bluuebunny/crossref_metadata_2025 huggingface dataset:
Prognostic value of shock index in patients admitted with non-ST-segment elevation myocardial infarction: the ARIC study community surveillance
Authors: Chunawala Zainali S , Hall Michael E , Arora Sameer , Dai Xuming , Menon Venu , Smith Sidney C , Matsushita Kunihiro , Caughey Melissa C
Published: June 2021

Aims

Shock index (SI), defined as the ratio of heart rate (HR) to systolic blood pressure (SBP), is easily obtained and predictive of mortality in patients with ST-segment elevation myocardial infarction. However, large-scale evaluations of SI in patients with non-ST-segment elevation myocardial infarction (NSTEMI) are lacking.

Methods and results

Hospitalizations for acute myocardial infarction were sampled from four US areas by the Atherosclerosis Risk in Communities (ARIC) study and classified by physician review. Shock index was derived from the HR and SBP at first presentation and considered high when ≥0.7. From 2000 to 2014, 18 301 weighted hospitalizations for NSTEMI were sampled and had vitals successfully obtained. Of these, 5753 (31%) had high SI (≥0.7). Patients with high SI were more often female (46% vs. 39%) and had more prevalent chronic kidney disease (40% vs. 32%). TIMI (Thrombolysis in Myocardial Infarction) risk scores were similar between the groups (4.3 vs. 4.2), but GRACE (Global Registry of Acute Coronary Syndrome) score was higher with high SI (140 vs. 118). Angiography, revascularization, and guideline-directed medications were less often administered to patients with high SI, and the 28-day mortality was higher (13% vs. 5%). Prediction of 28-day mortality by SI as a continuous measurement [area under the curve (AUC): 0.68] was intermediate to that of the GRACE score (AUC: 0.87) and the TIMI score (AUC: 0.54). After adjustments, patients with high SI had twice the odds of 28-day mortality (odds ratio = 2.02; 95% confidence interval: 1.46–2.80).

Conclusion

The SI is easily obtainable, performs moderately well as a predictor of short-term mortality in patients hospitalized with NSTEMI, and may be useful for risk stratification in emergency settings.
Body weight and premature retirement: population-based evidence from Finland
Authors: Viinikainen Jutta , Tikka Santtu , Laaksonen Mikko , Jääskeläinen Tuija , Böckerman Petri , Karvanen Juha
Published: June 2021

Background

Health status is a principal determinant of labour market participation. In this study, we examined whether excess weight is associated with withdrawal from the labour market owing to premature retirement.

Methods

The analyses were based on nationally representative data from Finland over the period 2001–15 (N ∼ 2500). The longitudinal data included objective measures of body weight (i.e. body mass index and waist circumference) linked to register-based information on actual retirement age. The association between the body weight measures and premature retirement was modelled using cubic b-splines via logistic regression. The models accounted for other possible risk factors and potential confounders, such as smoking and education.

Results

Excess weight was associated with an increased risk of premature retirement for both men and women. A closer examination revealed that the probability of retirement varied across the weight distribution and the results differed between sexes and weight measures.

Conclusion

Body weight outside a recommended range elevates the risk of premature retirement.
Mapping key components of community-oriented strategies to facilitate alcohol-related early identification and brief intervention in general practice: a scoping review
Authors: Pussig Bram , Vandelanotte Sarah , Matheï Catharina , Pas Leo , Aertgeerts Bert , Vermandere Mieke
Published: June 2021

Hazardous alcohol use is one of the leading risk factors for morbidity and mortality in the world. Early identification and brief interventions (EIBIs) delivered in primary care is an effective but underutilized strategy to address this issue. Community-oriented strategies (COS) are suggested to facilitate EIBI delivery. COS are public health activities directed to the general population raising awareness and encouraging behaviour change. Unfortunately, it remains unclear what these COS should comprise and what their added value might be in EIBI delivery. To map the available information on COS aiming to facilitate alcohol-related EIBI delivery in general practice. A scoping review, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses for Scoping reviews guidelines, was used to map both grey and peer-reviewed literature. Of the 6586 information sources screened, 8 sources were retained in this review. Three COS are currently described in the literature, all with their different components. They include the use of mass media, self-assessment tools and waiting room actions. Waiting room actions comprising audio recordings or computerized self-assessment tools significantly increase the discussion on alcohol use in primary care. The effect of mass media and community-wide self-assessment tools on EIBI delivery remains to be determined. Currently, the described COS lack empirical justification to motivate their added value in facilitating EIBI delivery. However, a theoretical reflection showed the use of a limited set of behaviour change techniques, which might support the use of COS. There remains a lot of possible strategies to explore. This review highlights the current evidence gap and discusses the next steps.
Antibiotics for gastroenteritis in general practice and out-of-hour services in Norway 2006–15
Authors: Emberland Knut Erik , Wensaas Knut-Arne , Litleskare Sverre , Larsen Leo , Morch Kristine , Ruths Sabine , Rortveit Guri
Published: June 2021

Background

When patients with gastroenteritis (GE) seek health care, they are generally managed in primary care. Little is known about the use of antibiotic treatment in these cases.

