BIBSNet: A Deep Learning Baby Image Brain Segmentation Network for MRI Scans

Objectives

Brain segmentation of infant magnetic resonance (MR) images is vitally important in studying developmental mental health and disease. The infant brain undergoes many changes throughout the first years of postnatal life, making tissue segmentation difficult for most existing algorithms. Here, we introduce a deep neural network BIBSNet (Baby and Infant Brain Segmentation Neural Network), an open-source, community-driven model that relies on data augmentation and a large sample size of manually annotated images to facilitate the production of robust and generalizable brain segmentations.

Experimental Design

Included in model training and testing were MR brain images on 84 participants with an age range of 0-8 months (median postmenstrual ages of 13.57 months). Using manually annotated real and synthetic segmentation images, the model was trained using a 10-fold cross-validation procedure. Testing occurred on MRI data processed with the DCAN labs infant-ABCD-BIDS processing pipeline using segmentations produced from gold standard manual annotation, joint-label fusion (JLF), and BIBSNet to assess model performance.

Principal Observations

Using group analyses, results suggest that cortical metrics produced using BIBSNet segmentations outperforms JLF segmentations. Additionally, when analyzing individual differences, BIBSNet segmentations perform even better.

Conclusions

BIBSNet segmentation shows marked improvement over JLF segmentations across all age groups analyzed. The BIBSNet model is 600x faster compared to JLF and can be easily included in other processing pipelines.

Examining the factor structure and discriminative utility of the Infant Behavior Questionnaire-Revised in infant siblings of autistic children

Using the Infant Behavior Questionnaire-Revised in a longitudinal sample of infant siblings of autistic children (HR; n = 427, 171 female, 83.4% White) and a comparison group of low-risk controls (LR, n = 200, 86 female, 81.5% White), collected between 2007 and 2017, this study identified an invariant factor structure of temperament traits across groups at 6 and 12 months. Second, after partitioning the groups by familial risk and diagnostic outcome at 24 months, results reveal an endophenotypic pattern of Positive Emotionality at both 6 and 12 months, (HR-autism spectrum disorder [ASD] < HR-no-ASD < LR). Third, increased 'Duration of Orienting' at 12 months was associated with lower scores on the 24-month developmental outcomes in HR infants. These findings may augment efforts for early identification of ASD.

Resting-state functional connectivity identifies individuals and predicts age in 8-to-26-month-olds

Resting-state functional connectivity (rsFC) measured with fMRI has been used to characterize functional brain maturation in typically and atypically developing children and adults. However, its reliability and utility for predicting development in infants and toddlers is less well understood. Here, we use fMRI data from the Baby Connectome Project study to measure the reliability and uniqueness of rsFC in infants and toddlers and predict age in this sample (8-to-26 months old; n = 170). We observed medium reliability for within-session infant rsFC in our sample, and found that individual infant and toddler's connectomes were sufficiently distinct for successful functional connectome fingerprinting. Next, we trained and tested support vector regression models to predict age-at-scan with rsFC. Models successfully predicted novel infants' age within ± 3.6 months error and a prediction R² = .51. To characterize the anatomy of predictive networks, we grouped connections into 11 infant-specific resting-state functional networks defined in a data-driven manner. We found that connections between regions of the same network-i.e. within-network connections-predicted age significantly better than between-network connections. Looking ahead, these findings can help characterize changes in functional brain organization in infancy and toddlerhood and inform work predicting developmental outcome measures in this age range.

Real-time motion monitoring improves functional MRI data quality in infants

Imaging the infant brain with MRI has improved our understanding of early neurodevelopment. However, head motion during MRI acquisition is detrimental to both functional and structural MRI scan quality. Though infants are typically scanned while asleep, they commonly exhibit motion during scanning causing data loss. Our group has shown that providing MRI technicians with real-time motion estimates via Framewise Integrated Real-Time MRI Monitoring (FIRMM) software helps obtain high-quality, low motion fMRI data. By estimating head motion in real time and displaying motion metrics to the MR technician during an fMRI scan, FIRMM can improve scanning efficiency. Here, we compared average framewise displacement (FD), a proxy for head motion, and the amount of usable fMRI data (FD ≤ 0.2 mm) in infants scanned with (n = 407) and without FIRMM (n = 295). Using a mixed-effects model, we found that the addition of FIRMM to current state-of-the-art infant scanning protocols significantly increased the amount of usable fMRI data acquired per infant, demonstrating its value for research and clinical infant neuroimaging.

