The Genotype and Phenotypes in Families (GPF) platform manages the large and complex data at SFARI.

The exploration of genotypic variants impacting phenotypes is a cornerstone in genetics research. The emergence of vast collections containing deeply genotyped and phenotyped families has made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale datasets requires specialized computational tools tailored to organize and analyze the extensive data. GPF (Genotypes and Phenotypes in Families) is an open-source platform ( https://github.com/iossifovlab/gpf ) that manages genotypes and phenotypes derived from collections of families. The GPF interface allows interactive exploration of genetic variants, enrichment analysis for de novo mutations, and phenotype/genotype association tools. In addition, GPF allows researchers to share their data securely with the broader scientific community. GPF is used to disseminate two large-scale family collection datasets (SSC, SPARK) for the study of autism funded by the SFARI foundation. However, GPF is versatile and can manage genotypic data from other small or large family collections. Our GPF-SFARI GPF instance ( https://gpf.sfari.org/ ) provides protected access to comprehensive genotypic and phenotypic data for the SSC and SPARK. In addition, GPF-SFARI provides public access to an extensive collection of de novo mutations identified in individuals with autism and related disorders and to gene-level statistics of the protected datasets characterizing the genes' roles in autism. Here, we highlight the primary features of GPF within the context of GPF-SFARI.

Pyrazole derivatives of pyridine and naphthyridine as proapoptotic agents in cervical and breast cancer cells.

Cancer is one of the leading causes of death worldwide. The increasing prevalence and resistance to chemotherapy is responsible for driving the search of novel molecules to combat this disease. In search of novel compounds with pro-apoptotic potential, pyrazolo-pyridine and pyrazolo-naphthyridine derivatives were investigated against cervical cancer (HeLa) and breast cancer (MCF-7) cells. The anti-proliferative activity was determined through the MTT assay. Potent compounds were then analyzed for their cytotoxic and apoptotic activity through a lactate dehydrogenase assay and fluorescence microscopy after propidium iodide and DAPI staining. Flow cytometry was used to determine cell cycle arrest in treated cells and pro-apoptotic effect was verified through measurement of mitochondrial membrane potential and activation of caspases. Compounds 5j and 5k were found to be most active against HeLa and MCF-7 cells, respectively. G0/G1 cell cycle arrest was observed in treated cancer cells. Morphological features of apoptosis were also confirmed, and an increased oxidative stress indicated the involvement of reactive oxygen species in apoptosis. The compound-DNA interaction studies demonstrated an intercalative mode of binding and the comet assay confirmed the DNA damaging effects. Finally, potent compounds demonstrated a decrease in mitochondrial membrane potential and increased levels of activated caspase-9 and -3/7 confirmed the induction of apoptosis in treated HeLa and MCF-7 cells. The present work concludes that the active compounds 5j and 5k may be used as lead candidates for the development of lead drug molecules against cervical and breast cancer.

Gastroschisis Outcomes: Presence of Histologic Chorioamnionitis and the Impact on Time to Full Enteral Feeds and Length of Hospital Stay.

OBJECTIVE: Despite improvements in our ability for early diagnosis and providing supportive care for infants with gastroschisis, it continues to be associated with long length of stay and morbidity. Intestinal dysfunction secondary to chronic inflammatory insult to exposed bowel is well known; however, little research has been done on the impact of acute inflammation in the perinatal period on intestinal function. This study's aim was to investigate the impact of acute chorioamnionitis on the time to achieve full enteral feeds and length of hospital stay. STUDY DESIGN: Retrospective chart review of 60 mothers and their infants born with gastroschisis at a Level IV NICU from November 2011 to June 2020 was performed. Infants were divided into two groups based on the presence of histologic chorioamnionitis, and outcomes were compared. The primary outcome was delayed full enteral feeds (full enteral feeds after 28 days of life). The secondary outcomes were differences in their time to achieve full enteral feeds and time to hospital discharge, and prolonged length of hospital stay (discharge after 30 days of life). Univariate and multivariate logistic regression analyses were performed to assess the association between the dependent and the predictor variables. RESULT: Of the 60 infants enrolled, 23 (38%) had evidence of histologic chorioamnionitis. The median gestational age was 37 weeks. Fifty-four (90%) infants achieved full enteral feeds, with a median time of 24 days. Median length of hospital stay was 31 days. The presence of histologic chorioamnionitis was not associated with delayed full enteral feeds (odds ratio [OR] = 0.79; 95% confidence interval [CI] = 0.14-4.23; p = 0.80) or prolonged length of hospital stay (OR = 0.45; 95% CI = 0.1-0.23; p = 0.32) in the adjusted analysis. CONCLUSION: Acute placental inflammation during the perinatal period does not impact the infant's time to achieve full feeds or prolong their hospital stay. Larger studies are needed to confirm these findings. KEY POINTS: · Chronic inflammatory injury to exposed bowel in utero is well known in fetuses with gastroschisis.. · Acute inflammatory injury during perinatal period may impact enteral feeding outcomes.. · No impact of acute placental inflammation on time to full enteral feeds..

