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1 Table S1. Characteristics of the Included Fetuses and Neonates in Whom the Vertebral Pattern Could Be 1 Assessed and the Exclu

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1 Table S1. Characteristics of the included fetuses and neonates in whom the vertebral pattern could be 2 assessed and the excluded fetuses and neonates in whom the vertebral pattern could not be assessed. Vertebral pattern assessable Vertebral pattern not assessable p-value (n=374) (n=71) Gestational age at birth 22.7 (11.9-41.3) 21.4 (12.0-40.4) 0.06 (weeks) Presence congenital anomaly 256 (68.4) 49 (69.0) 0.36 No congenital anomaly 78 (20.9) 11 (15.5) Unknown 40 (10.7) 11 (15.5) Type congenital anomaly 0.24 Craniofacial 10 (3.9) 0 Nervous system 25 (9.8) 3 (5.7) Bronchopulmonary 4 (1.6) 1 (1.9) Cardiovascular 27 (10.6) 5 (9.4) Ventral body wall 3 (1.2) 1 (1.9) Digestive system 3 (1.2) 0 Urogenital 12 (4.7) 6 (11.3) Limb defects 9 (3.5) 1 (1.9) Skeletal 4 (1.6) 4 (7.5) Other 13 (5.1) 3 (5.7) Multiple 146 (57.3) 29 (54.7) Pregnancy outcome 0.79 Miscarriages and stillbirths 128 (34.2) 25 (35.2) Live births 58 (15.5) 13 (18.3) Termination of pregnancy 188 (50.3) 33 (46.5) 3 4 Data are presented as number (percentage) or median and (range). 5 6 7 8 9 10 11 12 13 1 14 Table S2. Gestational age at birth, age at death, presence of congenital abnormalities and cause of death of the included live births. GA at birth Age at death Cervical Congenital abnormalities Cause of death (weeks) (days) rib(s) 22.3 0 No. None. Immature delivery. 22.7 0 Yes. Transposition of the great arteries, Immature delivery. dysmorphic facial features. 23.6 0 No. None. Immature delivery. 23.9 0 No. Unknown (no autopsy, no advanced Immature delivery. anomaly scan). 24.0 0 No. Right isomerism left lung. Unsuccessful resuscitation. 24.4 0 No. Colpocephaly. Palliative care because of extremely preterm birth. 24.0 7 No. Mild retrognathia. NEC and sepsis. 24.6 7 Yes. None. Sepsis and septic thrombus and emboli in multiple organs, leading to multiorgan dysfunction. NEC. 24.6 12 No. Dysmorphic facial features. Sepsis leading to cardiorespiratory failure. 24.7 5 No. Unknown (no autopsy or advanced Bowel perforation, IRDS, discontinuation of anomaly scan). treatment due to bowel ischemia. 24.9 2 No. None. Discontinuation of treatment because of cardiorespiratory failure and refractory lactic acidosis, possibly due to NEC. 24.9 30 No. Ascites. Circulatory failure, likely due to NEC. 25.0 0 No. Bicuspid aortic valve. Pulmonary hypoplasia (anhydramnios from GA 17 weeks) 25.0 25 No. No malformations. Respiratory and hemodynamic insufficiency. Sepsis. Right atrial thrombus. 25.1 15 No. Hypertrophic left cardiac ventricle. Sepsis, circulatory insufficiency, hypovolemic shock eci. 26.1 0 Yes. Unknown (no autopsy, no advanced Emergency caesarian section because of placental anomaly scan). abruption. Unsuccessful resuscitation. 26.4 33 No. None. Cardiorespiratory insufficiency and sepsis (NEC). 27.4 0 Yes. Dysmorphic facial features, lateral PPROM, tachycardia and suspected intrauterine deviation foot, atrial septal defect. infection, for which emergency caesarian section. 2 Cardiorespiratory failure, unsuccessful resuscitation at birth. 27.4 1 No. Hydrops, periventricular Refractory cardiorespiratory failure in hydropic leukomalacia, left isomerism right neonates with anemia and thrombocytopenia. lung, dysmorphic facial features. 27.7 0 No. None. Cardiorespiratory failure due to septic shock (Klebsiella pneumoniae and NEC). 27.9 1 No. Omphalocele, dysmorphic facial Circulatory failure due to refractory hypotension. features, macroglossia, enlarged kidneys, open duct Botalli, periventricular leukomalacia. Beckwith Wiedemann syndrome. 27.9 31 No. Ambiguous genital, macroglossia, Cardiorespiratory failure due to NEC. short limbs. 28 5 No. None. Discontinuation of treatment because of severe asphyxia, pulmonary hypertension and immature lungs. 29.0 0 Yes. No autopsy. Advanced anomaly scan Palliative care. and babygram suggestive of lethal skeletal dysplasia. 29.3 0 No. Omphalocele, hypertelorism, left- Palliative care because of multiple congenital sided diaphragmatic hernia, anomalies hypoplastic lungs, ascites, hydronephrosis, dilated bladder. 29.7 2 No. Hydrops, neuronal heterotopia. Discontinuation of treatment because of poor prognosis due to extensive cystic periventricular leukomalacia. 30.0 0 Yes. Pulmonary hypoplasia, Respiratory failure. polymicrogyria, glioneuronal heterotopia, skin lesions, ascites, hepatosplenomegaly, cholestasis, enlarged small bowel loops. 3 30.7 0 No. Lissencephaly, hypoplastic corpus Unsuccessful resuscitation after emergency callosum, bicuspid aortic valve, caesarean section. pleural effusion. 30.7 0 No. Hydrops. Severe lung hypoplasia. Respiratory insufficiency. 