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MRI studies of the infant brain are critical for studying early neurodevelopment.

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Head motion diminishes MRI data quality, which can adversely affect infant imaging.

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We show that real-time head motion monitoring improves fMRI scan quality in infants.

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Being able to monitor motion during fMRI acquisition improves scanning efficiency.

The effect of chemical representation on active machine learning towards closed-loop optimization

Multivariate chemical reaction optimization involving catalytic systems is a non-trivial task due to the high number of tuneable parameters and discrete choices.

Caregivers' estimate of early childhood developmental status in rural Uganda: a cross-sectional study

OBJECTIVE

To characterise developmental milestones among young children living in rural communities in Uganda.

DESIGN

Cross-sectional study.

SETTING

Iganga-Mayuge Health and Demographic Surveillance Site in rural eastern Uganda.

PARTICIPANTS

A total of 720 caregivers of children aged 3-4 years old from a health and demographic surveillance site in rural eastern Uganda were recruited into this study. Caregivers reported on their child's developmental skills and behaviours using the 10-item Early Childhood Development Index (ECDI) developed by UNICEF. Childhood development was characterised based on the ECDI's four domains: literacy-numeracy, learning/cognition, physical and socioemotional development. As an exploratory analysis, we implemented a hierarchical agglomerative cluster analysis to identify homogenous subgroups of children based on the features assessed. The cluster analysis was performed to identify potential subgroups of children who may be at risk of developmental problems.

RESULTS

Between November 2017 and June 2018, 720 caregivers of children aged 3-4 years completed the ECDI. The proportions of children at risk of delay in each domain were as follows: literacy-numeracy: 75% (n=538); socioemotional development: 22% (n=157); physical: 3% (n=22); and cognitive: 4% (n=32). The cluster analysis revealed a three-cluster solution that included 93% of children assigned to a low-risk group, 4% assigned to a moderate-risk group and 3% assigned to a high-risk group characterised by low scores in almost all domains.

CONCLUSION

The findings suggest that a high proportion of children in rural eastern Uganda demonstrate poor literacy-numeracy skills. These results underscore the need to improve population-based screening and intervention efforts to improve early childhood developmental outcomes, particularly in literacy and socioemotional domains, in low-income and middle-income countries such as Uganda.

Comparison of Validity of Mapping between Drug Indications and ICD-10

Background: Mapping of drug indications to ICD-10 was undertaken in Korea by a public and a private institution for their own purposes. A different mapping approach was used by each institution, which presented a good opportunity to compare the validity of the two approaches.

Objectives: This study was undertaken to compare the validity of a direct mapping approach and an indirect terminology based mapping approach of drug indications against the gold standard drawn from the results of the two mapping processes.

Methods: Three hundred and seventy-five cardiovascular reference drugs were selected from all listed cardiovascular drugs for the study. In the direct approach, two experienced nurse coders mapped the free text indications directly to ICD-10. In the indirect terminology based approach, the indications were extracted and coded in the Korean Standard Terminology of Medicine. These terminology coded indications were then manually mapped to ICD-10. The results of the two approaches were compared to the gold standard. A kappa statistic was calculated to see the compatibility of both mapping approaches. Recall, precision and F1 score of each mapping approach were calculated and analyzed using a paired t-test.

Results: The mean number of indications for the study drugs was 5.42. The mean number of ICD-10 codes that matched in direct approach was 46.32 and that of indirect terminology based approach was 56.94. The agreement of the mapping results between the two approaches were poor (kappa = 0.19). The indirect terminology based approach showed higher recall (86.78%) than direct approach (p < 0.001). However, there was no difference in precision and F1 score between the two approaches.

Conclusions: Considering no differences in the F1 scores, both approaches may be used in practice for mapping drug indications to ICD-10. However, in terms of consistency, time and manpower, better results are expected from the indirect terminology based approach.

The impact of stress at different life stages on physical health and the buffering effects of maternal sensitivity

OBJECTIVE

Many studies indicate that early life stress leads to negative health outcomes in adulthood, and some suggest that high-quality parenting might buffer these effects. Most prior research, however, has relied on cross-sectional retrospective reports of stress and parenting. Our study tests how coder-rated stress and parenting quality assessed at different life stages predict adult health outcomes in a prospective, longitudinal study.

