Identifying bird species by their calls in Soundscapes

In many real data science problems, it is common to encounter a domain mismatch between the training and testing datasets, which means that solutions designed for one may not transfer well to the other due to their differences. An example of such was in the BirdCLEF2021 Kaggle competition, where participants had to identify all bird species that could be heard in audio recordings. Thus, multi-label classifiers, capable of coping with domain mismatch, were required. In addition, classifiers needed to be resilient to a long-tailed (imbalanced) class distribution and weak labels. Throughout the competition, a diverse range of solutions based on convolutional neural networks were proposed. However, it is unclear how different solution components contribute to overall performance. In this work, we contextualise the problem with respect to the previously existing literature, analysing and discussing the choices made by the different participants. We also propose a modular solution architecture to empirically quantify the effects of different architectures. The results of this study provide insights into which components worked well for this challenge.

Buoyancy affects stranding rate and dispersal distance of floating litter entering the sea from river mouths

Rivers are a major source of litter entering the sea but our understanding of the transport and fate of plastics in estuarine environments is poor. Marked blocks of varying buoyancy were released at three river mouths in South Africa. Of the 1400 blocks released, 80% were recovered on nearby beaches, with a higher recovery rate for more buoyant blocks. Dispersal distances increased with decreasing buoyancy at all sites; median dispersal distance of stranded items ranged from 20 to 90 m for expanded polystyrene (EPS) to 70-90 m for wood and 60-1042 m for high density polyethylene (HDPE) blocks. Floating litter in estuaries is subject to bidirectional flow and export is largely controlled by hydrodynamic conditions such as tides, winds, and wave action, as well as coastal structure and vegetation. Cleaning beaches around river mouths will help to reduce leakage of plastic and other litter into the sea.

Global COVID-19 lockdown highlights humans as both threats and custodians of the environment

The global lockdown to mitigate COVID-19 pandemic health risks has altered human interactions with nature. Here, we report immediate impacts of changes in human activities on wildlife and environmental threats during the early lockdown months of 2020, based on 877 qualitative reports and 332 quantitative assessments from 89 different studies. Hundreds of reports of unusual species observations from around the world suggest that animals quickly responded to the reductions in human presence. However, negative effects of lockdown on conservation also emerged, as confinement resulted in some park officials being unable to perform conservation, restoration and enforcement tasks, resulting in local increases in illegal activities such as hunting. Overall, there is a complex mixture of positive and negative effects of the pandemic lockdown on nature, all of which have the potential to lead to cascading responses which in turn impact wildlife and nature conservation. While the net effect of the lockdown will need to be assessed over years as data becomes available and persistent effects emerge, immediate responses were detected across the world. Thus, initial qualitative and quantitative data arising from this serendipitous global quasi-experimental perturbation highlights the dual role that humans play in threatening and protecting species and ecosystems. Pathways to favorably tilt this delicate balance include reducing impacts and increasing conservation effectiveness.

The Impact of the COVID-19 Lockdown on Urban Street Litter in South Africa

Abstract

The lockdowns instigated to slow the spread of the COVID-19 pandemic offered a unique opportunity to assess how restrictions on human activity affect street litter. We recorded daily litter arrival rates for 50 days in two South African cities from the time of strictest lockdown through two successive easings in regulations. The strict lockdown had no marked impact on litter composition, which was dominated by convenience foods and beverages (29% by number, 34% by mass) and tobacco products (33% by number, 3% by mass). The ban on the sale of tobacco products during the lockdown did not greatly reduce the number of cigarette butts and associated packaging. Vehicle parts accounted for <1% of litter items (2% by mass) whereas household waste spilled from bins prior to or during collection accounted for 3% of litter items (14% by mass). Street litter loads decreased roughly by a factor of three during the strict lockdown. The increase in litter was gradual, suggesting a reduction in compliance with regulations as the lockdown continued. Our results show a clear link between human activity levels and littering.

Highlights

• Street litter loads increased three-fold in two cities as Covid lockdowns eased.

• Cigarette butts made up 33% of litter by number despite a ban on tobacco sales.