31.0 0 No. Lissencephaly, neuronal heterotopia, Discontinuation of treatment because of multiple ventriculomegaly, coarctation of the abnormalities. aorta, persistent left superior vena cava, ureteropelvic junction, dysmorphic facial features. 31.0 1 No. Hydrops, hypertrophic dilated Cardiac failure. cardiomyopathy 32.0 6 No. Hydrops, transient Discontinuation of treatment because of myeloproliferative disorder, trisomy pulmonary hypertension not responsive to therapy. 21. 32.1 0 Yes. Pleural effusion, dysplastic aortic Cardiorespiratory failure. and pulmonary valves, ductus venosus agenesis, dysmorphic facial features, Noonan syndrome. 32.1 0 No. Suspicion of urethral valves. Placental abruption, emergency caesarian section. Unsuccessful resuscitation. 32.3 0 No. No autopsy. Advanced anomaly scan Palliative care because of multiple abnormalities. and prenatal MRI: right diaphragmatic hernia, Dandy Walker malformation, ventriculomegaly, persistent left superior vena cava. 32.3 1 No. Hydrops. IRDS. 32.7 0 Yes. Macrosomia. Uterine rupture. Unsuccessful resuscitation. 33.6 22 No. Pontocerebellar dysplasia. Respiratory failure due to central apnea. 33.7 9 No. Hydrops. Discontinuation of treatment because of respiratory insufficiency and brain injury following asphyxia. 34.0 0 Yes. Cystic kidney dysplasia, lung Pulmonary hypoplasia hypoplasia (anhydramnios), cardiomegaly, ascites, sandal gap. 4 34.0 0 Yes. No autopsy. Babygram showed Palliative treatment. abnormalities suggestive of Jeune syndrome. 34.0 0 No. Omphalocele, bladder exstrophy, Palliative care because of multiple abnormalities. anorectal malformation, meningomyelocele, ventricular septal defect, hypoplastic lungs. 34.1 12 No. Hydrops, dysplastic kidneys, pyloric Discontinuation of treatment because of multiple stenosis, uterus bicornis, abnormalities. dysmorphic facial features, rocker bottom feet. 34.6 0 Yes. Laryngeal atresia, esophageal Unsuccessful resuscitation due to unexpected high atresia, truncus arteriosus. airway obstruction. 34.6 5 No. Hydrops, ventricular septal defect. Sepsis and multiorgan dysfunction. 34.7 0 No. No autopsy. Advanced anomaly Palliative care because of infaust prognosis. scan: bilateral multicystic dysplastic kidneys and anhydramnios. 35.1 0 Yes. Anorectal malformation, bilateral Respiratory insufficiency due to pulmonary multicystic dysplastic kidneys, hypoplasia. tracheoesophageal fistula. 36.3 4 No. Hydrocephalus, cerebellar dentate Discontinuation of treatment because of dysplasia, neuronal heterotopia. hydrocephalus, severe pulmonary hypertension and convulsions. 36.7 4 Yes. Hepatic haemangioendothelioma, High-output failure. cardiomegaly. 37.3 0 No. Coarctation of the aorta, atrial Respiratory insufficiency. septal defect, mild pulmonary hypoplasia. 37.7 0 Yes. None. Multiorgan dysfunction after perinatal asphyxia. 38.6 0 No. Abdominal neuroblastoma, multiple Hypovolemic shock due to hemorrhage from liver metastases, perimembranous abdominal tumor. ventricular septal defect. 38.9 0 Yes. Omphalocele, left diaphragmatic Palliative care because of multiple abnormalities. hernia, persistent left superior vena 5 cava, absent processus xiphoideus, facial dysmorphic features, reduction defect left hand. 39.1 0 No. Ebstein’s anomaly Cardiorespiratory failure. 40.3 70 No. None. Sudden infant death syndrome. 40.9 1 Yes. None. Subgaleal hemorrhage leading to cardiorespiratory failure. 41.1 1 Yes. Small ventricular septal defect. Sudden and unexpected postnatal collapse. 41.3 25 Yes. Club feet, neuronal heterotopia. Discontinuation of treatment due to poor prognosis. Neurological abnormalities (facial nerve paresis, bilateral vocal cord paresis, bilateral hearing loss). Suggestive of variation of Moebius syndrome. 15 eci = e causa ignota, GA = Gestational age, IRDS = Infant respiratory distress syndrome, NEC = Necrotizing enterocolitis, PPROM = preterm 16 premature rupture of membranes 17 18 19 20 21 22 23 24 25 26 6 27 7 28 Table S3. The prevalence of cervical ribs and different vertebral patterns in fetuses and neonates with 29 pathogenic chromosomal abnormalities, likely deleterious CNVs and variants of uncertain significance 30 (N=374). One patient can have multiple CNVs, but is included only once in the most severe category. 31 Classification result Number of fetuses and Cervical ribs Vertebral pattern (number) chromosomal/ neonates (% within subgroup) CNV analysis (% of total) Pathogenic Aneuploidies 15 (4.0) 10 (66.7) Trisomy 21 7 (1.9) 4 (57.1) R (2), TL (1), CT (2), CT_TL (2) Trisomy 13 3 (0.8) 1 (33.3) R (1), CT_TL_LS (2) Trisomy 18 2 (0.5) 2 (100) CT_TL (1), CT_TL_LS (1) Monosomy X 2 (0.5) 2 (100) CT (1), CT_LS (1) 47, XYY 1 (0.3) 1 (100) CT (1) Triploidy 1 (0.3) 0 TL (1) Pathogenic CNVs 12 (3.2) 6 (50.0%) R (3) TL (3) CT (2) CT_LS (1) CT_TL (3) (Likely) deleterious Large rare CNVs 7/374 (1.9) 4 (57.1) R (2) LS (1) CT (1) CT_TL (2) CT_TL_LS (1) VOUS Rare small CNVs 37/374 (9.9) 23 (62.2)
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  • Sean Raspet – Molecules