METHOD

Participants were 163 individuals in the Minnesota Longitudinal Study of Risk and Adaptation studied since birth. Physical health was assessed at age 32 with body mass index, self-reports of symptoms and illnesses experienced, and self-ratings of overall physical health. Stress was assessed by coder-rated interviews involving participants or their mothers at 16 time points partitioned into 5 life stages: early childhood, middle childhood, adolescence, young adulthood, and at age 32 (when health was assessed). Parenting quality was measured by coder ratings of each mother's provision of sensitive, responsive support at 7 time points between birth and age 13.

RESULTS

Early childhood, adolescent, and concurrent stress predicted adult health outcomes at age 32. Early childhood and adolescent stress, and adolescent and concurrent stress, both showed a "dual-risk" pattern, such that experiencing higher stress at both of these life stages predicted the worst health outcomes. Higher maternal sensitivity, however, buffered these deleterious effects.

CONCLUSION

Our prospective data reveal that early childhood and adolescence are important developmental periods during which stress is influential for adult physical health. However, parenting interventions that promote greater sensitivity may help children in high-stress environments avoid negative adult health outcomes. (PsycINFO Database Record

Cognitive adaptations to stressful environments: When childhood adversity enhances adult executive function

Can growing up in a stressful childhood environment enhance certain cognitive functions? Drawing participants from higher-income and lower-income backgrounds, we tested how adults who grew up in harsh or unpredictable environments fared on 2 types of executive function tasks: inhibition and shifting. People who experienced unpredictable childhoods performed worse at inhibition (overriding dominant responses), but performed better at shifting (efficiently switching between different tasks). This finding is consistent with the notion that shifting, but not inhibition, is especially useful in unpredictable environments. Importantly, differences in executive function between people who experienced unpredictable versus predictable childhoods emerged only when they were tested in uncertain contexts. This catalyst suggests that some individual differences related to early life experience are manifested under conditions of uncertainty in adulthood. Viewed as a whole, these findings indicate that adverse childhood environments do not universally impair mental functioning, but can actually enhance specific types of cognitive performance in the face of uncertainty.

Secure Infant-Mother Attachment Buffers the Effect of Early-Life Stress on Age of Menarche

Prior research indicates that being reared in stressful environments is associated with earlier onset of menarche in girls. In this research, we examined (a) whether these effects are driven by exposure to certain dimensions of stress (harshness or unpredictability) during the first 5 years of life and (b) whether the negative effects of stress on the timing of menarche are buffered by secure infant-mother attachment. Results revealed that (a) exposure to greater harshness (but not unpredictability) during the first 5 years of life predicted earlier menarche and (b) secure infant-mother attachment buffered girls from this effect of harsh environments. By connecting attachment research to its evolutionary foundations, these results illuminate how environmental stressors and relationships early in life jointly affect pubertal timing.

An examination of the elastic properties of tissue-mimicking phantoms using vibro-acoustography and a muscle motor system

Tissue hardness, often quantified in terms of elasticity, is an important differentiating criterion for pathological identity and is extensively used by surgeons for tumor localization. Delineation of malignant regions from benign regions is typically performed by visual inspection and palpation. Although practical, this method is highly subjective and does not provide quantitative metrics. We have previously reported on Vibro-Acoustography (VA) for tumor delineation. VA is unique in that it uses the specific, non-linear properties of tumor tissue in response to an amplitude modulated ultrasound beam to generate spatially resolved, high contrast maps of tissue. Although the lateral and axial resolutions (sub-millimeter and sub-centimeter, respectively) of VA have been extensively characterized, the relationship between static stiffness assessment (palpation) and dynamic stiffness characterization (VA) has not been explicitly established. Here we perform a correlative exploration of the static and dynamic properties of tissue-mimicking phantoms, specifically elasticity, using VA and a muscle motor system. Muscle motor systems, commonly used to probe the mechanical properties of materials, provide absolute, quantitative point measurements of the elastic modulus, analogous to Young's modulus, of a target. For phantoms of varying percent-by-weight concentrations, parallel VA and muscle motor studies conducted on 18 phantoms reveal a negative correlation (p < - 0.85) between mean signal amplitude levels observed with VA and calculated elastic modulus values from force vs. indentation depth curves. Comparison of these elasticity measurements may provide additional information to improve tissue modeling, system characterization, as well as offer valuable insights for in vivo applications, specifically surgical extirpation of tumors.