Objective

The aim of this study was to investigate time trends and patient characteristics associated with antibiotic treatment for GE in Norwegian primary care in a 10-year period.

Methods

We linked data from two nationwide registries, reimbursement claims data from Norwegian primary care (the KUHR database) and The Norwegian Prescription Database, for the period 2006–15. GE consultations were extracted, and courses of systemic antibiotics dispensed within 1 day were included for further analyses.

Results

Antibiotic treatment was linked to 1.8% (n = 23 663) of the 1 279 867 consultations for GE in Norwegian primary care in the period 2006–15. The proportion of GE consultations with antibiotic treatment increased from 1.4% in 2006 to 2.2% in 2012 and then decreased to 1.8% in 2015. Fluoroquinolones (28.9%) and metronidazole (26.8%) were most frequently used. Whereas the number of fluoroquinolones courses decreased after 2012, the number of metronidazole courses continued to increase until year 2015. The antibiotic treatment proportion of GE consultations was lowest in young children and increased with increasing age.

Conclusion

Antibiotic treatment is infrequently used in GE consultations in Norwegian primary care. Although there was an overall increase in use during the study period, we observed a reduction in overall use after year 2012. Young children were treated with antibiotics in GE consultations less frequent than older patients.
34S enrichment as a signature of thiosulfate oxidation in the “Proteobacteria”
Authors: Alam Masrure , Fernandes Svetlana , Mandal Subhrangshu , Rameez Maida Jameela , Bhattacharya Sabyasachi , Peketi Aditya , Mazumdar Aninda , Ghosh Wriddhiman
Published: June 2021

Kinetics of thiosulfate oxidation, product and intermediate formation, and 34S fractionation, were studied for the members of Alphaproteobacteria Paracoccus sp. SMMA5 and Mesorhizobium thiogangeticum SJTT, the Betaproteobacteria member Pusillimonas ginsengisoli SBO3, and the Acidithiobacillia member Thermithiobacillus sp. SMMA2, during chemolithoautotrophic growth in minimal salts media supplemented with 20 mM thiosulfate. The two Alphaproteobacteria oxidized thiosulfate directly to sulfate, progressively enriching the end-product with 34S; Δ34Sthiosulfate-sulfate values recorded at the end of the two processes (when no thiosulfate was oxidized any further) were −2.9‰ and −3.5‰, respectively. Pusillimonas ginsengisoli SBO3 and Thermithiobacillus sp. SMMA2, on the other hand, oxidized thiosulfate to sulfate via tetrathionate intermediate formation, with progressive 34S enrichment in the end-product sulfate throughout the incubation period; Δ34Sthiosulfate-sulfate, at the end of the two processes (when no further oxidation took place), reached −3.5‰ and −3.8‰, respectively. Based on similar 34S fractionation patterns recorded previously during thiosulfate oxidation by strains of Paracoccus pantotrophus, Advenella kashmirensis and Hydrogenovibrio crunogenus, it was concluded that progressive reverse fractionation, enriching the end-product sulfate with 34S, could be a characteristic signature of bacterial thiosulfate oxidation.
Using magnetic techniques to calibrate hydrocarbon migration in petroleum systems modelling: A Case Study from the Lower Tertiary, UK Central North Sea
Authors: Badejo S A , Muxworthy A R , Fraser A , Neumaier M , Perkins J R , Stevenson G R , Davey R
Published: June 2021

Magnetic minerals form or alter in the presence of hydrocarbons, making them a potential magnetic proxy for identifying hydrocarbon migration pathways. In this paper we test this idea by magnetically measuring core samples from the Tay Fan in the Western Central Graben in the Central North Sea. In a companion paper, 3D petroleum systems modelling has been carried out to forward model migration pathways within the Tay Fan. Rock magnetic experiments identified a range of magnetite, maghemite, iron sulphides, siderite, goethite and titanohematite, some of which are part of the background signal, and some due to the presence of hydrocarbons. Typical concentrations of the magnetic minerals were ∼10–200 ppm. Importantly, we have identified an increasing presence of authigenic iron sulphides (likely pyrite and greigite) along the identified lateral hydrocarbon migration pathway (east to west). This is likely caused by biodegradation resulting in the precipitation of iron sulphides, however, though less likely, it could alternatively be caused by mature oil generation, which subsequently travelled with the migrating oil to the traps in the west. These observations suggest mineral magnetic techniques could be a rapid alternative method for identifying the severity of biodegradation or oil maturity in core sample, which can then be used to calibrate petroleum systems models.
Structure and properties of the giant reed (Arundo donax) lectin (ADL)
Authors: Perduca Massimiliano , Bovi Michele , Destefanis Laura , Nadali Divina , Fin Laura , Parolini Francesca , Sorio Daniela , Carrizo Maria E , Monaco Hugo L
Published: June 2021