• There is a clear link between human activity levels and littering.

Electronic supplementary material

The online version of this article (10.1007/s40710-020-00472-1) contains supplementary material, which is available to authorized users.

Treatment of central serous chorioretinopathy with topical NSAIDs

Purpose

Central serous chorioretinopathy (CSCR) is a common retinopathy that is often observed until resolution. The purpose of this study is to evaluate the effects of topical nonsteroidal anti-inflammatory drugs (NSAIDs) on timing of CSCR recovery.

Methods

An IRB-approved retrospective review was conducted on patients that had been diagnosed with a new-onset, symptomatic case of CSCR. Patients were either observed only (13 untreated eyes) or treated with topical bromfenac or nepafenac (14 eyes) over an average of about a 4-5 week follow-up period.

Results

There was no statistical significance between central macular thickness (CMT) and visual acuity of treatment and control groups at the initial presentation. However, at the follow-up visit, CMT reductions in the treatment group were significantly higher than in the control group (p<0.006).

Conclusion

Use of topical NSAIDs in the treatment of acute CSCR leads to a faster rate of reduction in the subretinal fluid volume over a follow-up period of a few weeks.

The Tayside insulin management course: an effective education programme in type 1 diabetes

AIMS

The Tayside insulin management (TIM) course is an intensive insulin management programme for adults with type 1 diabetes. The aim was to assess its effectiveness.

METHODS

Haemoglobin A1c (HbA1c) and body mass index (BMI) from individuals with type 1 diabetes were collected 3 months before, and 6 and 24 months after the programme. The programme involved a full day of education per week for 4 weeks in a row. Quality of life was assessed using the standardised Audit of Diabetes-Dependent Quality of Life (ADDQoL) questionnaire completed both before and 3 months after the course. Subjects were also asked to complete a pre- and postcourse questionnaire gathering information about aspects of their diabetes management. In addition, individual satisfaction with course content and delivery was recorded.

RESULTS

Participants had a median reduction in haemoglobin A1c (HbA1c) of 4 mmol/mol (0.4%) after 6 months and 5 mmol/mol (0.5%) 2 years after the course (p < 0.001). Mean daily dose of short-acting insulin decreased from 31.5 (1.9) units to 27.3 (1.9, p < 0.001). There was no significant change in BMI. There was an improvement in all 18 domains of the ADDQoL questionnaire. There was a decrease in hypoglycaemia unawareness from 34.3 ± 47.8% of patients to 8.6 ± 28% (p < 0.001), and a decrease in self-reported lipohypertrophy from 27.8% to 11.1% (p = 0.001). There was a significant reduction in the mean number of diabetic ketoacidosis and severe hypoglycaemic episodes. The number of blood glucose checks changed from 2.8 ± 2.1 to 3.2 ± 1.1 (p = 0.058) per day. Participant satisfaction with all aspects of course content and delivery was high.

CONCLUSIONS

TIM is an effective intensive education programme for patients with type 1 diabetes.

Electrical control of spin relaxation in a quantum dot

We demonstrate electrical control of the spin relaxation time T1 between Zeeman-split spin states of a single electron in a lateral quantum dot. We find that relaxation is mediated by the spin-orbit interaction, and by manipulating the orbital states of the dot using gate voltages we vary the relaxation rate W identical withT1(-1) by over an order of magnitude. The dependence of W on orbital confinement agrees with theoretical predictions, and from these data we extract the spin-orbit length. We also measure the dependence of W on the magnetic field and demonstrate that spin-orbit mediated coupling to phonons is the dominant relaxation mechanism down to 1 T, where T1 exceeds 1 s.