Intestinal failure-associated liver disease in the neonatal ICU: what we know and where we're going.

PURPOSE OF REVIEW: Parenteral nutrition is an integral part of the care of infants in the neonatal ICU. However, prolonged use of parenteral nutrition can be associated with adverse outcomes, most notably parenteral nutrition-associated liver disease, now known as intestinal failure-associated liver disease (IFALD). This review highlights pertinent developments in the epidemiology of IFALD as it pertains to neonates and showcases recent advances in the pathophysiology, treatment, and outcomes of neonates with IFALD. RECENT FINDINGS: The role of intravenous lipid emulsions in the pathogenesis, prevention, and treatment of IFALD remains a target for investigative studies. Recent data continues to support the use of fish-oil based intravenous lipids, but its use is limited due to concerns for essential fatty acid deficiency. Use of soy-based lipids and mixed lipids is not wrought with such concerns as these are often used at greater doses but their use is limited due to higher proinflammatory fatty acid content, increased phytosterols and decreased antioxidants, risk factors for the development of IFALD. SUMMARY: Hepatic complications may limit the use of parenteral nutrition in the neonatal ICU. However, the pathophysiology of IFALD is continuing to be further elucidated and novel targets are being developed for the treatment of IFALD. As noninvasive disease monitoring strategies continue to be developed, early enteral nutrition ameliorates the risk of IFALD and should be considered when possible.

Percent mother's own milk feedings for preterm neonates predicts discharge feeding outcomes.

INTRODUCTION: No studies have determined if there is a threshold whereby use of mother's own milk (MOM) during hospitalization predicts exclusive MOM feeding at discharge. METHODS: Among 113 very low birthweight neonates, the ratio of MOM to enteral feeds was measured in the first 14 days, 28 days, and overall hospital stay. The primary outcome was exclusive MOM feeding at discharge. RESULTS: For every 1% increase in MOM consumption in the first 14 and 28 days, the odds of being discharge home on an exclusive MOM diet increased nearly 7-fold (OR 7.01, 95% CI: 2.09-23.50) and 17-fold (OR 17.46, 95% CI 4.67-63.31), respectively. A threshold of >50%, >83%, and >85% MOM consumption compared to overall enteral feeds in the first 14 days, 28 days, and throughout hospitalization, respectively, is recommended. CONCLUSIONS: Promotion of MOM consumption in the first 2-4 weeks is of paramount importance, with negligible impact of increasing MOM consumption after 28 days.

Optimizing the Use of Human Milk Cream Supplement in Very Preterm Infants: Growth and Cost Outcomes.

BACKGROUND: An exclusive human milk-based diet has been shown to decrease necrotizing enterocolitis and improve outcomes for infants ≤1250 g birth weight. Studies have shown that infants who received an exclusive human milk diet with a donor-human milk-derived cream supplement (cream) had improved weight and length velocity when the cream was added to mother's own milk or donor-human milk when energy was <20 kcal/oz using a human milk analyzer. Our objective was to compare growth and cost outcomes of infants ≤1250 g birth weight fed with an exclusive human milk diet, with and without human milk cream, without the use of a human milk analyzer. METHODS: Two cohorts of human milk-fed premature infants were compared from birth to 34 weeks postmenstrual age. Group 1 (2010-2011) received a donor-human milk fortifier, whereas Group 2 (2015-2016) received donor-human milk fortifier plus the commercial cream supplement, if weight gain was <15 g/kg/d. RESULTS: There was no difference in growth between the 2 groups for weight (P = 0.32) or head circumference (P = 0.90). Length velocity was greater for Group 1 (P = 0.03). The mean dose of donor-human milk fortifier was lower in Group 2 (P < 0.001). Group 2 saved an average of $2318 per patient on the cost of human milk products (P < 0.01). CONCLUSIONS: Infants receiving a human milk diet with cream supplementation for growth faltering achieve appropriate growth in a cost-effective feeding strategy.