Arundo donax lectin (ADL) is a 170 amino acid protein that can be purified from the rhizomes of the giant reed or giant cane by exploiting its selective binding to chitin followed by elution with N-acetylglucosamine. The lectin is listed in the UniProt server, the largest protein sequence database, as an uncharacterized protein with chitin-binding domains (A0A0A9P802). This paper reports the purification, structure and ligand-binding properties of ADL. The lectin is a homodimer in which the two protomers are linked by two disulfide bridges. Each polypeptide chain presents four carbohydrate-binding modules that belong to carbohydrate-binding module family 18. A high degree of sequence similarity is observed among the modules present in each protomer. We have determined the X-ray structure of the apo-protein to a resolution of 1.70 Å. The carbohydrate-binding modules, that span a sequence of approximately 40 amino acids, present four internal disulfide bridges, a very short antiparallel central beta sheet and three short alpha helices, two on one side of the beta sheet and one on the other. The structures of the complexes of the lectin with N-acetylglucosamine, N-acetyllactosamine, N-acetylneuraminic acid and N-N’diacetylchitobiose reveal that ADL has two primary and two secondary carbohydrate-binding sites per dimer. They are located at the interface between the two protomers, and each binding site involves residues of both chains. The lectin presents structural similarity to the wheat germ agglutinin family, in particular, to isoform 3.
Evaluating urban–rural access to pathology and laboratory medicine services in Tanzania
Authors: Iyer Hari S , Wolf Nicholas G , Flanigan John S , Castro Marcia C , Schroeder Lee F , Fleming Kenneth , Vuhahula Edda , Massambu Charles
Published: June 2021

Placement of pathology and laboratory medicine (PALM) services requires balancing efficiency (maximizing test volume) with equitable urban–rural access. We compared the association between population density (proxy for efficiency) and travel time to the closest facility (proxy for equitable access) across levels of Tanzania’s public sector health system. We linked geospatial data for Tanzania from multiple sources. Data on facility locations and other geographic measures were collected from government and non-governmental databases. We classified facilities assuming increasing PALM availability by tier: (1) dispensaries, (2) health centres, (3) district hospitals and (4) regional/referral hospitals. We used the AccessMod 5 algorithm to estimate travel time to the closest facility for each tier across Tanzania with 500-m resolution. District-level average population density and travel time to the closest facility were calculated and presented using medians and interquartile ranges. Spatial correlations between these variables were estimated using the global Moran’s I and bivariate Local Indicator of Spatial Autocorrelation, specifying a queen’s neighbourhood matrix. Spatial analysis was restricted to 171 contiguous districts. The study included 5406 dispensaries, 675 health centres, 186 district hospitals and 37 regional/referral hospitals. District-level travel times were shortest for Tier 1 (median: [IQR]: 45.4 min [30.0–74.7]) and longest for Tier 4 facilities (160.2 min [107.3–260.0]). There was a weak spatial autocorrelation across tiers (Tier 1: −0.289, Tier 2: −0.292, Tier 3: −0.271 and Tier 4: −0.258) and few districts were classified as significant spatial outliers. Across tiers, geographic patterns of populated districts surrounded by neighbours with short travel time and sparsely populated districts surrounded by neighbours with long travel time were observed. Similar spatial correlation measures across health system levels suggest that Tanzania’s health system reflects equitable urban–rural access to different PALM services. Longer travel times to hospital-based care could be ameliorated by shifting specialized diagnostics to more accessible lower tiers.
Mitochondrial DNA disorders: from pathogenic variants to preventing transmission
Authors: Bernardino Gomes Tiago M , Ng Yi Shiau , Pickett Sarah J , Turnbull Doug M , Vincent Amy E
Published: June 2021

Mitochondrial DNA (mtDNA) disorders are recognized as one of the most common causes of inherited metabolic disorders. The mitochondrial genome occurs in multiple copies resulting in both homoplasmic and heteroplasmic pathogenic mtDNA variants. A biochemical defect arises when the pathogenic variant level reaches a threshold, which differs between variants. Moreover, variants can segregate, clonally expand, or be lost from cellular populations resulting in a dynamic and tissue-specific mosaic pattern of oxidative deficiency. MtDNA is maternally inherited but transmission patterns of heteroplasmic pathogenic variants are complex. During oogenesis, a mitochondrial bottleneck results in offspring with widely differing variant levels to their mother, whilst highly deleterious variants, such as deletions, are not transmitted. Complemented by a complex interplay between mitochondrial and nuclear genomes, these peculiar genetics produce marked phenotypic variation, posing challenges to the diagnosis and clinical management of patients. Novel therapeutic compounds and several genetic therapies are currently under investigation, but proven disease-modifying therapies remain elusive. Women who carry pathogenic mtDNA variants require bespoke genetic counselling to determine their reproductive options. Recent advances in in vitro fertilization techniques, have greatly improved reproductive choices, but are not without their challenges. Since the first pathogenic mtDNA variants were identified over 30 years ago, there has been remarkable progress in our understanding of these diseases. However, many questions remain unanswered and future studies are required to investigate the mechanisms of disease progression and to identify new disease-specific therapeutic targets.
Examining Cultural Structures and Functions in Biology
Authors: Tanner Richelle L , Grover Neena , Anderson Michelle L , Crocker Katherine C , Dutta Shuchismita , Horner Angela M , Hough Loren E , Moore Talia Y , Rosen Gail L , S Whitney Kaitlin , Summers Adam P
Published: June 2021

