Riding the waves from epidemic to endemic: Viral mutations, immunological change and policy responses

Nonpharmaceutical interventions (NPI) are an important tool for countering pandemics such as COVID-19. Some are cheap; others disrupt economic, educational, and social activity. The latter force governments to balance the health benefits of reduced infection and death against broader lockdown-induced societal costs. A literature has developed modeling how to optimally adjust lockdown intensity as an epidemic evolves. This paper extends that literature by augmenting the classic SIR model with additional states and flows capturing decay over time in vaccine-conferred immunity, the possibility that mutations create variants that erode immunity, and that protection against infection erodes faster than protecting against severe illness. As in past models, we find that small changes in parameter values can tip the optimal response between very different solutions, but the extensions considered here create new types of solutions. In some instances, it can be optimal to incur perpetual epidemic waves even if the uncontrolled infection prevalence would settle down to a stable intermediate level.

Prospective evaluation of NGS-based sequencing in epilepsy patients: results of seven NASGE-associated diagnostic laboratories

Background

Epilepsy is one of the most common and disabling neurological disorders. It is highly prevalent in children with neurodevelopmental delay and syndromic diseases. However, epilepsy can also be the only disease-determining symptom. The exact molecular diagnosis is essential to determine prognosis, comorbidity, and probability of recurrence, and to inform therapeutic decisions.

Methods and materials

Here, we describe a prospective cohort study of patients with epilepsy evaluated in seven diagnostic outpatient centers in Germany. Over a period of 2 months, 07/2022 through 08/2022, 304 patients (317 returned result) with seizure-related human phenotype ontology (HPO) were analyzed. Evaluated data included molecular results, phenotype (syndromic and non-syndromic), and sequencing methods.

Results

Single exome sequencing (SE) was applied in half of all patients, followed by panel (P) testing (36%) and trio exome sequencing (TE) (14%). Overall, a pathogenic variant (PV) (ACMG cl. 4/5) was identified in 22%; furthermore, a significant number of patients (12%) carried a reported clinically meaningful variant of unknown significance (VUS). The average diagnostic yield in patients ≤ 12 y was higher compared to patients >12 y cf. Figure 2B vs. Figure 3B. This effect was more pronounced in cases, where TE was applied in patients ≤ 12 vs. >12 y [PV (PV + VUS): patients ≤ 12 y: 35% (47%), patients > 12 y: 20% (40%)]. The highest diagnostic yield was achieved by TE in syndromic patients within the age group ≤ 12 y (ACMG classes 4/5 40%). In addition, TE vs. SE had a tendency to result in less VUS in patients ≤ 12 y [SE: 19% (22/117) VUS; TE: 17% (6/36) VUS] but not in patients >12 y [SE: 19% (8/42) VUS; TE: 20% (2/10) VUS]. Finally, diagnostic findings in patients with syndromic vs. non-syndromic symptoms revealed a significant overlap of frequent causes of monogenic epilepsies, including SCN1A, CACNA1A, and SETD1B, confirming the heterogeneity of the associated conditions.

Conclusion

In patients with seizures-regardless of the detailed phenotype-a monogenic cause can be frequently identified, often implying a possible change in therapeutic action (36.7% (37/109) of PV/VUS variants); this justifies early and broad application of genetic testing. Our data suggest that the diagnostic yield is highest in exome or trio-exome-based testing, resulting in a molecular diagnosis within 3 weeks, with profound implications for therapeutic strategies and for counseling families and patients regarding prognosis and recurrence risk.

The hammer and the jab: Are COVID-19 lockdowns and vaccinations complements or substitutes?

The COVID-19 pandemic has devastated lives and economies around the world. Initially a primary response was locking down parts of the economy to reduce social interactions and, hence, the virus' spread. After vaccines have been developed and produced in sufficient quantity, they can largely replace broad lock downs. This paper explores how lockdown policies should be varied during the year or so gap between when a vaccine is approved and when all who wish have been vaccinated. Are vaccines and lockdowns substitutes during that crucial time, in the sense that lockdowns should be reduced as vaccination rates rise? Or might they be complementary with the prospect of imminent vaccination increasing the value of stricter lockdowns, since hospitalization and death averted then may be permanently prevented, not just delayed? We investigate this question with a simple dynamic optimization model that captures both epidemiological and economic considerations. In this model, increasing the rate of vaccine deployment may increase or reduce the optimal total lockdown intensity and duration, depending on the values of other model parameters. That vaccines and lockdowns can act as either substitutes or complements even in a relatively simple model casts doubt on whether in more complicated models or the real world one should expect them to always be just one or the other. Within our model, for parameter values reflecting conditions in developed countries, the typical finding is to ease lockdown intensity gradually after substantial shares of the population have been vaccinated, but other strategies can be optimal for other parameter values. Reserving vaccines for those who have not yet been infected barely outperforms simpler strategies that ignore prior infection status. For certain parameter combinations, there are instances in which two quite different policies can perform equally well, and sometimes very small increases in vaccine capacity can tip the optimal solution to one that involves much longer and more intense lockdowns.

Biallelic variants in PIGN cause Fryns syndrome, multiple congenital anomalies-hypotonia-seizures syndrome, and neurologic phenotypes: A genotype-phenotype correlation study

PURPOSE

Biallelic PIGN variants have been described in Fryns syndrome, multiple congenital anomalies-hypotonia-seizure syndrome (MCAHS), and neurologic phenotypes. The full spectrum of clinical manifestations in relation to the genotypes is yet to be reported.

METHODS

Genotype and phenotype data were collated and analyzed for 61 biallelic PIGN cases: 21 new and 40 previously published cases. Functional analysis was performed for 2 recurrent variants (c.2679C>G p.Ser893Arg and c.932T>G p.Leu311Trp).