    Sean Raspet – Molecules

    1. Commercial name: Fructaplex© IUPAC Name: 2-(3,3-dimethylcyclohexyl)-2,5,5-trimethyl-1,3-dioxane SMILES: CC1(C)CCCC(C1)C2(C)OCC(C)(C)CO2 Molecular weight: 240.39 g/mol Volume (cubic Angstroems): 258.88 Atoms number (non-hydrogen): 17 miLogP: 4.43 Structure: Biological Properties: Predicted Druglikenessi: GPCR ligand -0.23 Ion channel modulator -0.03 Kinase inhibitor -0.6 Nuclear receptor ligand 0.15 Protease inhibitor -0.28 Enzyme inhibitor 0.15 Commercial name: Fructaplex© IUPAC Name: 2-(3,3-dimethylcyclohexyl)-2,5,5-trimethyl-1,3-dioxane SMILES: CC1(C)CCCC(C1)C2(C)OCC(C)(C)CO2 Predicted Olfactory Receptor Activityii: OR2L13 83.715% OR1G1 82.761% OR10J5 80.569% OR2W1 78.180% OR7A2 77.696% 2. Commercial name: Sylvoxime© IUPAC Name: N-[4-(1-ethoxyethenyl)-3,3,5,5tetramethylcyclohexylidene]hydroxylamine SMILES: CCOC(=C)C1C(C)(C)CC(CC1(C)C)=NO Molecular weight: 239.36 Volume (cubic Angstroems): 252.83 Atoms number (non-hydrogen): 17 miLogP: 4.33 Structure: Biological Properties: Predicted Druglikeness: GPCR ligand -0.6 Ion channel modulator -0.41 Kinase inhibitor -0.93 Nuclear receptor ligand -0.17 Protease inhibitor -0.39 Enzyme inhibitor 0.01 Commercial name: Sylvoxime© IUPAC Name: N-[4-(1-ethoxyethenyl)-3,3,5,5tetramethylcyclohexylidene]hydroxylamine SMILES: CCOC(=C)C1C(C)(C)CC(CC1(C)C)=NO Predicted Olfactory Receptor Activity: OR52D1 71.900% OR1G1 70.394% 0R52I2 70.392% OR52I1 70.390% OR2Y1 70.378% 3. Commercial name: Hyperflor© IUPAC Name: 2-benzyl-1,3-dioxan-5-one SMILES: O=C1COC(CC2=CC=CC=C2)OC1 Molecular weight: 192.21 g/mol Volume
  • Kenneth Martin Rosenberg Email: Kenneth.Rosenberg@Som.Umaryland.Edu, Kenny.M.Rosenberg@Gmail.Com 660 West Redwood Street, Howard Hall Room 332D, Baltimore, MD, 21201