Synopsis

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity—we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access—a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together—this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate—not reintegrate—the nuances of biology into our field.
Hybrid Metachronal Rowing Augments Swimming Speed and Acceleration via Increased Stroke Amplitude
Authors: Ford Mitchell P , Ray William J , DiLuca Erika M , Patek S N , Santhanakrishnan Arvind
Published: June 2021

Synopsis

Numerous aquatic invertebrates use drag-based metachronal rowing for swimming, in which closely spaced appendages are oscillated starting from the posterior, with each appendage phase-shifted in time relative to its neighbor. Continuously swimming species such as Antarctic krill generally use “pure metachronal rowing” consisting of a metachronal power stroke and a metachronal recovery stroke, while burst swimming species such as many copepods and mantis shrimp typically use “hybrid metachronal rowing” consisting of a metachronal power stroke followed by a synchronous or nearly synchronous recovery stroke. Burst swimming organisms need to rapidly accelerate in order to capture prey and/or escape predation, and it is unknown whether hybrid metachronal rowing can augment acceleration and swimming speed compared to pure metachronal rowing. Simulations of rigid paddles undergoing simple harmonic motion showed that collisions between adjacent paddles restrict the maximum stroke amplitude for pure metachronal rowing. Hybrid metachronal rowing similar to that observed in mantis shrimp (Neogonodactylus bredini) permits oscillation at larger stroke amplitude while avoiding these collisions. We comparatively examined swimming speed, acceleration, and wake structure of pure and hybrid metachronal rowing strategies by using a self-propelling robot. Both swimming speed and peak acceleration of the robot increased with increasing stroke amplitude. Hybrid metachronal rowing permitted operation at larger stroke amplitude without collision of adjacent paddles on the robot, augmenting swimming speed and peak acceleration. Hybrid metachronal rowing generated a dispersed wake unlike narrower, downward-angled jets generated by pure metachronal rowing. Our findings suggest that burst swimming animals with small appendage spacing, such as copepods and mantis shrimp, can use hybrid metachronal rowing to generate large accelerations via increasing stroke amplitude without concern of appendage collision.
Impaired T-Lymphocyte Responses During Childhood Staphylococcus aureus Infection
Authors: Li Zhaotao , Beesetty Pavani , Gerges George , Kleinhenz Maureen , Moore-Clingenpeel Melissa , Yang Ching , Ahmed Luul B , Hensley Josey , Steele Lisa , Chong Anita S , Montgomery Christopher P
Published: June 2021

Background

Staphylococcus aureus infections are common throughout the lifespan, with recurrent infections occurring in nearly half of infected children. There is no licensed vaccine, underscoring the need to better understand how S. aureus evades protective immunity. Despite much study, the relative contributions of antibodies and T cells to protection against S. aureus infections in humans are not fully understood.

Methods

We prospectively quantified S. aureus-specific antibody levels by ELISA and T-cell responses by ELISpot in S. aureus-infected and healthy children.

Results

S. aureus-specific antibody levels and T-cell responses increased with age in healthy children, suggesting a coordinated development of anti-staphylococcal immunity. Antibody levels against leukotoxin E (LukE) and Panton-Valentine leukocidin (LukS-PV), but not α-hemolysin (Hla), were higher in younger infected children, compared with healthy children; these differences disappeared in older children. We observed a striking impairment of global and S. aureus-specific T-cell function in children with invasive and noninvasive infection, suggesting that S. aureus-specific immune responses are dysregulated during childhood infection regardless of the infection phenotype.

Conclusions

These findings identify a potential mechanism by which S. aureus infection actively evades adaptive immune responses, thereby preventing the development of protective immunity and maintaining susceptibility to recurrent infection.
Social Determinants of Poor Outcomes Following Frostbite Injury: A Study of the National Inpatient Sample
Authors: Endorf Frederick W , Nygaard Rachel M
Published: June 2021

Severe frostbite injury can result in significant disability from amputation of limbs and digits which may be mitigated through prompt medical care. The reported rates of amputation vary widely between centers. Our aim was to describe the incidence and factors associated with amputation secondary to frostbite injury in the United States using a national sample of hospitalizations. Admissions for frostbite injury were identified in the National Inpatient Sample (2016–2018). Factors associated with amputation were assessed by multivariable logistic regression and clustered by hospital. The overall incidence of frostbite injury in the United States is 0.83 of 100,000 people. Of the social factors associated with frostbite injury, homelessness and the black race were independently associated with a higher likelihood of amputation at the primary admission. Diagnosis of cellulitis was a predictor of amputation. Homeless frostbite patients were more frequently discharged against medical advice and were less likely to discharge with supportive medical care, despite having a higher rate of more severe injury. Disability from amputation following frostbite injury affects at least 20% of frostbite-injured patients and disproportionally affects the homeless population. Further study is needed to ascertain the decision making that leads to early amputation following frostbite injury, especially in the homeless and black population. Outreach and education efforts should be initiated to promote salvage of functional limb length following frostbite injury.
Adherence of Burn Outpatient Clinic Referrals to ABA Criteria in a Tertiary Center: Creating Unnecessary Referrals?
Authors: Chambers Spencer B , Garland Katie , Dai Cecilia , DeLyzer Tanya
Published: June 2021

Initial assessment and triage of burns are guided by the American Burn Association criteria for referral to a burn center. These criteria are sensitive but not specific and can potentially lead to over-triage and “unnecessary” clinic visits. We are a Level 1 trauma center with burn subspecialty care, and due to the COVID-19 pandemic, referrals to our multidisciplinary outpatient burn clinic required triaging for virtual care appointments. In order to improve the triage process, we retrospectively reviewed our outpatient burn clinic referrals over a 2-year period, 2018 to 2019, for adherence to American Burn Association criteria. We collected data pertaining to patient and burn characteristics, as well as treatment outcome, to characterize referrals not requiring an in-person appointment. Of the 244 patients referred, 73% met the referral criteria, with 45% of these patients being healed at the first visit and 14.6% requiring surgical management. Mean time from injury to first visit was 9.7 days (mode 6), and the average number of visits was 2. Overall, mean burn size was 2%, with the majority of injuries being partial thickness (71%), located in the hand or extremity (77%). There was a fairly equal distribution of contact (36%), flame (21%), and scald (26%) burns. This study highlights the nonspecific nature of the American Burn Association referral criteria. We found that pediatric and hand burns in particular were over-triaged and lead to “unnecessary” appointments. This information is useful to help adjust referral criteria and to guide triaging of appointments with the evolution of telehealth and virtual care.
The Average and Heterogeneous Effects of Transportation Investments: Evidence from Sub-Saharan Africa 1960–2010
Authors: Jedwab Rémi , Storeygard Adam
Published: June 2021

Previous work on transportation investments has focused on average impacts in high- and middle-income countries. We estimate average and heterogeneous effects in a poor continent, Africa, using roads and cities data spanning 50 years in 39 countries. Using changes in market access due to distant road construction as a source of exogenous variation, we estimate a 30-year elasticity of city population with respect to market access of about 0.08–0.13. Our results suggest that this elasticity is stronger for small and remote cities, and weaker in politically favored and agriculturally suitable areas. Access to foreign cities besides international ports matters little. Additional evidence points suggestively to rural-to-urban migration as the primary source of this population increase, though we cannot fully rule out natural increase or reallocation across cities.
Can regular follow-up imaging contribute to the determination of appropriate timing of surgery in patients with undiagnosed mucinous cystic neoplasm? A multicenter retrospective study
Authors: Satoh Tatsunori , Ishiwatari Hirotoshi , Kawaguchi Shinya , Sato Junya , Kaneko Junichi , Kanemoto Hideyuki , Sugiura Teiichi , Sasaki Keiko , Matsubayashi Hiroyuki , Uesaka Katsuhiko , Ono Hiroyuki
Published: June 2021

Objective

Guidelines suggest that patients with undiagnosed pancreatic cystic lesions should be monitored despite a lack of evidence supporting surveillance for undiagnosed mucinous cystic neoplasms (MCNs). We aimed to investigate the pre- and post-operative clinical course of patients with MCN and the utility of follow-up for patients who were not diagnosed with MCN at initial examination.

Patients and Methods

This multicenter retrospective study enrolled 28 patients with resected pathology-proven MCN; 12 and 16 patients underwent surgery within and after 6 months from the initial examination (Groups A and B, respectively). Outcome measures included changes in imaging findings until surgery in Group B, pathological findings between both groups and differences in pathological findings between patients with and without regular follow-up imaging in Group B.

Results

In Group B, the median cyst size was 30 and 48 mm at the initial examination and immediately before surgery, respectively. The incidence of mural cysts, thickened walls and mural nodules were 25, 19 and 0%, respectively, at the initial examination and 69, 56 and 31%, respectively, immediately before surgery. There were no significant differences in the invasive carcinoma rates between Groups A and B (13 vs. 17%). Regular follow-up imaging was offered to Group B. Among these, invasive carcinoma was found in one patient exhibiting no recurrence. One patient without follow-up imaging had invasive carcinoma recurrence post-operatively.

Conclusions

MCNs increased in size, and typical imaging findings appeared over time. For undiagnosed MCN, regular follow-up examination contributed to the determination of the appropriate surgical timing.
Slingshot prominences: a hidden mass loss mechanism
Authors: Waugh Rose F P , Jardine Moira M , Morin J , Donati J-F
Published: June 2021

Whilst ‘slingshot’ prominences have been observed on M-dwarfs, most if not all theoretical studies have focused on solar-like stars. We present an investigation into stellar prominences around rapidly rotating young M-dwarfs. We have extrapolated the magnetic field in the corona from Zeeman-Doppler maps and determined the sites of mechanical stability where prominences may form. We analyse the prominence mass that could be supported and the latitude range over which this material is distributed. We find that for these maps, much of this prominence mass may be invisible to observation – typically <1 per cent transits the stellar disc. On the rapidly rotating M-dwarf V374 Peg (Prot = 0.45 d) where prominences have been observed, we find the visible prominence mass to be around only 10 per cent of the total mass supported. The mass loss rate per unit area for prominences scales with the X-ray surface flux as $\dot{M}/A \propto \, F_\mathrm{ X}^{1.32}$ that is very close to the observationally derived value for stellar winds. This suggests that prominence ejection may contribute significantly to the overall stellar wind loss and spin-down. A planet in an equatorial orbit in the habitable zone of these stars may experience intermittent enhancements of the stellar wind due to prominence ejections. On some stars, this may occur throughout 20 per cent of the orbit.
Supercritical dusty BH growth in the early Universe
Authors: Ishibashi W
Published: June 2021

Supermassive black holes (with ${M_{\rm BH} \sim 10^9\, \mathrm{M}_{\odot }}$) are observed in the first Gyr of the Universe, and their host galaxies are found to contain unexpectedly large amounts of dust and metals. In light of the two empirical facts, we explore the possibility of supercritical accretion and early black hole growth occurring in dusty environments. We generalize the concept of photon trapping to the case of dusty gas and analyse the physical conditions leading to ‘dust photon trapping’. Considering the parameter space dependence, we obtain that the dust photon trapping regime can be more easily realized for larger black hole masses, higher ambient gas densities, and lower gas temperatures. The trapping of photons within the accretion flow implies obscured active galactic nuclei, while it may allow a rapid black hole mass build-up at early times. We discuss the potential role of such dust photon trapping in the supercritical growth of massive black holes in the early Universe.
Primordial black hole origin for thermal gamma-ray bursts
Authors: Barco Oscar
Published: June 2021

A binary black hole (BH) astrophysical scenario where a mass-constrained (2.5 × 10−13M⊙) primordial black hole (PBH) undergoes a radial fall on to its heavier component (such as a supermassive black hole, SMBH) is described as an intense gamma-ray emission event. As the relativistic PBH approaches the Schwarschild SMBH event horizon, its Lorentz-boosted Hawking radiation progressively reduces to a near-zero emission cone resulting in a highly collimated thermal beam. Accordingly, our numerically calculated PBH flux density Sν and νSν fluence spectrum show a decreasing Planck-like spectral dependence consistent with the cooling behaviour of thermal-dominant gamma-ray bursts (GRBs). Our results might provide an alternative explanation for thermal GRBs based on PBH origin.
Reverse transcription priming methods affect normalisation choices for gene expression levels in oocytes and early embryos
Authors: Yu Bo , van Tol Helena T A , Stout Tom A E , Roelen Bernard A J
Published: June 2021

Mammalian oocytes and embryos rely exclusively on maternal mRNAs to accomplish early developmental processes. Since oocytes and early embryos are transcriptionally silent after meiotic resumption, most of the synthesised maternal mRNA does not undergo immediate translation but is instead stored in the oocyte. Quantitative RT-PCR is commonly used to quantify mRNA levels, and correct quantification relies on reverse transcription and the choice of reference genes. Different methods for reverse transcription may affect gene expression determination in oocytes. In this study, we examined the suitability of either random or oligo(dT) primers for reverse transcription to be used for quantitative RT-PCR. We further looked for changes in poly(A) length of the maternal mRNAs during oocyte maturation. Our data indicate that depending on the method of reverse transcription, the optimal combination of reference genes for normalisation differed. Surprisingly, we observed a shortening of the poly(A) tail lengths of maternal mRNA as oocytes progressed from germinal vesicle to metaphase II. Overall, our findings suggest dynamic maternal regulation of mRNA structure and gene expression during oocyte maturation and early embryo development.
Organoids for toxicology and genetic toxicology: applications with drugs and prospects for environmental carcinogenesis
Authors: Caipa Garcia Angela L , Arlt Volker M , Phillips David H
Published: June 2021

Advances in three-dimensional (3D) cell culture technology have led to the development of more biologically and physiologically relevant models to study organ development, disease, toxicology and drug screening. Organoids have been derived from many mammalian tissues, both normal and tumour, from adult stem cells and from pluripotent stem cells. Tissue organoids can retain many of the cell types and much of the structure and function of the organ of origin. Organoids derived from pluripotent stem cells display increased complexity compared with organoids derived from adult stem cells. It has been shown that organoids express many functional xenobiotic-metabolising enzymes including cytochrome P450s (CYPs). This has benefitted the drug development field in facilitating pre-clinical testing of more personalised treatments and in developing large toxicity and efficacy screens for a range of compounds. In the field of environmental and genetic toxicology, treatment of organoids with various compounds has generated responses that are close to those obtained in primary tissues and in vivo models, demonstrating the biological relevance of these in vitro multicellular 3D systems. Toxicological investigations of compounds in different tissue organoids have produced promising results indicating that organoids will refine future studies on the effects of environmental exposures and carcinogenic risk to humans. With further development and standardised procedures, advancing our understanding on the metabolic capabilities of organoids will help to validate their use to investigate the modes of action of environmental carcinogens.
Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries
Authors: Lietard Jory , Leger Adrien , Erlich Yaniv , Sadowski Norah , Timp Winston , Somoza Mark M
Published: June 2021

Nucleic acid microarrays are the only tools that can supply very large oligonucleotide libraries, cornerstones of the nascent fields of de novo gene assembly and DNA data storage. Although the chemical synthesis of oligonucleotides is highly developed and robust, it is not error free, requiring the design of methods that can correct or compensate for errors, or select for high-fidelity oligomers. However, outside the realm of array manufacturers, little is known about the sources of errors and their extent. In this study, we look at the error rate of DNA libraries synthesized by photolithography and dissect the proportion of deletion, insertion and substitution errors. We find that the deletion rate is governed by the photolysis yield. We identify the most important substitution error and correlate it to phosphoramidite coupling. Besides synthetic failures originating from the coupling cycle, we uncover the role of imperfections and limitations related to optics, highlight the importance of absorbing UV light to avoid internal reflections and chart the dependence of error rate on both position on the array and position within individual oligonucleotides. Being able to precisely quantify all types of errors will allow for optimal choice of fabrication parameters and array design.
TRAPID 2.0: a web application for taxonomic and functional analysis ofde novotranscriptomes
Authors: Bucchini François , Del Cortona Andrea , Kreft Łukasz , Botzki Alexander , Van Bel Michiel , Vandepoele Klaas
Published: June 2021

Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
The synaptonemal complex central region modulates crossover pathways and feedback control of meiotic double-strand break formation
Authors: Lee Min-Su , Higashide Mika T , Choi Hyungseok , Li Ke , Hong Soogil , Lee Kangseok , Shinohara Akira , Shinohara Miki , Kim Keun P
Published: June 2021

The synaptonemal complex (SC) is a proteinaceous structure that mediates homolog engagement and genetic recombination during meiosis. In budding yeast, Zip-Mer-Msh (ZMM) proteins promote crossover (CO) formation and initiate SC formation. During SC elongation, the SUMOylated SC component Ecm11 and the Ecm11-interacting protein Gmc2 facilitate the polymerization of Zip1, an SC central region component. Through physical recombination, cytological, and genetic analyses, we found that ecm11 and gmc2 mutants exhibit chromosome-specific defects in meiotic recombination. CO frequencies on a short chromosome (chromosome III) were reduced, whereas CO and non-crossover frequencies on a long chromosome (chromosome VII) were elevated. Further, in ecm11 and gmc2 mutants, more double-strand breaks (DSBs) were formed on a long chromosome during late prophase I, implying that the Ecm11–Gmc2 (EG) complex is involved in the homeostatic regulation of DSB formation. The EG complex may participate in joint molecule (JM) processing and/or double-Holliday junction resolution for ZMM-dependent CO-designated recombination. Absence of the EG complex ameliorated the JM-processing defect in zmm mutants, suggesting a role for the EG complex in suppressing ZMM-independent recombination. Our results suggest that the SC central region functions as a compartment for sequestering recombination-associated proteins to regulate meiosis specificity during recombination.
The Association of California’s Proposition 56 Tobacco Tax Increase With Smoking Behavior Across Racial and Ethnic Groups and by Income
Authors: Keeler Courtney , Wang Yingning , Max Wendy , Yao Tingting , Gu Dian , Sung Hai-Yen
Published: June 2021

Introduction

On April 1, 2017, California Proposition 56 (Prop 56) was implemented, increasing the excise tax on cigarettes by $2/pack. This study compares the association of Prop 56 with smoking prevalence and smoking intensity across racial/ethnic groups, further examining distinctions across income subgroups within each racial/ethnic group.

Aims and Methods

The study used pooled cross-sectional data from the 2012–2018 California Behavioral Risk Factor Surveillance System. We examined two outcomes: current smoking prevalence and smoking intensity conditional on current smoking. A two-part econometric model was used to estimate the association of Prop 56 with smoking prevalence and intensity using multiple logistic regression and multiple linear regression, respectively. The two-part model was run separately for all adults (full sample) and each racial/ethnic group. Within each racial/ethnic group, we ran stratified analyses by income subgroups.