RESULTS

Biallelic-truncating variants were detected in 16 patients-10 with Fryns syndrome, 1 with MCAHS1, 2 with Fryns syndrome/MCAHS1, and 3 with neurologic phenotype. There was an increased risk of prenatal or neonatal death within this group (6 deaths were in utero or within 2 months of life; 6 pregnancies were terminated). Incidence of polyhydramnios, congenital anomalies (eg, diaphragmatic hernia), and dysmorphism was significantly increased. Biallelic missense or mixed genotype were reported in the remaining 45 cases-32 showed a neurologic phenotype and 12 had MCAHS1. No cases of diaphragmatic hernia or abdominal wall defects were seen in this group except patient 1 in which we found the missense variant p.Ser893Arg to result in functionally null alleles, suggesting the possibility of an undescribed functionally important region in the final exon. For all genotypes, there was complete penetrance for developmental delay and near-complete penetrance for seizures and hypotonia in patients surviving the neonatal period.

CONCLUSION

We have expanded the described spectrum of phenotypes and natural history associated with biallelic PIGN variants. Our study shows that biallelic-truncating variants usually result in the more severe Fryns syndrome phenotype, but neurologic problems, such as developmental delay, seizures, and hypotonia, present across all genotypes. Functional analysis should be considered when the genotypes do not correlate with the predicted phenotype because there may be other functionally important regions in PIGN that are yet to be discovered.

Incidence of fatigue associated with immune checkpoint inhibitors in patients with cancer: a meta-analysis

Background

Fatigue is one of the most common adverse effects associated with cancer immunotherapy using checkpoint inhibitors (CPIs). Because treatment-related fatigue also frequently occurs in patients treated with non-immunological therapies, our study aimed to compare the incidence of fatigue in CPI-treated patients with that associated with non-immune therapies in randomised trials.

Methods

PubMed and ClinicalTrials.gov were searched for phase III studies using a CPI alone or in combination with chemotherapy or non-immunologic targeted therapy in the experimental arm and control arm using inactive therapies such as placebo or observation, chemotherapy, or non-immunologic targeted therapy. Adverse events listed in the full texts as well as those available from clinicaltrials.gov were reviewed for all identified studies.

Results

A total of 60 studies involving 41 435 patients were included in the analysis. All-grade fatigue was reported in 30.4% of patients [95% confidence interval (CI) 29.9% to 31.0%] in the immunotherapy arms of the analysed studies. Using anti-programmed cell death protein 1 agents as reference, the odds ratio (OR) for fatigue was significantly higher both for anti-cytotoxic T lymphocyte-associated antigen 4 agents (OR 1.46, 95% CI 1.04-2.04) and the combination of anti-cytotoxic T lymphocyte-associated antigen 4 and anti-programmed cell death protein agents (OR 1.43, 95% CI 1.12-1.83). Fatigue was significantly less likely to occur in patients treated with CPI compared with patients receiving chemotherapy (OR 0.79, 95% CI 0.73-0.85), but significantly was more common in patients receiving the combination of CPI/chemotherapy compared with patients receiving chemotherapy alone (OR 1.12, 95% CI 1.03-1.22).

Conclusions

Although immunotherapy using CPIs was associated with treatment-related fatigue, the occurrence of all-grade fatigue was significantly higher in patients treated with chemotherapy compared with patients receiving CPIs. The risk of fatigue was higher for CPI/chemotherapy combinations than for chemotherapy alone. These results suggest that although the effects of CPIs and chemotherapy are additive, chemotherapy was the dominant cause of treatment-related fatigue in the analysed trials.

•

Fatigue is a common adverse event associated with cancer immunotherapy but also with other therapies and with cancer itself.

•

This meta-analysis analysed the incidence of fatigue reported in phase III trials of checkpoint inhibitors.

•

Fatigue was more common in patients treated with chemotherapy compared with patients receiving checkpoint inhibitors.

•

Chemotherapy was the dominant cause of fatigue in combinations of chemotherapy and checkpoint inhibitors.

Testing a knowledge-based approach for inferring spatio-temporal characteristics of groundwater in the Australian State of Victoria

Groundwater spatio-temporal characteristics are important information for groundwater development and management. However, such information is usually insufficient or even unavailable in many regions around the world due to insufficient or even lack of in-situ data such as from boreholes. Recently, a knowledge-based approach was proposed to infer 'where' and 'when' to find groundwater using Lake Victoria Basin (LVB) as an example for data-deficient regions. In this knowledge-based approach, groundwater model and inversion analysis of groundwater impact factors are used to infer groundwater storage potential and recharge timing. In the LVB's case, only 10 borehole data were used to test the spatio-temporal behaviours of groundwater, which are insufficient. In this contribution, therefore, using the Australian State of Victoria as an example, with over 15,000 boreholes data, the performance of the same knowledge-based approach is further tested in a well-controlled area. The results indicate that the knowledge-based approach is able to correctly infer regions with large groundwater storage potential suitable for extraction. The recharge timing of groundwater is also correctly indicated as the results show consistency with the borehole data. This provides further evidence of the reliability of the knowledge-based approach for inferring spatio-temporal characteristics of groundwater.

Effectiveness of Child-Focused Interventions for Externalizing Behavior: a Rapid Evidence Review

Parent behavior management training (BMT) is well established as an effective, evidence-based treatment for children with externalizing behavior. Despite the wealth of data supporting BMT, many community providers use a variety of child-focused and non-directive interventions to target behavior problems. There is lack of clarity as to whether the evidence supporting child-focused externalizing treatments is sufficiently compelling to support offering these treatments rather than or in addition to BMT. This rapid evidence review compares the effectiveness of BMT with several common child-focused interventions for externalizing behavior including cognitive behavioral (CBT), social skill (SS), and play/dynamic (PT) approaches. PubMed, PsychINFO, and Web of Science were searched for English-language articles from year 2000 onwards for each intervention type. Inclusion criteria were child age (12 and under), presence of a child-focused behavioral treatment condition, and externalizing behavior as an outcome variable. A total of 30 studies met inclusion criteria and were coded (13 CBT, 10 SS, 7 PT). Results supported social skills interventions with accompanying BMT as effective in improving externalizing problems, with generally moderate effect sizes. Individual social skills interventions were promising but needing further evaluation compared to treatment as usual. CBT treatments with and without accompanying BMT showed moderate effects over waitlist but produced less consistently significant effects compared to more robust controls. Play therapy approaches showed inconsistent effects and require further evaluation. This review supports social skills plus BMT treatments as a child-focused intervention with probable efficacy for child externalizing problems. Implications for policy and community practice are discussed.