SLUG (SNAI2) overexpression in embryonic development

The Snail-related zinc-finger transcription factor, SLUG (SNAI2), is critical for the normal development of neural crest-derived cells and loss-of-function SLUG mutations have been proven to cause piebaldism and Waardenburg syndrome type 2 in a dose-dependent fashion. However, little is known about the consequences of SLUG overexpression in embryonic development. We report SLUG duplication in a child with a unique de novo 8q11.2-->q13.3 duplication associated with tetralogy of Fallot, submucous cleft palate, renal anomalies, hypotonia and developmental delay. To investigate the effects of Slug overexpression on development, we analyzed mice carrying a Slug transgene. These mice were morphologically normal at birth, inferring that Slug overexpression is not sufficient to cause overt morphogenetic defects. In the adult mice, there was a 20% incidence of sudden death, cardiomegaly and cardiac failure associated with incipient mesenchymal tumorigenesis. These findings, while not directly implicating Slug in congenital and acquired heart disease, raise the possibility that Slug overexpression may contribute to specific cardiac phenotypes and cancer development.

Loss of Cited2 affects trophoblast formation and vascularization of the mouse placenta

Cited2 is widely expressed in the developing embryo and in extraembryonic tissues including the placenta. Gene expression can be induced by a number of factors; most notably by the hypoxia inducible transcription factor, HIF1, under low oxygen conditions. Cited2 encodes for a transcriptional co-factor that in vitro can act as both a positive and negative regulator of transcription. This function is due to its interaction with CBP/p300 and appears to depend on whether Cited2 enables CBP/p300 to interact with the basic transcriptional machinery, or if its binding prevents such an interaction from occurring. Here, we report a novel function for Cited2 in placenta formation, following gene deletion in mouse. In the absence of Cited2 the placenta and embryo are significantly small from 12.5 and 14.5 dpc respectively, and death occurs in utero. Cited2 null placentas have fewer differentiated trophoblast cell types; specifically there is a reduction in trophoblast giant cells, spongiotrophoblasts and glycogen cells. In addition, the fetal vasculature of the placenta is disorganised and there are fewer anastomosing capillaries. Given that Cited2 is expressed in both trophoblasts and the fetal vasculature, the observed defects fit well with the sites of gene expression. We conclude that Cited2 is required for normal placental development and vascularisation, and hence for embryo viability.

Pulmonary haemorrhage and cardiac dysfunction in a neonate with medium-chain acyl-CoA dehydrogenase (MCAD) deficiency

We report on a favourable case of MCAD deficiency (homozygous 985A > G) that presented as lethargy, poor feeding, pulmonary haemorrhage and cardiac arrest without hypoglycaemia. The cessation of intralipid and the commencement of carnitine supplementation were associated with a rapid clinical improvement.

CONCLUSION

Mild carnitine depletion and secondary impairment of long-chain fatty acid metabolism may have contributed to post-asphyxial myocardial dysfunction and ventricular arrhythmias. Metabolic disorders must be kept in mind as a differential diagnosis in acutely ill infants, but it must also be emphasized that carnitine therapy is not uniformly effective in all MCAD patients.

Kousseff syndrome: a causally heterogeneous disorder

The existence of Kousseff syndrome as a distinct entity has been thrown into doubt by a recent study conducted on the family originally reported by Kousseff. In all cases where chromosome 22q11.2 FISH testing has been undertaken, including the original sibship, a chromosome 22q11.2-microdeletion has been identified. We report two cases of sacral myelomeningocele associated with a conotruncal cardiac anomaly or "Kousseff syndrome." The first case, a 4-year-old girl, had a sacral myelomeningocele, tetralogy of Fallot, microcephaly, hydrocephalus, hypoplasia of the corpus callosum and mild-moderate developmental delay. Chromosome 22q11.2 FISH was normal and the facial phenotype was not that of velocardiofacial syndrome. Sequencing of the entire coding region of CITED2 did not reveal a mutation. The second case, a male infant, was found to have a 22q11.2-microdeletion. These cases confirm Kousseff syndrome to be a causally heterogeneous disorder.

Breaking symmetry: a clinical overview of left-right patterning

It is increasingly recognized that mutations in genes and pathways critical for left-right (L-R) patterning are involved in common isolated congenital malformations such as congenital heart disease, biliary tract anomalies, renal polycystic disease, and malrotation of the intestine, indicating that disorders of L-R development are far more common than a 1 in 10,000 incidence of heterotaxia might suggest. Understanding L-R patterning disorders requires knowledge of molecular biology, embryology, pediatrics, and internal medicine and is relevant to day-to-day clinical genetics practice. We have reviewed data from mammalian (human and mouse) L-R patterning disorders to provide a clinically oriented perspective that might afford the clinician or researcher additional insights into this diagnostically challenging area.

