Vowels production by Cantonese-speaking children with cochlear implant

"A dissertation submitted in partial fulfillment of the requirements for the Bachelor of Science (Speech and Hearing Sciences), The University of Hong Kong, 30th June, 2010."Includes bibliographical references (p. 28-32).Thesis (B.Sc)--University of Hong Kong, 2010.This study investigated vowels production by Cantonese-speaking children with cochlear implant. Nineteen subjects with cochlear implant age ranged 2;05 to 6;01 years old were compared to 19 hearing children. All participants were required to produce 51 words, covering seven Cantonese monophthongs /a, i, E, O, u, y, J/ and ten Cantonese diphthongs /ui, Oi, ai, iu, Ey, Ai, ou, ei, au, Au/. The production accuracy was compared. Error patterns were investigated by phonological process and acoustic analysis. The production accuracy from cochlear implant subjects with hearing experience less than two years was significantly different than that of hearing children with similar hearing experience. A developmental and universal phonological acquisition process was observed. Developmental phonological rules were found in erroneous production. Articulatory complexity played an important role in vowels acquisition in CI groups. The result demonstrated a positive influence of cochlear implant on vowels production in Cantonese-speaking children.published_or_final_versionSpeech and Hearing SciencesBachelorBachelor of Science in Speech and Hearing Science

Predictive Associations Between Prenatal and Postnatal Risk Factors and Developmental and Temperamental Outcomes Among Infants in Foster Care

Infants detained for maltreatment present with a number of prenatal and perinatal risk factors, including prenatal exposure to substances, prematurity, low birth weight, birth complications, and prolonged hospital stay. These factors pose significant risk for a broad range of infant outcomes critically linked to later functioning, including cognitive, language, motor, socio-emotional, and temperamental development (Del Giudice, 2012; Singer et al., 2008). However, many infants exposed to prenatal risk also develop normatively, highlighting the need to better understand how the postnatal environment influences individual differences in response to prenatal risk. Importantly, prior to adoptive placement, infants placed in foster care often face unique stressors, including multiple foster placements and trial stays with birth families. Exposure to these pre-placement postnatal factors vary substantially across individuals, and they likely have unique and cumulative effects on developmental outcomes (Fisher et al., 2005; Waterman et al., 2013). Emerging evidence from normative samples suggests that prenatal and postnatal factors may interact to influence developmental outcomes, potentially through prenatal programming of infant responses to postnatal environments (Pluess & Belsky, 2011). These theoretical models have yet to be tested among infants in foster care, despite a need to better understand which prenatal and postnatal risk factors influence outcomes for these high-risk children. Thus, the present study aims to disentangle prenatal and postnatal risk factors to examine their unique and interactive associations with differentiated developmental outcomes (cognitive, language, motor, socioemotional) and early temperament among high-risk infants transitioning from foster care to adoption. Participants include 68 infants aged 0-28 months (race-ethnicity: 26% Hispanic, 14% African-American, 11% Caucasian, 1% Asian/Pacific Islander, 26% Mixed, 22% Unknown) referred for developmental assessment within two months of placement in adoptive homes. Prenatal/perinatal risk factors (prematurity, substance exposure, birth weight, birth complications, hospital stay) and postnatal risk factors (birth parent stay, age detained, number of placements, age at adoption) were coded from previous medical, DCFS, and court records. Infants were assessed using the Bayley Scales of Infant Development (BSID-III) to evaluate cognitive, motor (fine and gross), language (receptive and expressive), and socioemotional development. In addition, the primary adoptive parent completed the Infant/Toddler Temperament Questionnaire to measure temperament domains (e.g., sensitivity, reactivity, regularity). Preliminary correlations revealed that cognitive and motor development were most robustly associated with prenatal risk (i.e., prematurity, birth weight) and perinatal risk factors (i.e., birth complications, duration of hospital stay), whereas infant temperament domains were additionally linked to postnatal risk factors (i.e., birth parent placement, age detained, age of adoption, number of placements). Furthermore, differential associations between individual risk factors and outcomes were observed, suggesting there are likely unique risk factors predictive of different infant outcomes. Next, stepwise regressions will be employed to examine the independent, cumulative, and interactive associations between prenatal and postnatal risk factors on each developmental and temperamental outcome. Results will provide insight into the individual and cumulative effects of prenatal and preplacement postnatal risk factors for infants transitioning from foster care to adoption. Implications for key prevention and intervention targets among high-risk infants will be discussed