PIGN encephalopathy: Characterizing the epileptology

OBJECTIVE

Epilepsy is common in patients with PIGN diseases due to biallelic variants; however, limited epilepsy phenotyping data have been reported. We describe the epileptology of PIGN encephalopathy.

METHODS

We recruited patients with epilepsy due to biallelic PIGN variants and obtained clinical data regarding age at seizure onset/offset and semiology, development, medical history, examination, electroencephalogram, neuroimaging, and treatment. Seizure and epilepsy types were classified.

RESULTS

Twenty six patients (13 female) from 26 families were identified, with mean age 7 years (range = 1 month to 21 years; three deceased). Abnormal development at seizure onset was present in 25 of 26. Developmental outcome was most frequently profound (14/26) or severe (11/26). Patients presented with focal motor (12/26), unknown onset motor (5/26), focal impaired awareness (1/26), absence (2/26), myoclonic (2/26), myoclonic-atonic (1/26), and generalized tonic-clonic (2/26) seizures. Twenty of 26 were classified as developmental and epileptic encephalopathy (DEE): 55% (11/20) focal DEE, 30% (6/20) generalized DEE, and 15% (3/20) combined DEE. Six had intellectual disability and epilepsy (ID+E): two generalized and four focal epilepsy. Mean age at seizure onset was 13 months (birth to 10 years), with a lower mean onset in DEE (7 months) compared with ID+E (33 months). Patients with DEE had drug-resistant epilepsy, compared to 4/6 ID+E patients, who were seizure-free. Hyperkinetic movement disorder occurred in 13 of 26 patients. Twenty-seven of 34 variants were novel. Variants were truncating (n = 7), intronic and predicted to affect splicing (n = 7), and missense or inframe indels (n = 20, of which 11 were predicted to affect splicing). Seven variants were recurrent, including p.Leu311Trp in 10 unrelated patients, nine with generalized seizures, accounting for nine of the 11 patients in this cohort with generalized seizures.

SIGNIFICANCE

PIGN encephalopathy is a complex autosomal recessive disorder associated with a wide spectrum of epilepsy phenotypes, typically with substantial profound to severe developmental impairment.

Inference of the spatio-temporal variability and storage potential of groundwater in data-deficient regions through groundwater models and inversion of impact factors on groundwater, as exemplified by the Lake Victoria Basin

Groundwater is an important resource for supporting domestic water use for people's livelihoods and for maintaining ecosystems. Borehole observations provide the first-hand data that characterise the fluctuation, depth, and aquifer conditions of the groundwater. Unfortunately, such observations are not available or are insufficient for scientific use in many regions. Taking the Lake Victoria Basin (LVB) as an example of data-deficient regions, this study proposes a simple knowledge-based approach that uses the Global Land Data Assimilation System (GLDAS) Catchment Land Surface Model (CLSM) for the main data, with rainfall, hydrological, topographical and geological datasets as supports, by which to infer the spatio-temporal variability and storage potential of groundwater. The method is based on analysis and inversion of impact factors on groundwater, and the feasibility of such a method is proven by showing that the groundwater results from GLDAS CLSM can correctly indicate the seasonality, as well as the link to topographical and geological features. For example, both results from the water balance equation (WBE) and GLDAS CLSM indicate that there are two groundwater recharge seasons in the basin, e.g., March to May and September to November. Compared to the eastern side of the LVB, the western side has mountains blocking surface runoff, and thus, reasonably, has larger storage potential estimates in GLDAS CLSM. Due to the low degree of weathering of the basement rocks, it is expected that there is only small storage potential and variation of groundwater in the southeastern parts of the LVB. GLDAS CLSM also correctly reflects this behaviour. Additionally, the largest groundwater storage potential over the LVB is found in regions near the Kagera River and the western shoreline, since it associates with unconsolidated rocks and behaviours of large groundwater recharge from GLDAS CSLM during the wet year of 2006. The major limitation of this knowledge-based method is that the uncertainty in terms of magnitude on GLDAS CLSM groundwater changes cannot be assessed, in addition to the fact that the reliability of the results cannot be quantified in terms of specific numbers. Therefore, the results and interpretation of groundwater behaviours using such methods can only be a guide for 'where' and 'when' to find groundwater.

Impacts of extreme climate on Australia's green cover (2003-2018): A MODIS and mascon probe

Australia as a continent represents a semi-arid environment that is generally water-limited. Changes in rainfall pattern will inevitably occur due to rising temperatures caused by climate change, which has a direct impact on the distribution of Australia's vegetation (green cover). As variability in rainfall continues to increase, i.e., in frequency and/or magnitude, due to climate change, extreme climate events such as droughts are predicted to become more pervasive and severe that will have an adverse effect on vegetation. This study investigates the effects of extreme climate on Australia's green cover during 2003-2018 for the end of rainy seasons of April and October in the northern and southern parts, respectively, to (i) determine the state of vegetation and its changes, (ii) identify "hotspots", i.e., regions that constantly experienced statistically significant decrease in NDVI, and (iii), relate changes in the identified hotspots to GRACE-hydrological changes. These are achieved through the exploitation of the statistical tools of Principal Component Analysis (PCA) and Mann-Kendel Test on Gravity Recovery and Climate Experiment (GRACE) hydrological products on the one hand, and the utilization of Australia's rainfall product and Moderate Resolution Imaging Spectroradiometer Normalized Difference Vegetation Index (MODIS-NDVI) used here with its native spatial resolution of 0.002413^∘ × 0.002413^∘ on the other hand. Differences between 3-year intervals from 2003 to 2018 for both April and October datasets are used to quantify vegetation variations. Through area change analysis, the vegetation differences (2003-2018) indicate that April exhibited larger increase (13.77% of total vegetation area) than decrease (7.83%) compared to October, which experienced slightly larger decrease (9.41%) than increase (8.71%). South Australia and Western Australia emerge as "hotspots" in which vegetation statistically decreased in October, with no noticeable change in April. GRACE-based hydrological changes in both hotspots reflect a decreasing trend (2003-2009) and increasing trend (2009-2012) that peaks in 2011, which then transitions towards a gradually decreasing trend after 2012. Australia-wide climate variability (ENSO and IOD) influenced vegetation variations during the data period 2003 to 2018.

