bluuebunny/crossref_metadata_2025_split huggingface dataset:
metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality
Authors: Zinger Lucie , Lionnet Clément , Benoiston Anne‐Sophie , Donald Julian , Mercier Céline , Boyer Frédéric 
Published: January 2021

Abstract

DNA metabarcoding is becoming the tool of choice for biodiversity assessment across taxa and environments. Yet, the artefacts present in metabarcoding datasets often preclude a proper interpretation of ecological patterns. Bioinformatic pipelines to remove experimental noise exist. However, these often only partially target produced artefacts, or are marker specific. In addition, assessments of data curation quality and chosen filtering thresholds are seldom available in existing pipelines, partly due to the lack of appropriate visualisation tools.

Here, we present metabaR, an r package that provides a comprehensive suite of tools to effectively curate DNA metabarcoding data after basic bioinformatic analyses. In particular, metabaR uses experimental negative or positive controls to identify different types of artefactual sequences, that is, contaminants and tag‐jumps. It also flags potentially dysfunctional PCRs based on PCR replicate similarities when those are available. Finally, metabaR provides tools to visualise DNA metabarcoding data characteristics in their experimental context as well as their distribution, and facilitates assessment of the appropriateness of data curation filtering thresholds.

metabaR is applicable to any DNA metabarcoding experimental design but is most powerful when the design includes experimental controls and replicates. More generally, the simplicity and flexibility of the package makes it applicable any DNA marker, and data generated with any sequencing platform, and pre‐analysed with any bioinformatic pipeline. Its outputs are easily usable for downstream analyses with any ecological r package.

metabaR complements existing bioinformatics pipelines by providing scientists with a variety of functions to effectively clean DNA metabarcoding data and avoid serious misinterpretations. It thus offers a promising platform for automatised data quality assessments of DNA metabarcoding data for environmental research and biomonitoring.
A five‐channel LED display to investigate UV perception
Authors: Powell Samuel B. , Mitchell Laurie J. , Phelan Amelia M. , Cortesi Fabio , Marshall Justin , Cheney Karen L. 
Published: January 2021

Abstract

The ability to see ultraviolet (UV) light (<400 nm) may have importance for foraging, communication or navigation in many taxa including insects, crustaceans, fishes, amphibians, reptiles, birds and mammals. Behavioural experiments reveal how vision mediates such behaviour; however, our knowledge of UV perception is constrained by the challenge of creating and calibrating stimuli that reflect or emit UV. Commonly used technologies for displaying visual stimuli—such as computer screens and printers—are designed for human vision and thus are unsuitable for testing UV perception.

To overcome this limitation, we designed and constructed a display with five spectral channels with peak wavelengths as follows: red at 629 nm, green at 526 nm, blue at 466 nm, violet at 395 nm and UV at 367 nm. Each pixel of the display consists of five LEDs with a baffle to prevent crosstalk from adjacent pixels and a diffuser to promote uniform colour mixing. The LEDs are driven by high‐performance pulse‐width‐modulated constant‐current drivers with a maximum flicker rate of 64 kHz and a maximum frame rate of 6.5 kHz. This method allows colour mixing with wavelengths as low as 350 nm to be calibrated and tested rapidly and concurrently.

To demonstrate the utility of this display, we conducted colour detection tests using the anemonefish, Amphiprion ocellaris, a species known to have UV‐sensitive cones. Fish were able to associate pecking all target colours (‘Blue’, ‘UV‐grey’ and ‘UV’) with a food reward, demonstrating for the first time, UV perception in A. ocellaris.