The occurrence of dystonia in upper-limb multiple sclerosis tremor

BACKGROUND

The pathophysiology of multiple sclerosis (MS) tremor is uncertain with limited phenotypical studies available.

OBJECTIVE

To investigate whether dystonia contributes to MS tremor and its severity.

METHODS

MS patients (n = 54) with and without disabling uni- or bilateral upper limb tremor were recruited (39 limbs per group). We rated tremor severity, writing and Archimedes spiral drawing; cerebellar dysfunction (SARA score); the Global Dystonia Scale (GDS) for proximal and distal upper limbs, dystonic posturing, mirror movements, geste antagoniste, and writer's cramp.

RESULTS

Geste antagoniste, mirror dystonia, and dystonic posturing were more frequent and severe (p < 0.001) and dystonia scores were correlated with tremor severity in tremor compared to non-tremor patients. A 1-unit increase in distal dystonia predicted a 0.52-Bain unit (95% confidence interval (CI) 0.08-0.97), p = 0.022) increase in tremor severity and a 1-unit (95% CI 0.48-1.6, p = 0.001) increase in drawing scores. A 1-unit increase in proximal dystonia predicted 0.93-Bain unit increase (95% CI 0.45-1.41, p < 0.001) in tremor severity and 1.5-units (95% CI 0.62-2.41, p = 0.002) increase in the drawing score. Cerebellar function in the tremor limb and tremor severity was correlated (p < 0.001).

CONCLUSIONS

Upper limb dystonia is common in MS tremor suggesting that MS tremor pathophysiology involves cerebello-pallido-thalamo-cortical network dysfunction.

Symptom differences and pretreatment asymptomatic interval affect outcomes of stenting for intracranial atherosclerotic disease

BACKGROUND AND PURPOSE

Different types of symptomatic intracranial stenosis may respond differently to interventional therapy. We investigated symptomatic and pathophysiologic factors that may influence clinical outcomes of patients with intracranial atherosclerotic disease who were treated with stents.

MATERIALS AND METHODS

A retrospective analysis was performed of patients treated with stents for intracranial atherosclerosis at 4 centers. Patient demographics and comorbidities, lesion features, treatment features, and preprocedural and postprocedural functional status were noted. χ(2) univariate and multivariate logistic regression analysis was performed to assess technical results and clinical outcomes.

RESULTS

One hundred forty-two lesions in 131 patients were analyzed. Lesions causing hypoperfusion ischemic symptoms were associated with fewer strokes by last contact [χ(2) (1, n = 63) = 5.41, P = .019]. Nonhypoperfusion lesions causing symptoms during the 14 days before treatment had more strokes by last contact [χ(2) (1, n = 136), 4.21, P = .047]. Patients treated with stents designed for intracranial deployment were more likely to have had a stroke by last contact (OR, 4.63; P = .032), and patients treated with percutaneous balloon angioplasty in addition to deployment of a self-expanding stent were less likely to be stroke free at point of last contact (OR, 0.60; P = .034).

CONCLUSIONS

More favorable outcomes may occur after stent placement for lesions causing hypoperfusion symptoms and when delaying stent placement 7-14 days after most recent symptoms for lesions suspected to cause embolic disease or perforator ischemia. Angioplasty performed in addition to self-expanding stent deployment may lead to worse outcomes, as may use of self-expanding stents rather than balloon-mounted stents.

Intracortical visual prosthesis research - approach and progress

Following the early work of Brindley in the late 1960's, the NIH began intramural and extramural funding for stimulation of the primary visual coretex using fine-wire electrodes that are inserted into area VI for the prupose of restoring vision in individuals with blindness. More recently researchers with experience in this projectbecame part of our multi-institutional team with the intention to identify and close technological gaps so that the intracortical approach might be tested in humans on a chronic basis. Our team has formulated an approach for testing a prototype system in a human volunteer. Here, we describe our progress and expectations.