Scanning Compton X-ray microscopy

X-ray microscopy offers the opportunity to image biological and radiosensitive materials without special sample preparations, bridging optical and electron microscopy capabilities. However, the performance of such microscopes, when imaging radiosensitive samples, is not limited by their intrinsic resolution, but by the radiation damage induced on such samples. Here, we demonstrate a novel, to the best of our knowledge, radio-efficient microscope, scanning Compton X-ray microscopy (SCXM), which uses coherently and incoherently (Compton) scattered photons to minimize the deposited energy per unit of mass for a given imaging signal. We implemented SCXM, using lenses capable of efficiently focusing 60 keV X-ray photons into the sub-micrometer scale, and probe its radio-efficient capabilities. SCXM, when implemented in high-energy diffraction-limited storage rings, e.g., European Synchrotron Radiation Facility Extremely Brilliant Source and PETRA IV, will open the opportunity to explore the nanoscale of unstained, unsectioned, and undamaged radiosensitive materials.

Efficacy of Retreatment After Failed Direct-acting Antiviral Therapy in Patients With HCV Genotype 1-3 Infections

Hepatitis C virus infection is causing chronic liver disease, cirrhosis, and hepatocellular carcinoma. By combining direct-acting antivirals (DAAs), high sustained virologic response rates (SVRs) can be achieved. Resistance-associated substitutions (RASs) are commonly observed after DAA failure, and especially nonstructural protein 5A (NS5A) RASs may impact retreatment options.^1-3 Data on retreatment of DAA failure patients using first-generation DAAs are limited.^4-7 Recently, a second-generation protease- and NS5A-inhibitor plus sofosbuvir (voxilaprevir/velpatasvir/sofosbuvir [VOX/VEL/SOF]) was approved for retreatment after DAA failure.⁸ However, this and other second-generation regimens are not available in many resource-limited countries or are not reimbursed by regular insurance, and recommendations regarding the selection of retreatment regimens using first-generation DAAs are very important. This study aimed to analyze patients who were re-treated with first-generation DAAs after failure of a DAA combination therapy.

Improved Criteria for the Classification of Titin Variants in Inherited Skeletal Myopathies

BACKGROUND

Extensive genetic screening results in the identification of thousands of rare variants that are difficult to interpret. Because of its sheer size, rare variants in the titin gene (TTN) are detected frequently in any individual. Unambiguous interpretation of molecular findings is almost impossible in many patients with myopathies or cardiomyopathies.

OBJECTIVE

To refine the current classification framework for TTN-associated skeletal muscle disorders and standardize the interpretation of TTN variants.

METHODS

We used the guidelines issued by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) to re-analyze TTN genetic findings from our patient cohort.

RESULTS

We identified in the classification guidelines three rules that are not applicable to titin-related skeletal muscle disorders; six rules that require disease-/gene-specific adjustments and four rules requiring quantitative thresholds for a proper use. In three cases, the rule strength need to be modified.

CONCLUSIONS

We suggest adjustments are made to the guidelines. We provide frequency thresholds to facilitate filtering of candidate causative variants and guidance for the use and interpretation of functional data and co-segregation evidence. We expect that the variant classification framework for TTN-related skeletal muscle disorders will be further improved along with a better understanding of these diseases.

Spatio-temporal groundwater variations associated with climatic and anthropogenic impacts in South-West Western Australia

South-West Western Australia (SWWA) is a critical agricultural region that heavily relies on groundwater for domestic, agricultural and industrial use. However, the behaviours of groundwater associated with climate variability/change and anthropogenic impacts within this region are not well understood. This study investigates the spatio-temporal variability of groundwater in SWWA based on 2997 boreholes over the past 36 years (1980-2015). Results identify the decline in groundwater level (13 mm/month) located in the central coastal region of SWWA (i.e., north and south of Perth) to be caused by anthropogenic impacts (primary factor) and climate variability/change (secondary). In detail, anthropogenic impacts are mainly attributed to substantial groundwater abstraction, e.g., hotspots (identified by above 7 m/month groundwater level change) mostly occur in the central coastal region, as well as close to dams and mines. Impacts of climate variability/change indicate that coupled ENSO and positive IOD cause low-level rainfall in the coastal regions, subsequently, affecting groundwater recharge. In addition, correlation between groundwater and rainfall is significant at 0.748 over entire SWWA (at 95% confidence level). However, groundwater in northeastern mountainous regions hardly changes with rainfall because of very small amounts of rainfall (average 20-30 mm/month) in this region, potentially coupled with terrain and geological impacts. A marked division for groundwater bounded by the Darling and Gingin Scarps is found. This is likely due to the effects of the Darling fault, dams, central mountainous terrain and geology. For the region south of Perth and southern coastal regions, a hypothesis through multi-year analysis is postulated that rainfall of at least 60 and 65-70 mm/month, respectively, are required during the March-October rainfall period to recharge groundwater.

GRACE-derived groundwater changes over Greater Horn of Africa: Temporal variability and the potential for irrigated agriculture

Greater Horn of Africa (GHA) is projected to face negative impacts on per capita food production due to dwindling nature of water resources forced by climate change and rising population growth. The region has limited groundwater irrigated agriculture and also lacks groundwater monitoring infrastructure. This study (i) employs Independent Component Analysis (ICA) to localize Gravity Recovery and Climate Experiment (GRACE)-derived groundwater changes and analyses the corresponding temporal variabilities and their link to climate indices (Indian Ocean Dipole (IOD) and El Niño-Southern Oscillation (ENSO)), and (ii), explores the irrigation potentials of the localized groundwater. Monthly GRACE-derived groundwater changes showed similar temporal variability to WaterGap Hydrological Model (WGHM), i.e., a correlation of 0.7 (significant at 95% confidence level), highlighting GRACE's potential to provide GHA-wide changes in groundwater. Based on GHA aquifer location maps, the study associated the localized groundwater changes to nine major aquifers namely; Nubian sandstone, Karoo Carbonate, Upper Nile, Ethiopian highlands, Lake Tana region, Kenya-Somalia, Central Tanzania, Karoo sandstone, and Ruvuma. All temporal groundwater changes, except Nubian sandstone and Kenya-Somalia, showed an annual (cyclic) pattern indicating an annual (yearly) recharge cycle. Weak relationships with rainfall and both climate indices were noted. Maximum correlation occurred when rainfall preceded the temporal groundwater changes by several months. Based on water availability (from GRACE), water quality (indicated by the total dissolved substance) and dominant soil types, potential for groundwater irrigated agriculture results showed: low potentials for Nubian Sandstone and Kenya-Somalia areas; low to moderate potentials for Karoo Carbonate, Lake Tana region, central Tanzania, and Ruvuma; moderate to high potentials for Upper Nile and Karoo Sandstone; and high potential for Ethiopian highland. Even though the study has considered relatively short time period (10 years), these results are critical to the sustainable management of the region's groundwater resources and appropriate/informed policy formulation.