A variant microcephalic osteodysplastic slender-bone disorder with growth hormone deficiency and a pigmentary retinopathy

We present the case of a 3-year-old boy with post-natal growth failure, microcephaly, developmental delay, facial dysmorphism, an evolving pigmentary retinopathy, pituitary hypoplasia, micropenis, and growth hormone (GH) deficiency. He has a microcephalic osteodysplastic slender-bone disorder with disharmonic delayed osseous maturation, most closely resembling patients with microcephalic osteodysplastic primordial dwarfism type II (MOPD II). Intrauterine growth retardation, a universal finding in the MOPD II, was absent in our patient.

Serum suppresses myeloid progenitor apoptosis by regulating iron homeostasis

The growth and survival of committed hematopoietic progenitors is dependent upon cytokine signaling. However, serum is also required for optimal growth of these progenitors in culture ex vivo. Here we report that serum withdrawal leads to myeloid progenitor cell apoptosis. Although serum deprivation-induced cell death has many hallmarks typical of apoptosis, these cell deaths were not inhibited by hemopoietins, survival factors such as IGF-I, or treatment with a broad-spectrum caspase inhibitor. Rather, apoptosis due to serum withdrawal was associated with damage to mitochondria. Surprisingly the serum factor required for myeloid cell survival was identified as iron, and loss of iron led to marked reductions in ATP production. Furthermore, supplementing serum-deprived myeloid cells with bound or free iron promoted cell survival and prevented mitochondrial damage. Therefore, serum suppresses hematopoietic cell apoptosis by providing an obligate source of iron and iron homeostasis is critical for proper myeloid cell metabolism and survival.

Splenic abscess in a patient with type 3 Gaucher's disease receiving enzyme replacement therapy

We report the rare complication of a splenic abscess in an 11-year-old girl with type 3 Gaucher's disease, massive splenomegaly, and a splenic cyst after commencement of enzyme replacement therapy. This case highlights potential difficulties in establishing the diagnosis of splenic abscess in the presence of pre-existing splenic pathology.

Evaluation of a low-threshold clinic for opiate-dependent drug users

This study reports on the development and outcome of a Low Threshold Clinic (LTC) for opiate-dependent drug users. The service originated as a nursing initiative within an inner city Drug Dependency Centre (DDC) and its rationale and treatment approach are explored in relation to the literature and local circumstances. Client baseline and outcome data were systematically gathered to assess service uptake and service efficacy in terms of client outcome. Data are presented for the first two years of operation during which a total of 59 clients entered the LTC. The sociodemographic characteristics and patterns of drug use among this group suggest the service was successful in targeting clients who previously failed to enter traditional treatment programmes despite initial referral to the DDC. Outcome data indicate a tendency for clients to inject less frequently, engage in less criminal activity and, by 12 months, to reduce their dose of prescribed methadone whilst attending the LTC. Tentative conclusions are drawn concerning the value of this service for 'hard-to-reach' drug users and those who may be at a precontemplation stage of change. Recommendations are made for a more comprehensive evaluative study that involves comparison with other treatment approaches.

Association of extended in vitro proliferative potential with loss of p16INK4 expression