The RGB‐V‐UV LED display is a useful device for behavioural tests of colour vision across a broad spectrum (350–650 nm) visible to many animals and can be used to investigate various questions concerning animal perception, including colour discrimination and categorisation. We include design documents and source code so this system can be further developed and modified to investigate other visual behaviours in a variety of taxa.
Testing the validity of national drug surveys: comparison between a general population cohort and household surveys
Authors: Charles Hannah , Heron Jon , Hickman Matthew , Brown Jamie , Hines Lindsey 
Published: January 2021

ABSTRACTBackground and AimsThere are concerns that national population‐based estimates of illicit drug use are underestimated. We investigated this by comparing estimates of illicit substance use at age 24 from the Crime Survey for England and Wales (CSEW) with a birth cohort (Avon Longitudinal Study of Parents and Children, ALSPAC) and by comparing the Smoking and Alcohol Toolkit Studies (STS/ATS) to ALSPAC.DesignCross‐sectional household survey and cross‐sectional data from one wave of a longitudinal birth cohort.SettingEngland and Wales.ParticipantsYoung adults aged 23–25 reporting on substance use in 2017 to CSEW (n = 1165), ALSPAC (n = 3389) and STS/ATS (n = 950).MeasurementsLifetime and past‐year illicit drug use, smoking status and hazardous drinking at age 24.FindingsThe 2017 CSEW estimate of lifetime illicit drug use was 40.6%, compared with 62.8% in ALSPAC (risk difference % [RD%] = 22.2%; 95% CI = 18.9–25.5%; P ≤ 0.001). The RD in lifetime use between ALSPAC and the CSEW was 23.2% (95% CI = 20.0–26.4%) for cannabis, 16.9% (95% CI = 14.4–19.4%) for powder cocaine and 24.8% (95% CI = 22.6–27.0%) for amphetamine. Past‐year drug use was 16.4% in CSEW, compared with 36.7% in ALSPAC (RD% = 20.3%; 95% CI = 17.6–23.0%; P ≤ 0.001). For past‐year substance use, the RD between ALSPAC and the CSEW was 15.4% (95% CI = 12.9–17.9%) for cannabis, 14.8% (95% CI = 13.0%–16.6%) for powder cocaine and 15.9% (95% CI = 14.5–17.4%) for amphetamine. Levels of current smoking were similar between STS (27.4%) and ALSPAC (29.4%). Hazardous drinking was substantially higher in ALSPAC (60.3%) than the ATS (32.1%; RD% = 28.2%; 95% CI = 24.8–31.6%; P ≤ 0.001).ConclusionsThe Avon Longitudinal Study of Parents and Children provides one source of validation for measurements of drug use in government household surveys and indicates that illicit drug use may be underestimated in the Crime Survey for England and Wales.
Longitudinal study of intravenous versus subcutaneous immunoglobulin replacement therapy in hematological malignancy
Authors: Windegger Tanja M , English Janine , Weston Helen , Morwood Karen , Kynn Mary , Scuffham Paul , Fung Yoke‐Lin 
Published: January 2021

AbstractAimTo present findings from a longitudinal study on infection risk, mortality, and patient perspective of intravenous immunoglobulin (IVIg) and subcutaneous immunoglobulin (SCIg) treatment for patients with hypogammaglobulinemia secondary to hematological malignancy or its treatment (abbreviated as SID).MethodsObservational study period included final year of IVIg (13 patients) and of the first 3 years of SCIg (17 patients) with SID. Data were collected on clinical outcomes from medical records and patient perception via study specific questionnaire.ResultsThe median age was 63 years (53‐76 years), and for 82.4% of patients their hematological malignancy was in complete remission. The annual mean serum IgG trough levels remained stable over the 4 years and were 7.0 g/L (±2.77 g/L) with IVIg, and 8.0 g/L (±1.75 g/L), 8.7 g/L (±2.75 g/L), and 7.6 g/L (±2.89 g/L) (year 1, 2, and 3, respectively) with SCIg. While the annual infection rate was similar, the rate of hospitalization due to infection fluctuated, with 37%, 9%, 15%, and 32% in year 1, 2, 3, and 4 respectively. There were no systemic adverse events with IVIg or SCIg. Patients reported a strong preference for SCIg. One patient died due to progression of underlying disease and infection within the study period.ConclusionSCIg was the preferred treatment mode over IVIg in our cohort, but both were well tolerated without any systemic adverse events in 4‐year follow up. The dosage and serum IgG levels were stable throughout. However, the number of infections requiring hospitalization fluctuated. It is anticipated that these findings encourage more hospitals to offer SCIg for SID patients.
A rare case of epithelial‐myoepithelial carcinoma arising from pleomorphic adenoma of the lacrimal gland
Authors: Van Rooij Nicholas , Newman Alexander , Sullivan Timothy 
Published: January 2021