Early-Onset Myopathies: Clinical Findings, Prevalence of Subgroups and Diagnostic Approach in a Single Neuromuscular Referral Center in Germany

BACKGROUND

Early-onset myopathies are a heterogeneous group of neuromuscular diseases with broad clinical, genetic and histopathological overlap. The diagnostic approach has considerably changed since high throughput genetic methods (next generation sequencing, NGS) became available.

OBJECTIVE

We present diagnostic subgroups in a single neuromuscular referral center and describe an algorithm for the diagnostic work-up.

METHODS

The diagnostic approach of 98 index patients was retrospectively analysed. In 56 cases targeted sequencing of a known gene was performed, in 44 patients NGS was performed using large muscle specific panels, and in 12 individuals whole exome sequencing (WES) was undertaken. One patient was diagnosed via array CGH. Clinical features of all patients are provided.

RESULTS

The final diagnosis could be found in 63 out of 98 patients (64%) with molecular genetic analysis. In 55% targeted gene sequencing could establish the genetic diagnosis. However, this rate largely depended on the presence of distinct histological or clinical features. NGS (large myopathy-related panels and WES) revealed genetic diagnosis in 58.5% (52% and 67%, respectively). The genes detected by WES in our cohort of patients were all covered by the panels. Based on our findings we propose an algorithm for a practical diagnostic approach.Prevalences:MTM1- and LAMA2-patients are the two biggest subgroups, followed by SEPN1-, RYR1- and Collagen VI-related diseases. 31% of genetically confirmed cases represents a group with overlap between "congenital myopathies (CM)" and "congenital muscular dystrophies (CMD)". In 36% of the patients a specific genetic diagnosis could not be assigned.

CONCLUSIONS

A final diagnosis can be confirmed by high throughput genetic analysis in 58.5% of the cases, which is a higher rate than reported in the literature for muscle biopsy and should in many cases be considered as a first diagnostic tool. NGS cannot replace neuromuscular expertise and a close discussion with the geneticists on NGS is mandatory. Targeted candidate gene sequencing still plays a role in selected cases with highly suspicious clinical or histological features. There is a relevant clinical and genetic overlap between the entities CM and CMD.

Assessing data assimilation frameworks for using multi-mission satellite products in a hydrological context

With a growing number of available datasets especially from satellite remote sensing, there is a great opportunity to improve our knowledge of the state of the hydrological processes via data assimilation. Observations can be assimilated into numerical models using dynamics and data-driven approaches. The present study aims to assess these assimilation frameworks for integrating different sets of satellite measurements in a hydrological context. To this end, we implement a traditional data assimilation system based on the Square Root Analysis (SQRA) filtering scheme and the newly developed data-driven Kalman-Takens technique to update the water components of a hydrological model with the Gravity Recovery And Climate Experiment (GRACE) terrestrial water storage (TWS), and soil moisture products from the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E) and Soil Moisture and Ocean Salinity (SMOS) in a 5-day temporal scale. While SQRA relies on a physical model for forecasting, the Kalman-Takens only requires a trajectory of the system based on past data. We are particularly interested in testing both methods for assimilating different combination of the satellite data. In most of the cases, simultaneous assimilation of the satellite data by either standard SQRA or Kalman-Takens achieves the largest improvements in the hydrological state, in terms of the agreement with independent in-situ measurements. Furthermore, the Kalman-Takens approach performs comparably well to dynamical method at a fraction of the computational cost.

New insights into the crystallization of polymorphic materials: from real-time serial crystallography to luminescence analysis

This article unravels reaction conditions governing the formation of polymorphic structures in solution down to the single particle level applying, for instance, unprecedented real-time serial crystallography measurements during a synthesis process.

Understanding the association between climate variability and the Nile's water level fluctuations and water storage changes during 1992-2016

With the construction of the largest dam in Africa, the Grand Ethiopian Renaissance Dam (GERD) along the Blue Nile, the Nile is back in the news. This, combined with Bujagali Dam on the White Nile are expected to bring ramification to the downstream countries. A comprehensive analysis of the Nile's waters (surface, soil moisture and groundwater) is, therefore, essential to inform its management. Owing to its shear size, however, obtaining in-situ data from "boots on the ground" is practically impossible, paving way to the use of satellite remotely sensed and models' products. The present study employs multi-mission satellites and surface models' products to provide, for the first time, a comprehensive analysis of the changes in Nile's stored waters' compartments; surface, soil moisture and groundwater, and their association to climate variability (El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD)) over the period 1992-2016. In this regard, remotely sensed altimetry data from TOPEX/Poseidon (T/P), Jason-1, and Jason-2 satellites along with the Gravity Recovery And Climate Experiment (GRACE) mission, and the Tropical Rainfall Measuring Mission Project (TRMM) rainfall products are applied to analyze the compartmental changes over the Nile River Basin (NRB). This is achieved through the creation of 62 virtual gauge stations distributed throughout the Nile River that generate water levels, which are used to compute surface water storage changes. Using GRACE total water storage (TWS), soil moisture data from multi-models based on the Triple Collocation Analysis (TCA) method, and altimetry derived surface water storage, Nile basin's groundwater variations are estimated. The impacts of climate variability on the compartmental changes are examined using TRMM precipitation and large-scale ocean-atmosphere ENSO and IOD indices. The results indicate a strong correlation between the river level variations and precipitation changes in the central part of the basin (0.77 on average) in comparison to the northern (0.64 on average) and southern parts (0.72 on average). Larger water storages and rainfall variations are observed in the Upper Nile in contrast to the Lower Nile. A negative groundwater trend is also found over the Lower Nile, which could be attributed to a significantly lower amount of rainfall in the last decade and extensive irrigation over the region.