    Kenneth Martin Rosenberg Email: [email protected], [email protected] 660 West Redwood Street, Howard Hall Room 332D, Baltimore, MD, 21201

    The impact of the non-immune chemiome on T cell activation Item Type dissertation Authors Rosenberg, Kenneth Publication Date 2020 Abstract T cells are critical organizers of the immune response and rigid control over their activation is necessary for balancing host defense and immunopathology. It takes 3 signals provided by dendritic cells (DC) to fully activate a T cell response – T ce... Keywords signaling; T cell; T-Lymphocytes--immunology Download date 02/10/2021 13:41:58 Link to Item http://hdl.handle.net/10713/14477 Kenneth Martin Rosenberg Email: [email protected], [email protected] 660 West Redwood Street, Howard Hall Room 332D, Baltimore, MD, 21201 EDUCATION MD, University of Maryland, Baltimore, MD Expected May 2022 PhD, University of Maryland, Baltimore, MD December 2020 Graduate Program: Molecular Microbiology and Immunology (MMI) BS, University of Maryland, College Park, MD May 2013 Major: Bioengineering, cum laude University Honors Citation, Gemstone Citation RESEARCH EXPERIENCE UMSOM Microbiology and Immunology Baltimore, MD July 2016-present PhD Candidate Principal Investigator: Dr. Nevil Singh Thesis: The impact of the non-immune chemiome on T cell activation Examined environmental stimuli from classically “non-immune” sources – growth factors, hormones, neurotransmitters, etc. – act to modulate T cell signaling pathways and the functional effects of activating encounters with dendritic cells. UMSOM Anatomy and Neurobiology Baltimore, MD May-August 2015 Rotating student Principal Investigator: Dr. Asaf Keller Studied the role of descending modulation pathways on affective pain transmission. Performed tract- tracing experiments using targeted injection of Cholera toxin subunit B into the lateral parabrachial nucleus and ventrolateral periaqueductal gray of anesthetized transgenic mice.
  • 1 1 2 3 Cell Type-Specific Transcriptomics of Hypothalamic

    1 1 2 3 Cell Type-Specific Transcriptomics of Hypothalamic

    1 2 3 4 Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to 5 weight-loss 6 7 Fredrick E. Henry1,†, Ken Sugino1,†, Adam Tozer2, Tiago Branco2, Scott M. Sternson1,* 8 9 1Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 10 20147, USA. 11 2Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, 12 Cambridge CB2 0QH, UK 13 14 †Co-first author 15 *Correspondence to: [email protected] 16 Phone: 571-209-4103 17 18 Authors have no competing interests 19 1 20 Abstract 21 Molecular and cellular processes in neurons are critical for sensing and responding to energy 22 deficit states, such as during weight-loss. AGRP neurons are a key hypothalamic population 23 that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific 24 transcriptomics can be used to identify pathways that counteract weight-loss, and here we 25 report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived 26 young adult mice. For comparison, we also analyzed POMC neurons, an intermingled 27 population that suppresses appetite and body weight. We find that AGRP neurons are 28 considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell 29 type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion 30 channels, neuropeptides, and receptors. Combined with methods to validate and manipulate 31 these pathways, this resource greatly expands molecular insight into neuronal regulation of 32 body weight, and may be useful for devising therapeutic strategies for obesity and eating 33 disorders.