AbstractPurposeEpithelial‐myoepithelial carcinoma (EMC) is a low‐grade salivary gland tumour which is very rarely reported in the lacrimal gland. Hybrid carcinomas such as EMC, defined by Seifert and Donath (1996),1 comprise two histological subtypes of carcinoma within the same topographic field. Hybrid tumours constitute <1% of all salivary gland tumours, with only eight previous documented cases of lacrimal gland EMC reported in the literature.2 The diagnosis of EMC is histological, demonstrating a biphasic dual morphology of luminal cuboidal ductal epithelial cells and outer myoepithelial cells with clear cytoplasm.1,2Methods/ResultsWe describe the case of a 92‐year‐old transgender man that presented with progressively worsening left‐sided headaches, eye pain and with a clinical enlargement of the left lacrimal region. The patient underwent superior‐lateral orbitotomy with excisional biopsy of the left lacrimal gland and was found to have EMC arising from a pleomorphic adenoma, which was subsequently managed with adjuvant rotation therapy.ConclusionsPatient prognostication and optimal management of these tumours provide a challenge for clinicians due to their inherent rarity. We describe the first case of EMC arising within a pleomorphic adenoma in the Australian population.References1. Seifert G, Donath K. Hybrid tumours of salivary glands. Definition and classification of five rare cases. European Journal Of Cancer Part B, Oral Oncology 1996; 32B: 251‐259.Li E, Distefano A, Sinard J, Wong A, Pointdujour‐Lim R. Epithelial‐myoepithelial carcinoma presenting as a pseudo veno‐lymphatic malformation. Ophthalmic Plastic And Reconstructive Surgery 2018; 34: e157‐e60.
New data in a mouse model of spontaneous choroidal neovascularisation support the role of angiopoietin‐2 inhibition in driving sustained vascular stabilisation and reduced fibrosis progression
Authors: Canonica Jérémie , Uhles Sabine , Foxton Richard , Revelant Franco , Cole Nadine , Westenkow Peter , Scheidl Stefan , Ullmer Christoph 
Published: January 2021