A study of Bangladesh's sub-surface water storages using satellite products and data assimilation scheme

Climate change can significantly influence terrestrial water changes around the world particularly in places that have been proven to be more vulnerable such as Bangladesh. In the past few decades, climate impacts, together with those of excessive human water use have changed the country's water availability structure. In this study, we use multi-mission remotely sensed measurements along with a hydrological model to separately analyze groundwater and soil moisture variations for the period 2003-2013, and their interactions with rainfall in Bangladesh. To improve the model's estimates of water storages, terrestrial water storage (TWS) data obtained from the Gravity Recovery And Climate Experiment (GRACE) satellite mission are assimilated into the World-Wide Water Resources Assessment (W3RA) model using the ensemble-based sequential technique of the Square Root Analysis (SQRA) filter. We investigate the capability of the data assimilation approach to use a non-regional hydrological model for a regional case study. Based on these estimates, we investigate relationships between the model derived sub-surface water storage changes and remotely sensed precipitations, as well as altimetry-derived river level variations in Bangladesh by applying the empirical mode decomposition (EMD) method. A larger correlation is found between river level heights and rainfalls (78% on average) in comparison to groundwater storage variations and rainfalls (57% on average). The results indicate a significant decline in groundwater storage (∼32% reduction) for Bangladesh between 2003 and 2013, which is equivalent to an average rate of 8.73 ± 2.45mm/year.

Post-stroke insomnia in community-dwelling patients with chronic motor stroke: Physiological evidence and implications for stroke care

Questionnaire studies suggest that stroke patients experience sustained problems with sleep and daytime sleepiness, but physiological sleep studies focussing specifically on the chronic phase of stroke are lacking. Here we report for the first time physiological data of sleep and daytime sleepiness obtained through the two gold-standard methods, nocturnal polysomnography and the Multiple Sleep Latency Test. Data from community-dwelling patients with chronic right-hemispheric stroke (>12 months) were compared to sex- and age-matched controls. Behavioural and physiological measures suggested that stroke patients had poorer sleep with longer sleep latencies and lower sleep efficiency. Patients further spent more time awake during the night, and showed greater high-frequency power during nonREM sleep than controls. At the same time the Multiple Sleep Latency Test revealed greater wake efficiency in patients than controls. Importantly these findings were not due to group differences in sleep disordered breathing or periodic limb movements. Post-stroke insomnia is presently not adequately addressed within the care pathway for stroke. A holistic approach to rehabilitation and care provision, that includes targeted sleep interventions, is likely to enhance long-term outcome and quality of live in those living with chronic deficits after stroke.

Modulation of defensive reactivity by GLRB allelic variation: converging evidence from an intermediate phenotype approach

Representing a phylogenetically old and very basic mechanism of inhibitory neurotransmission, glycine receptors have been implicated in the modulation of behavioral components underlying defensive responding toward threat. As one of the first findings being confirmed by genome-wide association studies for the phenotype of panic disorder and agoraphobia, allelic variation in a gene coding for the glycine receptor beta subunit (GLRB) has recently been associated with increased neural fear network activation and enhanced acoustic startle reflexes. On the basis of two independent healthy control samples, we here aimed to further explore the functional significance of the GLRB genotype (rs7688285) by employing an intermediate phenotype approach. We focused on the phenotype of defensive system reactivity across the levels of brain function, structure, and physiology. Converging evidence across both samples was found for increased neurofunctional activation in the (anterior) insular cortex in GLRB risk allele carriers and altered fear conditioning as a function of genotype. The robustness of GLRB effects is demonstrated by consistent findings across different experimental fear conditioning paradigms and recording sites. Altogether, findings provide translational evidence for glycine neurotransmission as a modulator of the brain's evolutionary old dynamic defensive system and provide further support for a strong, biologically plausible candidate intermediate phenotype of defensive reactivity. As such, glycine-dependent neurotransmission may open up new avenues for mechanistic research on the etiopathogenesis of fear and anxiety disorders.

Neural correlates of behavioral inhibition in healthy people and in patients with borderline personality disorder and ADHD

Introduction

Deficits in behavioral inhibition leading to impulsivity occur frequently in many otherwise different psychiatric diseases, mainly ADHD and borderline personality disorder (BPD). However, the research is complicated by using of different tests and their parameters. Further, the role of frontoparietal network in behavioral inhibition has been questioned recently.

Objectives

The aims of our studies were:

– to present the influence of differences in inhibition tasks parameters;

– to describe neural correlates of behavioral inhibition in healthy people;

– to compare them with BPD and ADHD patients.

Methods

We implemented two different variants of Go/NoGo Task, one designed for behavioral research and the second for neuroimaging. Thirty healthy participants (37% of women, age range 15 to 33 years) underwent behavioral and fMRI measurement. Further, groups of patients with BPD, ADHD and their healthy controls underwent the Go/NoGo Task under both fMRI and EEG.

Results

The results show differences in behavioral performance based on different task parameters. The fMRI results in healthy people show specific activation patterns within the frontoparietal network associated with inhibition trials (mainly inferior frontal gyrus, insula, cingulate gyrus, SMA, inferior parietal lobule). Further, we present differences between patients with BPD, ADHD and controls in BOLD signal and ERPs.