Improved feeding tolerance and growth are linked to increased gut microbial community diversity in very-low-birth-weight infants fed mother's own milk compared with donor breast milk.

BACKGROUND: Mother's own milk (MOM) is protective against gut microbiota alterations associated with necrotizing enterocolitis (NEC) and feeding intolerance among preterm infants. It is unclear whether this benefit is preserved with donor milk (DM) feeding. OBJECTIVE: We aimed to compare microbiota development, growth, and feeding tolerance in very-low-birth-weight (VLBW) infants fed an exclusively human milk diet of primarily MOM or DM. METHODS: One hundred and twenty-five VLBW infants born at Texas Children's Hospital were enrolled and grouped into cohorts based on percentage of MOM and DM in enteral feeds. Feeds were fortified with DM-derived fortifier per unit protocol. Weekly stool samples were collected for 6 wk for microbiota analysis [16S ribosomal RNA (rRNA) sequencing]. A research nurse obtained weekly anthropometrics. Clinical outcomes were compared via Wilcoxon's rank-sum test and Fisher's exact test, as well as multivariate analysis. RESULTS: The DM cohort (n = 43) received on average 14% mothers' milk compared with 91% for the MOM cohort (n = 74). Diversity of gut microbiota across all time points (n = 546) combined was increased in MOM infants (P < 0.001). By 4 and 6 wk of life, microbiota in MOM infants contained increased abundance of Bifidobacterium (P = 0.02) and Bacteroides (P = 0.04), whereas DM-fed infants had increased abundance of Staphylococcus (P = 0.02). MOM-fed infants experienced a 60% reduction in feeding intolerance (P = 0.03 by multivariate analysis) compared with DM-fed infants. MOM-fed infants had greater weight gain than DM-fed infants. CONCLUSIONS: Compared with DM-fed infants, MOM-fed infants have increased gut microbial community diversity at the phylum and genus levels by 4 and 6 wk of life, as well as better feeding tolerance. MOM-fed infants had superior growth. The incidence of NEC and other gastrointestinal morbidity is low among VLBW infants fed an exclusively human milk diet including DM-derived fortifier. This trial was registered at clinicaltrials.gov as NCT02573779.

Optoacoustic Imaging Detects Hormone-Related Physiological Changes of Breast Parenchyma.

PURPOSE: Optoacoustic imaging with ultrasound (OPUS) can assess in-vivo perfusion/oxygenation through surrogate measures of oxy, deoxy and total hemoglobin content in tissues. The primary aim of our study was to evaluate the ability of OPUS to detect physiological changes in the breast during the menstrual cycle and to determine qualitative/quantitative metrics of normal parenchymal tissue in pre-/post-menopausal women. The secondary aim was to assess the technique's repeatability. MATERIALS AND METHODS: We performed a prospective ethically approved study in volunteers using OPUS (700, 800 and 850 nm wavelengths) in the proliferative/follicular and secretory phase of the menstrual cycle. Regions of interest (ROIs) were drawn on the most superficial region of fibroglandular tissue and same-day intra-observer repeatability was assessed. We used t-tests to interrogate differences in the OPUS measurements due to hormonal changes and interclass correlation coefficients/Bland-Altman plots to evaluate the repeatability of mean ROI signal intensities. RESULTS: 22 pre-menopausal and 8 post-menopausal volunteers were recruited. 21 participants underwent repeatability examinations. OPUS intensity values were significantly higher (p < 0.0001) at all excitation wavelengths in the secretory compared to the proliferative/follicular phase. Post-menopausal volunteers showed similar optoacoustic values to the proliferative/follicular phase of pre-menopausal volunteers. The repeatability of the technique was comparable to other handheld ultrasound modalities. CONCLUSION: OPUS detects changes in perfusion/vascularity related to the menstrual cycle and menopausal status of breast parenchyma.

Multispectral optoacoustic tomography of the human breast: characterisation of healthy tissue and malignant lesions using a hybrid ultrasound-optoacoustic approach.