PurposeTo explore the vessel stabilisation potential of dual angiopoietin‐2 (Ang‐2)/vascular endothelial growth factor‐A (VEGF‐A) inhibition in a mouse model of spontaneous choroidal neovascularisation (sCNV) in the context of phase 2 clinical data on faricimab, a bispecific antibody that binds to and neutralises both Ang‐2 and VEGF‐A.MethodsSeven‐week‐old JR5558 mice, developing sCNV in both eyes, were treated intraperitoneally with mouse cross‐reactive tool antibodies against Ang‐2, VEGF‐A, or both (bispecific antibody VA2); n = 7–15 mice per group. Fluorescein angiography (FA)‐evaluated CNV leakage and fibronectin (fibrosis marker) deposition on the retinal pigment epithelium (RPE)/choroid and around CNV lesions were assessed at baseline and 1 (PT1), 3 (PT2) and 5 weeks (PT3) post treatment to assess the effects on CNV lesion activity relative to untreated/IgG‐exposed mice.ResultsAnti‐Ang‐2‐, anti‐VEGF‐A‐ and VA2‐treated mice showed a significant reduction in CNV leakage (p < 0.05 to p < 0.001) versus controls at PT1, maintained only in anti‐Ang‐2‐ and VA2‐treated mice at PT2/3 (p < 0.05 to p < 0.0001). Lesions treated with anti‐VEGF alone showed reactivation on FA at PT2. The area of fibronectin staining on RPE/choroid and around lesions was significantly reduced with VA2 (38%; p < 0.01) and anti‐Ang‐2 (41%; p < 0.001) versus IgG control at PT1; the effect of VEGF‐A inhibition alone was not significant. At PT2 and PT3, only VA2 inhibition showed significant reduction in fibronectin staining over both control groups (by 47%; p < 0.01 and 54%; p < 0.05, respectively).ConclusionsFaricimab's potential for extended durability observed in phase 2 clinical trials was further explored in a mouse model of sCNV. CNV leakage and fibronectin staining around CNV lesions were suppressed for longer with dual Ang‐2/VEGF‐A inhibition versus VEGF‐A alone. These findings support the hypothesis that the sustained efficacy of faricimab observed in phase 2 trials is due to vessel‐stabilising effects driven by Ang‐2 inhibition.
Intravitreal dexamethasone implant combined with bevacizumab versus intravitreal bevacizumab for diabetic macular edema
Authors: Gong Yeseul , Kang Kuidong 
Published: January 2021

PurposeTo compare the visual and anatomical outcomes of intravitreal bevacizumab combined with the dexamethasone intravitreal implant and bevacizumab monotherapy in eyes with diabetic macular edemaMethodsWe retrospectively reviewed 41 eyes of 41 patients with diabetic macular edema who underwent either intravitreal bevacizumab (1.25 mg) (20 eyes, IVB group) injection alone or simultaneous injection of bevacizumab (1.25 mg) and dexamethasone implant (0.7 mg) (21 eyes, IVD group). The best‐corrected visual acuity, central macular thickness (CMT), intraocular pressure, and retreatment percentages were accessed for 1, 3, and 6 months after injectionResultsAt 3 and 6 months, best‐corrected visual acuity (BCVA) showed significant improvements in the IVD group compared to the baseline. No significant improvement of the BCVA was observed in the IVB group during the initial 3 months; however, BCVA in this group at 6 months was significantly improved compared to baseline. There was a significant improvement in CMT in IVD group compared to IVB group during the first 3 months. In IVD group, CMT was 264.39 ± 54.95 µm at 1 month after initial injection while that of IVB group was 349.00 ± 112.18 µm (p = 0.011). At 3 months, CMT in the IVD group significantly improved compared to that of IVB group (p < 0.001). The average number of additional intravitreal injections during 6 months follow‐up period was 0.45 in the IVD group and 1.15 in the IVB group. In the IVD group, cortical (7%) and posterior subcapsular (15%) cataract developed by 2 grades or more during the follow‐up period in phakic eyes.ConclusionsIn patients with diabetic macular edema, simultaneous therapy combining a dexamethasone implant plus bevacizumab showed significant improvement in the visual acuity and CMT during the initial 3 months, and the number of additional intravitreal injections were less in combined treated group.
Detection and clinical course of choroidal neovascularization in central serous chorioretinopathy
Authors: Kim Raeyoung , Park Young‐Hoon 
Published: January 2021