Conclusions

Go/NoGo Task design substantially influences the subjects’ behavioral performance. Our results with methodologically upgraded Go/NoGo Task design provide support for the inhibition frontoparietal brain network and its different activations in BPD and ADHD patients. The research was supported by Ministry of Health of the Czech Republic, grant nr. 15-30062A.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

T cell receptor repertoires after adoptive transfer of expanded allogeneic regulatory T cells

Regulatory T cell (T_reg ) therapy has been exploited in autoimmune disease, solid organ transplantation and in efforts to prevent or treat graft-versus-host disease (GVHD). However, our knowledge on the in-vivo persistence of transfused T_reg is limited. Whether T_reg transfusion leads to notable changes in the overall T_reg repertoire or whether longevity of T_reg in the periphery is restricted to certain clones is unknown. Here we use T cell receptor alpha chain sequencing (TCR-α-NGS) to monitor changes in the repertoire of T_reg upon polyclonal expansion and after subsequent adoptive transfer. We applied TCR-α-NGS to samples from two patients with chronic GVHD who received comparable doses of stem cell donor derived expanded T_reg . We found that in-vitro polyclonal expansion led to notable repertoire changes in vitro and that T_reg cell therapy altered the peripheral T_reg repertoire considerably towards that of the infused cell product, to different degrees, in each patient. Clonal changes in the peripheral blood were transient and correlated well with the clinical parameters. We suggest that T cell clonotype analyses using TCR sequencing should be considered as a means to monitor longevity and fate of adoptively transferred T cells.

Genetic and neurodevelopmental spectrum of SYNGAP1-associated intellectual disability and epilepsy

OBJECTIVE

We aimed to delineate the neurodevelopmental spectrum associated with SYNGAP1 mutations and to investigate genotype-phenotype correlations.

METHODS

We sequenced the exome or screened the exons of SYNGAP1 in a total of 251 patients with neurodevelopmental disorders. Molecular and clinical data from patients with SYNGAP1 mutations from other centres were also collected, focusing on developmental aspects and the associated epilepsy phenotype. A review of SYNGAP1 mutations published in the literature was also performed.

RESULTS

We describe 17 unrelated affected individuals carrying 13 different novel loss-of-function SYNGAP1 mutations. Developmental delay was the first manifestation of SYNGAP1-related encephalopathy; intellectual disability became progressively obvious and was associated with autistic behaviours in eight patients. Hypotonia and unstable gait were frequent associated neurological features. With the exception of one patient who experienced a single seizure, all patients had epilepsy, characterised by falls or head drops due to atonic or myoclonic seizures, (myoclonic) absences and/or eyelid myoclonia. Triggers of seizures were frequent (n=7). Seizures were pharmacoresistant in half of the patients. The severity of the epilepsy did not correlate with the presence of autistic features or with the severity of cognitive impairment. Mutations were distributed throughout the gene, but spared spliced 3' and 5' exons. Seizures in patients with mutations in exons 4-5 were more pharmacoresponsive than in patients with mutations in exons 8-15.

CONCLUSIONS

SYNGAP1 encephalopathy is characterised by early neurodevelopmental delay typically preceding the onset of a relatively recognisable epilepsy comprising generalised seizures (absences, myoclonic jerks) and frequent triggers.

Diagnostic Impact of Bone-Subtraction CT Angiography for Patients with Acute Subarachnoid Hemorrhage

BACKGROUND AND PURPOSE

Detection and evaluation of ruptured aneurysms is critical for choosing an appropriate endovascular or neurosurgical intervention. Our aim was to assess whether bone-subtraction CTA is capable of guiding treatment for cerebral aneurysms in patients with acute SAH and could replace DSA.

MATERIALS AND METHODS

We prospectively studied 116 consecutive patients with SAH with 16-detector row bone-subtraction CTA and DSA before intracranial aneurysm treatment. Two independent neuroradiologists reviewed the bone-subtraction CTA blinded to DSA (reference standard). We determined the accuracy of bone-subtraction CTA for aneurysm detection and the measurement of aneurysm dimensions and compared the radiation doses of the 2 imaging modalities.

RESULTS

Seventy-one patients (61%) had 74 aneurysms on DSA. Bone-subtraction CTA detected 73 of these aneurysms, but it detected 1 additional aneurysm. On a per-aneurysm basis, sensitivity, specificity, and positive and negative predictive values for bone-subtraction CTA were 99%, 98%, and 99% and 98%, respectively. For aneurysms of ≤3 mm, sensitivity was 94% (95% CI, 73%-99%). Bone-subtraction CTA slightly overestimated neck and dome diameters by <0.2 mm and overestimated the dome-to-neck ratios by 2% on average. Dose-length product was 565 ± 201 mGy × cm for bone-subtraction CTA and 1609 ± 1300 mGy × cm for DSA.

CONCLUSIONS

Bone-subtraction CTA is as accurate as DSA in detecting cerebral aneurysms after SAH, provides similar information about aneurysm configuration and measures, and reduces the average effective radiation dose for vascular diagnostics by 65%. Diagnostic equivalence in association with dose reduction suggests replacing DSA with bone-subtraction CTA in the diagnostic work-up of spontaneous SAH.

Gastro-Intestinal Tolerance and Renal Safety of Protein Oral Nutritional Supplements in Nursing Home Residents: A Randomized Controlled Trial

BACKGROUND/OBJECTIVE

High protein oral nutritional supplements (ONS) are regularly prescribed to undernourished patients; however usage of these in older adults is being discussed, as their renal function might have declined with age. Therefore, the aim of the current study was to evaluate the effects of 8 week long consumption of high protein ONS on the renal function of nursing home residents in need of supplementation. Furthermore, within the same setup, differences in gastro-intestinal tolerance between a standard and a more concentrated version of an ONS were investigated.

DESIGN

Randomized, controlled, single-blind, parallel-group, multi-country trial (NTR2565).

SETTING

Nursing home.

PARTICIPANTS

67 nursing home residents in need of ONS (energy-dense, small volume group n=32; standard volume group n=35).

INTERVENTION

Protein supplementation was provided by either a standard (200ml, 300kcal, 20g protein) or an energy-dense, small volume (125ml, 300kcal, 18g protein) ONS during the 8 week long study.

MEASUREMENTS

Primary outcome was gastro-intestinal tolerance, assessed by daily stool frequency and consistency, and occurrence and intensity of self-reported gastro-intestinal symptoms. Safety was measured via the occurrence of (serious) adverse events, vital signs, as well as liver- and kidney function monitoring.