BACKGROUND AND AIM: Multispectral optoacoustic tomography (MSOT) represents a new in vivo imaging technique with high resolution (~250 µm) and tissue penetration (>1 cm) using the photoacoustic effect. While ultrasound contains anatomical information for lesion detection, MSOT provides functional information based on intrinsic tissue chromophores. We aimed to evaluate the feasibility of combined ultrasound/MSOT imaging of breast cancer in patients compared to healthy volunteers. METHODS: Imaging was performed using a handheld MSOT system for clinical use in healthy volunteers (n = 6) and representative patients with histologically confirmed invasive breast carcinoma (n = 5) and ductal carcinoma in situ (DCIS, n = 2). MSOT values for haemoglobin and oxygen saturation were assessed at 0.5, 1.0 and 1.5 cm depth and selected wavelengths between 700 and 850 nm. RESULTS: Reproducible signals were obtained in all wavelengths with consistent MSOT signals in superficial tissue in breasts of healthy individuals. In contrast, we found increased signals for haemoglobin in invasive carcinoma, suggesting a higher perfusion of the tumour and tumour environment. For DCIS, MSOT values showed only little variation compared to healthy tissue. CONCLUSIONS: This preliminary MSOT breast imaging study provided stable, reproducible data on tissue composition and physiological properties, potentially enabling differentiation of solid malignant and healthy tissue. KEY POINTS: • A handheld MSOT probe enables real-time molecular imaging of the breast. • MSOT of healthy controls provides a reproducible reference for pathology identification. • MSOT parameters allows for differentiation of invasive carcinoma and healthy tissue.

Noninvasive real-time characterization of non-melanoma skin cancers with handheld optoacoustic probes.

Currently, imaging technologies that enable dermsurgeons to visualize non-melanoma skin cancers (NMSC) in vivo preoperatively are lacking, resulting in excessive or incomplete removal. Multispectral optoacoustic tomography (MSOT) is a volumetric imaging tool to differentiate tissue chromophores and exogenous contrast agents, based on differences in their spectral signatures and used for high-resolution imaging of functional and molecular contrast at centimeter scale depth. We performed MSOT imaging with two- and three-dimensional handheld scanners on 21 Asian patients with NMSC. The tumors and their oxygenation parameters could be distinguished from normal skin endogenously. The lesion dimensions and depths were extracted from the spectral melanin component with three-dimensional spatial resolution up to 80 µm. The intraclass correlation coefficient correlating tumor dimension measurements between MSOT and ex vivo histology of excised tumors, showed good correlation. Real-time 3D imaging was found to provide information on lesion morphology and its underlying neovasculature, indicators of the tumor's aggressiveness.

Spiral volumetric optoacoustic tomography visualizes multi-scale dynamics in mice.

Imaging dynamics at different temporal and spatial scales is essential for understanding the biological complexity of living organisms, disease state and progression. Optoacoustic imaging has been shown to offer exclusive applicability across multiple scales with excellent optical contrast and high resolution in deep-tissue observations. Yet, efficient visualization of multi-scale dynamics remained difficult with state-of-the-art systems due to inefficient trade-offs between image acquisition time and effective field of view. Herein, we introduce the spiral volumetric optoacoustic tomography technique that provides spectrally enriched high-resolution contrast across multiple spatiotemporal scales. In vivo experiments in mice demonstrate a wide range of dynamic imaging capabilities, from three-dimensional high-frame-rate visualization of moving organs and contrast agent kinetics in selected areas to whole-body longitudinal studies with unprecedented image quality. The newly introduced paradigm shift in imaging of multi-scale dynamics adds to the multifarious advantages provided by the optoacoustic technology for structural, functional and molecular imaging.

Sphingomyelin Synthase 1 Is Essential for Male Fertility in Mice.

Sphingolipids and the derived gangliosides have critical functions in spermatogenesis, thus mutations in genes involved in sphingolipid biogenesis are often associated with male infertility. We have generated a transgenic mouse line carrying an insertion in the sphingomyelin synthase gene Sms1, the enzyme which generates sphingomyelin species in the Golgi apparatus. We describe the spermatogenesis defect of Sms1-/- mice, which is characterized by sloughing of spermatocytes and spermatids, causing progressive infertility of male homozygotes. Lipid profiling revealed a reduction in several long chain unsaturated phosphatidylcholins, lysophosphatidylcholins and sphingolipids in the testes of mutants. Multi-Spectral Optoacoustic Tomography indicated blood-testis barrier dysfunction. A supplementary diet of the essential omega-3 docosahexaenoic acid and eicosapentaenoic acid diminished germ cell sloughing from the seminiferous epithelium and restored spermatogenesis and fertility in 50% of previously infertile mutants. Our findings indicate that SMS1 has a wider than anticipated role in testis polyunsaturated fatty acid homeostasis and for male fertility.