PurposeThe objective of this study was to observe the detection of choroidal neovascularization (CNV) after central serous chorioretinopathy (CSC) diagnosis and to determine whether clinical features and prognosis differ in CNV eyes from chronic CSC after CNV detection.MethodsThe medical records of 30 eyes of 30 patients with CSC were retrospectively analyzed in this study. The presence of CNV was diagnosed using fluorescein angiography (FA), indocyanine green angiography (ICGA), or optical coherent tomography angiography (OCTA). The time of initial symptom diagnosis and the period from the diagnosis of CSC to the detection of CNV were estimated based on the medical records. We observed the clinical change pattern by measuring the best‐corrected visual acuity (BCVA), central macular thickness (CMT), and subfoveal choroidal thickness (SFCT) for one year since the detection of CNV.ResultsThe average period until CNV detection was 24.18 ± 29.43 months (mean ± standard deviation) from the initial symptom initiation and 20.10 ± 28.49 months from the first diagnosis of CSC. The CMT significantly decreased in patients with CSC in the one‐year follow‐up after CNV detection (p = 0.01), but no statistically significant changes were found in BCVA and SFCT.ConclusionsIn CSC patients, CNV detection was observed earlier than previously reported, and after CNV detection, there was no rapid deterioration of visual acuity or clinical features.
Swept‐source optical coherence tomography angiography findings in hypertensive chorioretinopathy
Authors: Braham Imene Zhioua , Kaouel Hela , Ammous Imen , Boukari Mejdi , Zhioua Raja 
Published: January 2021

PurposeTo study malignant hypertension ocular findings with swept source optical coherence tomography (SS‐OCT) and optical coherence tomography angiography (OCT‐A).MethodsIn this retrospective study, we included patients with malignant hypertension associated to hypertensive chorioretinopathy. Clinical characteristics with multimodal imaging including SS‐OCT and OCT‐A were evaluated at baseline and during follow‐up.ResultsSeventeen eyes of nine patients were included. Fundus examination revealed signs of hypertensive chorioretinopathy in all cases. At baseline, SS‐OCT showed serous retinal detachment in 7 eyes, macular edema in 15 eyes and hard exudates in 13 eyes. Central macular thickness was 403.33 ± 257.92 µm at baseline and 261.08 ± 62.43 µm after 3 months of mean follow‐up (p = 0.05). Central choroidal thickness decreased from 352.06 ± 87.62 µm at baseline to 319.58 ± 80.66 µm after follow‐up (p > 0.05). On OCT‐A, all patients showed nonperfusion capillary areas at the level of the superficial and deep capillary plexuses. The choriocapillaris layer showed dark areas corresponding to a shadowing effect of retinal lesions and flow voids corresponding to focal ischemia. During follow‐up, there was a partial reperfusion of the retinal layers and the choriocapillaris with persistence of ischemic areas.ConclusionsOCTA clearly visualizes ischemic changes in the retinal layers and in the choriocapillaris in hypertensive chorioretinopathy. During follow‐up, OCTA showed incomplete reperfusion of the retinal layers and the choriocapillaris.
Identification of characteristic subepithelial surface granulomatosis in immune‐related adverse event‐associated enterocolitis
Authors: Kubo Terufumi , Hirohashi Yoshihiko , Keira Yoshiko , Akimoto Mayuko , Ikeda Tatsuru , Kikuchi Noriaki , Iwaki Hiroyuki , Kikuchi Tomoki , Obata Masahiko , Morita Rena , Kasai Kiyoshi , Segawa Keiko , Tsukahara Tomohide , Kanaseki Takayuki , Murata Kenji , Kikuchi Yasuhiro , Shinkawa Tomoyo , Hasegawa Tadashi , Torigoe Toshihiko 
Published: January 2021

AbstractImmune checkpoint inhibitors (ICIs) have provided an additional treatment option for various types of human cancers. However, ICIs often induce various immune‐related adverse events (irAEs). Enterocolitis is a major irAE with poorly understood histopathological characteristics. In this study, we retrospectively investigated the histopathology of colon tissue samples from 17 patients treated with ICIs. There were two major histological patterns of colitis: an ulcerative colitis‐like pattern and a graft vs host disease‐like pattern. Although these two patterns of colitis were mutually exclusive, both patterns often showed a characteristic that we call “subepithelial surface granulomatosis” (SSG), which has not been reported in other types of colitis. SSG was found even in colon tissue without symptoms or endoscopic findings of colitis. Given the increasing reports of sarcoid reaction or exacerbation of tuberculosis after treatment with ICIs, granuloma formation could be a histological hallmark of systemic immune activation by ICIs. Although statistical significance was not obtained, probably because of the small sample size, SSG may be a surrogate biomarker of systemic anticancer immune activation. We propose that a prospective study with larger sample size be performed.
An Illusion of Self‐Sufficiency for Learning About Artifacts in Scaffolded Learners, But Not Observers
Authors: Richardson Emory , Sheskin Mark , Keil Frank C. 
Published: January 2021