Evolution, stress, and sensitive periods: the influence of unpredictability in early versus late childhood on sex and risky behavior

According to a recent evolutionary life history model of development proposed by Ellis, Figueredo, Brumbach, and Schlomer (2009), growing up in harsh versus unpredictable environments should have unique effects on life history strategies in adulthood. Using data from the Minnesota Longitudinal Study of Risk and Adaptation, we tested how harshness and unpredictability experienced in early childhood (age 0-5) versus in later childhood (age 6-16) uniquely predicted sexual and risky behavior at age 23. Findings showed that the strongest predictor of both sexual and risky behavior was an unpredictable environment between ages 0 and 5. Individuals exposed to more unpredictable, rapidly changing environments during the first 5 years of life displayed a faster life history strategy at age 23 by having more sexual partners, engaging in more aggressive and delinquent behaviors, and being more likely to be associated with criminal activities. In contrast, exposure to either harsh environments or experiencing unpredictability in later childhood (age 6-16) was, for the most part, not significantly related to these outcomes at age 23. Viewed together, these findings show that unpredictable rather than merely harsh childhood environments exert unique effects on risky behavior later in life consistent with a faster life history strategy. The findings also suggest that there is a developmentally sensitive period for assessing environmental unpredictability during the first 5 years of life.

Fragile X-associated tremor/ataxia phenotype in a male carrier of unmethylated full mutation in the FMR1 gene

The Fragile X syndrome is caused by a CGG repeat expansion >200 in the promoter of the Fragile X mental retardation 1 (FMR1) gene termed full mutation (FM). These alleles are silenced through methylation of the FMR1 promoter, leading to deficit of the FMR1 protein (FMRP), and neurodevelopmental changes. However, occasional FM individuals have a complete lack of methylation, and those typically have only minor deficit of FMRP levels compared with normal controls and their intelligence may be in the normal range. FM alleles are generated through expansion of the CGG repeat from the premutation (PM) range of 55-200 repeats, linked to the late onset Fragile X-associated tremor/ataxia syndrome (FXTAS). This disorder has been attributed to a 'toxicity' of the FMR1 mRNA, which is significantly elevated in male carriers of PM alleles and of unmethylated FM alleles. This is the first report of a 65-year-old male with an unmethylated FM allele and history of alcohol abuse, who developed symptoms of FXTAS. We postulate that, although the elevation of FMR1 transcripts associated with unmethylated FM alleles have a potential to cause FXTAS, in some cases this disorder may occur through an additional effect of exposure to neurotoxicants including alcohol.

Deleted in breast cancer 1 (DBC1) is a dynamically regulated protein

Deleted in breast cancer 1 (DBC1, KIAA1967, p30 DBC) is a novel protein that has been suggested to be a critical regulator of tumorigenesis. DBC1 modulates the activities of various proteins, including SIRT1, ERalpha, RARalpha, and AR. The functions of DBC1 with target molecules have been investigated, but little is known of its molecular characteristics. We found that DBC1 is homo-oligomerized and exhibits a dynamic expression pattern during cell cycle. In addition, DBC1 expression is higher in lung cancer cells than in normal lung fibroblasts and the protein recognized by anti-DBC1 antibodies in normal cells differs from that in lung and breast cancer cells. Further examination of the oligomerization and the dynamic expression of DBC1 during the cell cycle will help us to understand the mechanisms of DBC1 function. Moreover, the elucidation about differential expression of DBC1 between normal cells and cancer cells will aid the development of DBC1 as a diagnostic marker for cancers.

Predictive and prognostic functions of microtubule-associated protein-tau and topoisomerase IIα protein in early breast cancer

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Background: Topoisomerase IIα protein(topo II) is the molecular target of topo II inhibitors such as anthracyclines and Microtubule-Associated Protein(MAP)-tau protein is associated with taxane sensitivity. Anthracyclins and taxanes are major cytotoxic agents of breast cancer in the adjuvant setting. The aim of this study was to evaluate the predictive and prognostic functions of MAP-tau and topo II in early breast cancers. Methods: Representative breast tumor sections were constructed from paraffin embedded specimens from 78 node positive breast cancer patients. MAP-tau and topo II protein were assessed by immunochemistry using antibody clone 4F1(Affinity BioReagents,USA) and clone Ki-S1 antibody(Dakocytomation,USA). MAP-tau staining of tumor cells was semiquantatively scored as 0, 1+, 2+, 3+ and cases with 0 or 1+ staining intensity were considered MAP-tau negative. Topo II protein over- expression was defined as the detection of nuclear staining in more than median value of evaluated cells. Results: Thirty- four cases (43.6%) of 78 samples showed topo II overexpression and 35 cases(44.9%) showed MAP-tau overexpression in node positive breast cancers. HER2 overexpression was noted in 28 samples (35.9%) and 56 cases (71.8%) were compatible with the luminal type. In 43 patients (55.1%), anthracyclin and taxane were used as adjuvant therapy and in this group, both MAP-tau and topo II overexpression showed lower disease-free survival (DFS) than the others, but statistically not significant. In luminal type, MAP-tau overexpression was poor prognostic factor on DFS in Cox regression.(HR 5.644, 95% CI 1.14–28.07, p=0.034) Conclusions: Topo II overexpression and MAP-tau overexpression in node positive breast cancers were not significant predictive factors for anthracyclin and taxane therapies. As several investigators reported, MAP-tau is associated endocrine therapy sensitivity in patients without chemotherapy, but higher MAP-tau in luminal type was a strong poor prognostic factor in patients who were given chemotherapy and hormonal therapy.

No significant financial relationships to disclose.

Hydrogen production by anaerobic microbial communities exposed to repeated heat treatments

Biological hydrogen production by anaerobic mixed communities was studied in laboratory-scale bioreactors using sucrose as the substrate. A bioreactor in which a fraction of the return sludge was exposed to repeated heat treatments performed better than a control bioreactor without repeated heat treatment of return sludge and produced a yield of 2.15 moles of hydrogen per mole of sucrose, with 50% hydrogen in the biogas. Terminal restriction fragment length polymorphism analysis showed that two different Clostridium groups (comprised of one or more species) were dominant during hydrogen production. The relative abundance of two other non-Clostridium groups increased during periods of decreased hydrogen production. The first group consisted of Bifidobacterium thermophilum, and the second group included one or more of Bacillus, Melissococcus, Spirochaeta, and Spiroplasma spp.

Anaerobic membrane bioreactor for treatment of synthetic municipal wastewater at ambient temperature

Non-woven fabric filter and poly-tetrafluoroethylene (PTFE) composite membrane were investigated to determine their applicability to treat low strength wastewater in an anaerobic membrane bioreactor (AMBR). Sludge cake resistance of the membrane was quantified using pure water flux of anaerobic sludge cake accumulated on the glass fiber filter of similar pore size. It is hypothesized that the formation of thin cake layer on the porous medium, e.g. non-woven and PTFE acts as a dynamic membrane. Thus, the capture of thin sludge cake inside the non-woven fabric matrix and accumulation on the PTFE membrane surface forms a membrane system equivalent to a commercial membrane system. The permeate quality was found to improve as the cake became more dense with filtration time. The PTFE composite membrane coated with thin PTFE film on the non-woven fabric filter enhanced the filtration performance by improving flux and minimizing the propensity of bio-fouling. The membrane flux was restored by back-flushing with permeate. The AMBR coupled with PTFE laminated membrane was operated continuously during the experiment at a cross flow velocity (CFV) of 0.1-0.2 m/sec and a transmembrane pressure (TMP) of 0.5-3 psi. Although about a month of acclimation was required to reach steady state, the effluent chemical oxygen demand (COD), volatile fatty acids (VFAs) as acetic acid, and suspended solids (SS) concentrations were below 30, 20 and 10 mg/L, respectively, during 90 days of operation with intermittent back washing. The lower operation TMP and CFV were subjected to less shear stress on the microbial community during continuous AMBR operation. In addition, thin sludge film accumulated on the membrane surface also acted as a biofilm bioreactor to remove additional COD in this study.

Adsorption of arsenic(V) by activated carbon prepared from oat hulls

The efficiency of self-manufactured activated carbon (AC) produced from oat hulls in adsorbing arsenic(V) was tested in a batch reactor. The results indicated that the adsorptive capacity of AC was affected by initial pH value, with adsorption capacity decreasing from 3.09 to 1.57 mg As g(-1) AC when the initial pH values increased from 5 to 8. A modified linear driving force model conjugated with a Langmuir isotherm was created to describe the study's kinetics. The test results show that rapid adsorption and slow adsorption exist simultaneously when AC is used to remove arsenic(V).