RESULTS

No clinically relevant and, except for flatulence, no statistically significant differences in gastro-intestinal tolerance were observed between groups. No significant difference between groups was found for estimated glomerular filtration rate (eGFR) and urinary albumin/creatinine ratio at baseline and week 8, nor for the changes from baseline. Adverse events and the changes in monitored renal parameters over the study period did not point to a deterioration of renal function.

CONCLUSION

High protein ONS seems to be well-tolerated and safe; there is no indication that it affects renal function in nursing home residents, including patients with stage 3 chronic kidney disease, under the conditions tested. Results did not suggest a difference in the effect on renal function between standard and energy-dense small volume ONS format.

Rare KCNJ18 variants do not explain hypokalaemic periodic paralysis in 263 unrelated patients

OBJECTIVE

To examine rare KCNJ18 variations recently reported to cause sporadic and thyrotoxic hypokalaemic periodic paralysis (TPP).

METHODS

We sequenced KCNJ18 in 474 controls (400 Caucasians, 74 male Asians) and 263 unrelated patients with periodic paralysis (PP), including 30 patients with TPP without mutations in established PP genes.

RESULTS

In 10 patients without TPP, we identified 9 heterozygous, novel variations (c.-3G>A, L15S, R81C, E273X, T309I, I340T, N365S, G394R, R401W) and a questionable heterozygous causative R399X stop variant. Studies on 40 relatives of these 10 patients showed that none of the variants were de novo in the patients and that R399X occurred in 3 non-affected relatives. Most affected amino acids lacked conservation and several clinically affected relatives did not carry the patient's variant. T309I, however, could be pathogenic under the pre-requisite of strongly reduced penetrance in females. Of the controls, 17 revealed 12 novel rare variants including the heterozygous E273X stop variant in three individuals.

CONCLUSIONS

Our study shows many different, rare KCNJ18 alterations in patients as well as controls. Only perhaps one meets the requirements of a disease-causing mutation. Therefore, KCNJ18 alterations are seldom pathogenic. Additional studies are required before patients with PP can be genetically diagnosed on the basis of a KCNJ18 variant alone.

Long-Term Observations in an Affected Family with Neurogenic Scapuloperoneal Syndrome Caused by Mutation R269C in the TRPV4 Gene

Mutations in the TRPV4 gene, encoding a polymodal Ca(2+) permeable channel, are causative for several human diseases, affecting the skeletal and the peripheral nervous system with highly variable phenotypes. We report on a family with two affected individuals. The father clinically suffered from a classical scapuloperoneal syndrome, while the son presented with a severe neonatal onset with congenital respiratory distress, feeding problems and arthrogryposis multiplex. Multi-Gene Panel sequencing by next generation sequencing revealed the heterozygous mutation c.805C>T (p.R269C) in the TRPV4 gene. Long-term observation over two decades showed no relevant disease progression in the father and, after a dramatic neonatal period, a significant improvement in the son who became ambulant with orthoses at the age of 5 years, suggesting a reasonably good prognosis even in cases with severe neonatal onset. Long-term findings in muscle ultrasound correlated with the clinical course, showing stable or even slightly improved findings. Neurography revealed a late-onset sensory neuropathy in the father, which was so far not described in TRPV4 neuropathies.

Overlap phenotype between CMT1A and hereditary neuropathy with liability to pressure palsies caused by the novel small in-frame deletion c.407_418del12 in PMP22 gene

We report monozygotic twins, who presented with a clinical picture of Charcot-Marie-Tooth disease type 1 (CMT1) with bilateral foot drop, pes cavus, thoracic kyphosis, and scoliosis. Hereditary neuropathy with liability to pressure palsies (HNPP) showed up in one of them. Neurography showed demyelinating neuropathy, typical for CMT1, and transient conduction block in the ulnar nerve correlating with clinical ulnar palsy due to minor mechanical stress in only one of them. Genetic analysis revealed novel small de novo deletion c.407_418del12 in the PMP22 gene. Our patient shows the rarely reported combination of CMT1A and HNPP, caused by an in-frame deletion in the PMP22 gene. HNPP is in the majority of cases correlated with heterozygous deletion of the whole PMP22 gene or other mutations leading to functional haploinsufficiency. The cases give further evidence that pathogenesis of HNPP is not completely understood and can obviously result from existence of a defective protein, too. The intrafamiliar phenotypic variability, even in monozygotic twins, confirms the well-known fact that factors apart from genetics contribute to the clinical course.

Compliance of energy-dense, small volume oral nutritional supplements in the daily clinical practice on a geriatric ward--an observational study

INTRODUCTION

Compliance is important in optimizing the clinical effectiveness of oral nutritional supplements (ONS). Small volume, energy-dense ONS (ED-ONS; ≥ 2 kcal/ml) have been shown to improve compliance in clinical trial settings. However, data from clinical practice is still lacking. The aim of the present study was to evaluate the effect of ED-ONS on the compliance in an observational set-up to obtain data from daily clinical practice on a geriatric ward.

METHODS

Geriatric inpatients, undernourished or at risk of undernutrition received two servings of either ED-ONS (125 ml, 2.4 kcal/ml: Nutridrink Compact Energy, Nutricia) or a standard ONS (S-ONS; 200 ml, 1.5 kcal/ml: Nutridrink) as part of their daily routine care. Patients were allocated to a group according to availability of beds and placement on the ward. Compliance (kcal/day and % of prescribed volume) was assessed by weighing returned bottles. Data were analyzed via Mixed Model for Repeated Measures.

RESULTS

Forty-seven patients received ED-ONS, and 61 patients received S-ONS. Compliance was significantly higher with ED-ONS in geriatric inpatients compared to S-ONS ( 378 ± 14.0 kcal/day vs. 337 ± 13.6 kcal/day (mean ± SEM), p = 0.039, 63.0 ± 2.34% vs. 56.2 ± 2.26%, p = 0.039). Moreover, a trend (p=0.078) was observed towards an increasing difference in compliance over time.

CONCLUSION

This study shows that compliance to ED-ONS is significantly better than to S-ONS in daily clinical practice. Although small, the difference in compliance seems to increase over time, suggesting clinical relevance with longer treatment.

Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1

OBJECTIVES

An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates.

METHODS

Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes.

RESULTS

All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1.

CONCLUSIONS

There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens.