at 3 months follow-up.

Results

Among the 1957 participants, 671 (34.29%) patients suffered PSCI at 3 months follow-up. The highest GGT level quartile group exhibited a lower risk of PSCI in the fully adjusted model [OR (95% CI): 0.69 (0.50-0.96)], relative to the lowest group. Moreover, incorporation of GGT to the conventional model resulted in slight improvements in PSCI outcomes after 3 months (NRI: 12.00%; IDI: 0.30%).

Conclusions

Serum GGT levels are inversely associated with the risk of PSCI, with extremely low levels being viable risk factors for PSCI.
Breast cancer screening in sub-Saharan Africa: a systematic review and ethical appraisal
Authors: Martei Yehoda M. , Dauda Bege , Vanderpuye Verna
Published: February 2022

Background

The aim of this systematic review was to evaluate the evidence and clinical outcomes of screening interventions and implementation trials in sub-Saharan Africa (SSA) and also appraise some ethical issues related to screening in the region through quantitative and qualitative narrative synthesis of the literature.

Methods

We searched Pubmed, OvidMEDLINE, Embase, and Web of Science to identify studies published on breast cancer screening interventions and outcomes in SSA. Descriptive statistics were used to summarize the frequency and proportions of extracted variables, and narrative syntheses was used to evaluate the clinical outcomes of the different screening modalities. The mixed methods appraisal tool was used to assess the quality of studies included in the review.

Results

Fifteen studies were included, which consisted of 72,572 women in ten countries in SSA. 63% (8/15) of the included publications evaluated Clinical Breast Examination (CBE), 47% (7/15) evaluated mammography and 7% (1/15) evaluated ultrasound screening. The cancer detection rate was < 1/1000 to 3.3/1000 and 3.3/100 to 56/1000 for CBE and mammography screening respectively. There was a lot of heterogeneity in CBE methods, target age for screening and no clear documentation of screening interval. Cost-effective analyses showed that CBE screening linked to comprehensive cancer care is most cost effective. There was limited discussion of the ethics of screening, including the possible harms of screening in the absence of linkage to care. The gap between conducting good screening program and the appropriate follow-up with diagnosis and treatment remains one of the major challenges of screening in SSA.

Discussion

There is insufficient real-world data to support the systematic implementation of national breast cancer screening in SSA. Further research is needed to answer important questions about screening, and national and international partnerships are needed to ensure that appropriate diagnostic and treatment modalities are available to patients who screen positive.
Cooperation with rheumatologists on intensive systemic treatment for psoriatic arthritis-related panuveitis with retinal vasculitis: a case report
Authors: Wu Po-Ying , Kao Chia-Chen , Sheu Shwu-Jiuan
Published: February 2022

Background

Patients with psoriatic arthritis (PsA) may develop uveitis, a potentially serious ocular complication. PsA-related uveitis may result in significant morbidity and even vision loss if underdiagnosed or under-treated. We presented a case with long-standing recurrent uveitis and retinal vasculitis successfully managed by fortified systemic immunomodulators for systemic PsA.

Case presentation

A 47-year-old woman was referred under the impression of acute anterior uveitis in her right eye in recent one month. Ocular examinations showed panuveitis in both eyes with intense vitreous opacity in her right eye. Fundus fluorescence angiography revealed retinal vasculitis in both eyes. Systemic surveys excluded the possibility of infection but showed an elevated inflammation marker. With intensive immunosuppressive treatment, inflammation resolved and the vision improved.

Conclusion

Our case highlights not only the importance of intensified systemic therapy in treating PsA-related uveitis but the importance of multidisciplinary collaboration. Recurrent uveitis may be an indicator of disease activity prior to other inflammatory markers.
Biomechanical evaluation and comparison of clinically relevant versus non-relevant leg length inequalities
Authors: Michalik Roman , Rissel Viola , Migliorini Filippo , Siebers Hannah Lena , Betsch Marcel
Published: February 2022

Background

Leg length inequalities are a frequent condition in every population. It is common clinical practice to consider LLIs of 2 cm and more as relevant and to treat those. However, the amount of LLIs that need treatment is not clearly defined in literature and the effect of real LLIs on the musculoskeletal system above and below 2 cm have not been studied biomechanically before.

Methods

By using surface topography, we evaluated 32 patients (10 females, 22 male) with real LLIs of ≥ 2 cm (mean: 2.72 cm; n = 10) and compared their pelvic position and spinal posture to patients with LLIs < 2 cm (mean: 1.24 cm; n = 22) while standing and walking. All patients were measured with a surface topography system during standing and while walking on a treadmill. To compare patient groups, we used Student t-tests for independent samples.

Results

Pelvic obliquity was significantly higher in patients with LLI ≥ 2 cm during the standing trial (p = 0.045) and during the midstance phase of the longer leg (p = 0.023) while walking. Further measurements did not reveal any significant differences (p = 0.06–0.706).

Conclusions

The results of our study suggest that relevant LLIs of ≥ 2 cm mostly affect pelvic obliquity and do not lead to significant alterations in the spinal posture during a standing trial. Additionally, we demonstrated that LLIs are better compensated when walking, showing almost no significant differences in pelvic and spinal posture between patients with LLIs smaller and greater than 2 cm. This study shows that LLIs ≥ 2 cm can still be compensated; however, we do not know if the compensation mechanisms may lead to long-term clinical pathologies.
“I felt like she didn’t take me seriously”: a multi-methods study examining patient satisfaction and experiences with polycystic ovary syndrome (PCOS) in Canada
Authors: Ismayilova Miya , Yaya Sanni
Published: February 2022

Background

Polycystic ovary syndrome (PCOS) is a common and complex condition affecting metabolic, reproductive, cardiovascular, and psychological health in women. Previous studies point to widespread dissatisfaction and delays with the diagnosis of PCOS and a lack of information provision by doctors, with few studies on Canadian populations. This multi-methods study explored the perceptions and experiences of PCOS diagnosis in Canada using an online-distributed survey and follow-up, in-depth, semi-structured phone interviews.

Methods

The online questionnaire was completed by 296 women aged 18–60 with a self-reported diagnosis of PCOS. The survey measured time to diagnosis, number of doctors seen, and information provided. Descriptive statistics, Chi-square tests, Fisher’s exact tests, and Spearman’s rank correlations were used to analyze the sample characteristics and correlations between the demographic factors and the outcome measures. Twenty-five follow-up interviews were held over the phone and analyzed using thematic analysis and interpretive description methodology.

Results

Survey respondents were dissatisfied with the information provided about PCOS (66%), lifestyle management (34%), and medical therapy (38%) at the time of diagnosis. Approximately 34% of respondents waited for more than 2 years and 41% saw 3 or more doctors before attaining diagnosis. Many did not receive any information about lifestyle management (42%) or medical therapy (28%). Interview participants encountered doctors who lacked sufficient knowledge on PCOS to diagnose, chronically dismissed concerns, and did not provide necessary medical information about the condition. Women described benefitting from self-advocation to receive the care they needed from doctors, and self-educating about PCOS using materials they could find online. Younger interview participants whose symptoms began in adolescence would often not understand the significance of symptoms until much later in life, contributing to delayed diagnoses.

Conclusions

Greater education on PCOS for physicians, particularly in primary care, is needed to prevent delayed diagnoses and ensure that patients are provided with reliable medical information about their condition. Greater awareness of PCOS may be necessary for the general population to help women identify symptoms, especially for adolescents and their parental figures.
Transitions in general practice training: quantifying epidemiological variation in trainees’ experiences and clinical behaviours
Authors: Tran Michael , Wearne Susan , Tapley Amanda , Fielding Alison , Davey Andrew , van Driel Mieke , Holliday Elizabeth , Ball Jean , FitzGerald Kristen , Spike Neil , Magin Parker
Published: February 2022

Background

General Practice training in Australia is delivered through the apprenticeship model. General Practice supervisors support trainees transitioning from hospital-based work towards competent independent community-based practice. The timing and manner in which support should be provided is still not well understood. This study aimed to establish the variation in clinical and educational experiences and behaviours, and location, of general practice trainees’ consultations by stage of their vocational training. It was hypothesised that change is greater in earlier stages of training.

Methods

A cross-sectional analysis of data (2010–2018) from the Registrar Clinical Encounters in Training (ReCEnT) study, an ongoing cohort study of Australian GP registrars’ in-consultation clinical and educational experience and behaviours. Multinomial logistic regression assessed the association of demographic, educational, and clinical factors in different stages of training. The outcome factor was the training term.

Results

Two thousand four hundred sixteen registrars contributed data for 321,414 patient consultations. For several important variables (seeing patients with chronic disease; new patients; seeking in-consultation information or assistance; ordering pathology and imaging; and working in a small or regional practice), odds ratios were considerably greater for comparisons of Term 1 and 3, relative to comparisons of Term 2 and 3.

Conclusion

Differences experienced in demographic, clinical and educational factors are significantly more pronounced earlier in registrars’ training. This finding has educational and training implications with respect to resource allocation, trainee supervision and curriculum design. Sociocultural learning theory enables an understanding of the impact of transitions on, and how to support, general practice trainees and supervisors.