Two studies ask whether scaffolded children (n = 243, 5–6 years and 9–10 years) recognize that assistance is needed to learn to use complex artifacts. In Study 1, children were asked to learn to use a toy pantograph. While children recognized the need for assistance for indirect knowledge, 70% of scaffolded children claimed that they would have learned to use the artifact without assistance, even though 0% of children actually succeeded without assistance. In Study 2, this illusion of self‐sufficiency was significantly attenuated when observing another learner being scaffolded. Learners may fail to appreciate artifacts’ opacity because self‐directed exploration can be partially informative, such that learning to use artifacts is typically scaffolded instead of taught explicitly.
Obesity and polycystic ovary syndrome
Authors: Barber Thomas M. , Franks Stephen 
Published: January 2021

AbstractThe increased global prevalence of obesity over the last 40‐years has driven a rise in prevalence of obesity‐related co‐morbidities, including polycystic ovary syndrome (PCOS). On a background of genetic susceptibility, PCOS often becomes clinically manifest following weight gain, commonly during adolescence. A common endocrinopathy affecting between 6%‐10% of reproductive‐age women, PCOS presents with the cardinal features of hyperandrogenism, reproductive and metabolic dysfunction. PCOS associates with insulin resistance, independently of (but amplified by) obesity. Insulin resistance in PCOS is characterized by abnormal post‐receptor signalling within the phosphatidylinositol‐kinase (PI3‐K) pathway. Multiple factors (including most notably, weight gain) contribute towards the severity of insulin resistance in PCOS. Compensatory hyperinsulinaemia ensues, resulting in over‐stimulation of the (intact) post‐receptor mitogen‐activated protein kinase (MAP‐K) insulin pathway, with consequent implications for steroidogenesis and ovarian function. In this concise review, we explore the effects of weight gain and obesity on the pathogenesis of PCOS from the perspective of its three cardinal features of hyperandrogenism, reproductive and metabolic dysfunction, with a focus on the central mediating role of the insulin pathway. We also consider key lifestyle strategies for the effective management of obese and overweight women with PCOS.
Exosomes from adipose‐derived stem cells and application to skin wound healing
Authors: An Yang , Lin Shuyan , Tan Xiaojie , Zhu Shiou , Nie Fangfei , Zhen Yonghuan , Gu Luosha , Zhang Chunlei , Wang Baicheng , Wei Wei , Li Dong , Wu Junhao 
Published: January 2021

AbstractSkin wound healing is an intractable problem that represents an urgent clinical need. To solve this problem, a large number of studies have focused on the use of exosomes (EXOs) derived from adipose‐derived stem cells (ADSCs). This review describes the mechanisms whereby ADSCs‐EXOs regulate wound healing and their clinical application. In the wound, ADSCs‐EXOs modulate immune responses and inflammation. They also promote angiogenesis, accelerate proliferation and re‐epithelization of skin cells, and regulate collagen remodelling which inhibits scar hyperplasia. Compared with ADSCs therapeutics, ADSCs‐EXOs have highly stability and are easily stored. Additionally, they are not rejected by the immune system and have a homing effect and their dosage can be easily controlled. ADSCs‐EXOs can improve fat grafting and promote wound healing in patients with diabetes mellitus. They can also act as a carrier and combined scaffold for treatment, leading to scarless cutaneous repair. Overall, ADSCs‐EXOs have the potential to be used in the clinic to promote wound healing.