Results

The results indicated that Prop 56 was negatively associated with smoking prevalence among full sample, Hispanic, White, and African American adults and negatively associated with smoking intensity among full sample and White smokers. Stratified analyses by race/ethnicity and income showed that Prop 56 was negatively associated with smoking prevalence among low-income full sample and White adults and among middle-income smokers in the full, Hispanic, White, African American, and Asian samples. Prop 56 was negatively associated with smoking intensity among middle-income Hispanic and high-income White smokers. The association between Prop 56 and smoking intensity was positive among high-income African American smokers.

Conclusion

Prop 56 was associated with a reduction in smoking prevalence across multiple racial/ethnic groups, particularly within the low- and middle-income subgroups.

Implications

Our findings indicate that the reduction in smoking prevalence immediately following the implementation of Prop 56 tobacco tax increase was significant across a variety racial/ethnic groups, particularly low- and middle-income subgroups. We found differential responses in smoking prevalence across income groups among Whites but not among racial/ethnic minorities. We found no evidence of any significance association between Proposition 56 and smoking intensity among minorities and economically vulnerable populations, except for middle-income Hispanics. Researchers, policy makers, and advocates should consider the additional merits of targeted, community-based, noneconomic tobacco control interventions in reaching low- and middle-income groups within racial/ethnic minorities.
Plants, public health and the pandemic
Authors: Rivas Virgilio A , Biana Hazel T
Published: June 2021

At the onset of the pandemic, people resort to coping mechanisms to lessen the impact of social distancing enforced through quarantine protocols. Confined to their homes, despite recent relaxation of mobility and travel sanctions, many people find comfort and psychological reassurance in plant tending and gardening. Plants have been known for their medicinal and recreational purposes and their psychological therapeutic value. In the case of the Philippines, plant parenting has become a viral phenomenon.
Impact of the COVID-19 pandemic on treat-to-target strategies and physical consultations in >7000 patients with inflammatory arthritis
Authors: Glintborg Bente , Jensen Dorte Vendelbo , Terslev Lene , Pfeiffer Jensen Mogens , Hendricks Oliver , Østergaard Mikkel , Engel Sara , Horskjær Rasmussen Simon , Adelsten Thomas , Colic Ada , Danebod Kamilla , Kildemand Malene , Loft Anne Gitte , Munk Heidi Lausten , Pedersen Jens Kristian , Østgård René Drage , Møller Sørensen Christian , Krogh Niels Steen , Nørgaard Agerbo Jette , Ziegler Connie , Hetland Merete Lund
Published: June 2021

Objectives

To explore the impact of the COVID-19 pandemic on treat-to-target strategies (disease activity, remission rates) and access to physical consultations in patients with inflammatory rheumatic disease, as well as to explore characteristics of patients with/without physical consultations in the clinic and the impact of early vs established disease.

Methods

Patients with RA, PsA or axial SpA (axSpA) prospectively followed in the nationwide DANBIO registry answered online questionnaires and reported patient-reported outcomes (PROs) in June and November 2020. Patient characteristics, disease activity and physical consultations in the clinic before and during the pandemic were identified in DANBIO [all patients and subgroups with early disease (disease duration ≤2 years)]. In individual patients, changes in PROs before and during the pandemic were calculated. Characteristics of patients with/without physical consultations were described (age, gender, education level, comorbidities, disease duration, treatment).

Results

We included 7836 patients (22% of eligible patients), 12% of which had early disease. PROs were stable before and during the pandemic, with median changes approximating zero, as well as in patients with early disease. Remission rates were stable. The relative decrease in the number of patients with physical consultations was 21–72%, which was highest in axSpA. Characteristics of patients with/without physical consultations were similar. Self-reported satisfaction with treatment options and access was >70%; the preferred contact form was physical consultation (66%).

Conclusion

In this nationwide study performed during the first 8 months of the pandemic, patient satisfaction was high and the PROs and remission rates remained stable despite the remarkable reduction in physical consultations, as well as in patients with early disease. Characteristics of patients with/without physical consultations appeared similar.
Unlikely Feminist Coalitions: Islamist and Secularist Women’s Organizing in Tunisia
Authors: Youssef Maro
Published: June 2021

Following the 2010–2011 revolution, Islamist and secularist political parties and women’s rights organizations formed coalitions in Tunisia. Nothing of the sort had happened before in Tunisian history. This article considers the conditions that led feminists with different ideological beliefs to create what I call an “unlikely feminist coalition” in Tunisia. I argue that Islamists and secularists can form unlikely feminist coalitions when facing similar threats, working on similar tasks prior to formation of the coalition, the experience of common grievances, and a shared feminist identity. Drawing on the gender politics and social movement literature on coalitions, I suggest that more needs to be understood about unlikely feminist coalitions, especially in the Middle East.