This study addresses the question of whether loss of p16INK4 expression contributes to the immortalization of human cells. In vitro immortalization usually proceeds through two phases. In the first phase (lifespan extension), cells continue proliferating and their telomeres continue shortening beyond the point at which normal cells become senescent. In the second phase (immortalization), the cells activate a telomere maintenance mechanism and acquire an unlimited proliferative potential. It has previously been shown that immortalized cells containing viral oncoproteins that bind and inactivate p110RB contain wild-type p16INK4; we therefore examined the p16INK4 status of cell lines that became immortalized in vitro in the absence of these oncoproteins. Three such lines were identified: III-CF/.2A1 and III-CF/E6A2 (both derived from Li-Fraumeni syndrome fibroblasts, probably by spontaneous immortalization) and MePV-231 (normal mesothelial cells transfected with HPV-16 E6/E7 genes that underwent deletion of these genes before immortalization). In each case p16INK4 expression was lost at or before immortalization. Further, a cell strain was identified that had an extended but finite lifespan associated with loss of p16INK4 (and p53) expression. Thus loss of p16INK4 expression was associated with extended in vitro lifespan but was not sufficient for immortalization, even in the absence of wild-type p53.

Structure-activity relationships in the peptide antibiotic nisin: role of dehydroalanine 5

A mutant of the peptide antibiotic nisin in which the dehydroalanine residue at position 5 has been replaced by an alanine has been produced and structurally characterized. It is shown to have activity very similar to that of wild-type nisin in inhibiting growth of Lactococcus lactis and Micrococcus luteus but is very much less active than nisin as an inhibitor of the outgrowth of spores of Bacillus subtilis. These observations, which parallel those of W. Liu and J. N. Hansen (Appl. Environ. Microbiol. 59:648-651, 1993) on the corresponding mutant of the related antibiotic subtilin, are discussed in terms of the mechanism(s) of action of these antibiotics.

Alterations in p53 and p16INK4 expression and telomere length during spontaneous immortalization of Li-Fraumeni syndrome fibroblasts

Normal cells have a strictly limited growth potential and senesce after a defined number of population doublings (PDs). In contrast, tumor cells often exhibit an apparently unlimited proliferative potential and are termed immortalized. Although spontaneous immortalization of normal human cells in vitro is an extremely rare event, we observed this in fibroblasts from an affected member of a Li-Fraumeni syndrome kindred. The fibroblasts were heterozygous for a p53 mutation and underwent senescence as expected at PD 40. In four separate senescent cultures (A to D), there were cells that eventually recommenced proliferation. This was associated with aneuploidy in all four cultures and either loss (cultures A, C, and D) or mutation (culture B) of the wild-type (wt) p53 allele. Loss of wt p53 function was insufficient for immortalization, since cultures A, B, and D subsequently entered crisis from which they did not escape. Culture C has continued proliferating beyond 400 PDs and thus appears to be immortalized. In contrast to the other cultures, the immortalized cells have no detectable p16INK4 protein. A culture that had a limited extension of proliferative potential exhibited a progressive decrease in telomere length with increasing PD. In the culture that subsequently became immortalized, the same trend occurred until PD 73, after which there was a significant increase in the amount of telomeric DNA, despite the absence of telomerase activity. Immortalization of these cells thus appears to be associated with loss of wt p53 and p16INK4 expression and a novel mechanism for the elongation of telomeres.

In vitro transformation of Li-Fraumeni syndrome fibroblasts by SV40 large T antigen mutants

Transfection of SV40 early region DNA into normal human diploid fibroblasts (NHDFs) increases their proliferative potential to a limited extent. We have investigated the roles of the SV40 large T antigen (LTAg) regions responsible for binding to the protein products of the retinoblastoma (Rb) and p53 genes in this temporary escape from senescence. Patients encoding LTAg mutants were transfected into NHDFs and into Li-Fraumeni syndrome (LFS) fibroblasts which are heterozygous wild-type (wt)/null-mutant for p53. A LTAg mutated in the p53-binding region (T402DE) had greatly reduced efficiency of focus formation, and a p110Rb-binding mutant was unable to induce any foci. T402DE-induced NHDF foci senesced at the same time as untransfected cells, but the equivalent LFS foci all had increased proliferative potentials, with the greatest increase being seen in clones that lost the wt p53 allele. One LFS clone expressed the T402DE mutant during focus formation, but later lost both the T402DE DNA and the wt p53 allele. We conclude that SV40-induced focus formation in NHDFs requires the LTAg p110Rb-binding region, and is enhanced by loss of normal p53 function. In contrast, increased proliferative potential is primarily due to loss of p53 function.