RNA-seq: impact of RNA degradation on transcript quantification

Background The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be corrected via data normalization, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples (for example, samples collected in the course of fieldwork) are at times the sole means of addressing specific questions. Results We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. Conclusions While standard normalizations failed to account for the effects of degradation, we found that by explicitly controlling for the effects of RIN using a linear model framework we can correct for the majority of these effects. We conclude that in instances in which RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.American Heart Association (Predoctoral Fellowship

What Should I Learn First: Introducing LectureBank for NLP Education and Prerequisite Chain Learning

Recent years have witnessed the rising popularity of Natural Language Processing (NLP) and related fields such as Artificial Intelligence (AI) and Machine Learning (ML). Many online courses and resources are available even for those without a strong background in the field. Often the student is curious about a specific topic but does not quite know where to begin studying. To answer the question of "what should one learn first," we apply an embedding-based method to learn prerequisite relations for course concepts in the domain of NLP. We introduce LectureBank, a dataset containing 1,352 English lecture files collected from university courses which are each classified according to an existing taxonomy as well as 208 manually-labeled prerequisite relation topics, which is publicly available. The dataset will be useful for educational purposes such as lecture preparation and organization as well as applications such as reading list generation. Additionally, we experiment with neural graph-based networks and non-neural classifiers to learn these prerequisite relations from our dataset

RNA-seq profiling of Fugacium kawagutii reveals strong responses in metabolic processes and symbiosis potential to deficiencies of iron and other trace metals

Abstract(#br)A healthy symbiotic relationship between corals and Symbiodiniaceae relies on suitable temperature and adequate nutrients including trace metals. Besides global warming, trace metal deficiency has been shown to cause coral bleaching, a phenomenon responsible for extensive coral reef degradation around the world. How trace metal deficiency impacts Symbiodiniaceae and coral symbiosis is poorly understood, however. In this study, we applied RNA-seq to investigate how Fugacium kawagutii responds to the deficiency of five trace metals (Fe 2+ , Zn 2+ , Cu 2+ , Mn 2+ , Ni 2+ ). We identified 685 to 2805 differentially expressed genes (DEGs) from these trace metal deficiency conditions, among which 372 were commonly regulated by all the five trace metals and were significantly enriched in energy metabolism (e.g. fatty acid synthesis). Furthermore, genes associated with extracellular matrix (ECM), cell surface structure and cell adhesion were impacted, suggesting that the ability of recognition and adhesion of F. kawagutii may be altered by trace metal deficiencies. In addition, among the five metals, Fe 2+ deficiency exhibited the strongest influence, with Fe-rich redox elements and many antioxidant synthesis genes being markedly down-regulated, indicative of adaptive reduction of Fe demand but a compromised ability to combat oxidative stress. Overall, deficiency of trace metals (especially Fe) seems to repress growth and ability of ROS scavenging, elevate energy metabolism and innate immunity, and alter cell adhesion capability, with implications in symbiosis disruption and coral bleaching

Prediction Accuracy of Serial Lung Ultrasound in COVID-19 Hospitalized Patients (Pred-Echovid Study)

The value of serial lung ultrasound (LUS) in patients with COVID-19 is not well defined. In this multicenter prospective observational study, we aimed to assess the prognostic accuracy of serial LUS in patients admitted to hospital due to COVID-19. The serial LUS protocol included two examinations (0–48 h and 72–96 h after admission) using a 10-zones sequence, and a 0 to 5 severity score. Primary combined endpoint was death or the need for invasive mechanical ventilation. Calibration (Hosmer–Lemeshow test and calibration curves), and discrimination power (area under the ROC curve) of both ultrasound exams (SCORE1 and 2), and their difference (DIFFERENTIAL-SCORE) were performed. A total of 469 patients (54.2% women, median age 60 years) were included. The primary endpoint occurred in 51 patients (10.9%). Probability risk tertiles of SCORE1 and SCORE2 (0–11 points, 12–24 points, and ≥25 points) obtained a high calibration. SCORE-2 showed a higher discrimination power than SCORE-1 (AUC 0.72 (0.58–0.85) vs. 0.61 (0.52–0.7)). The DIFFERENTIAL-SCORE showed a higher discrimination power than SCORE-1 and SCORE-2 (AUC 0.78 (0.66–0.9)). An algorithm for clinical decision-making is proposed. Serial lung ultrasound performing two examinations during the first days of hospitalization is an accurate strategy for predicting clinical deterioration of patients with COVID-19

The liver-enriched transcription factor CREB-H is a growth suppressor protein underexpressed in hepatocellular carcinoma

We have previously characterized transcription factor LZIP to be a growth suppressor targeted by hepatitis C virus oncoprotein. In search of proteins closely related to LZIP, we have identified a liver-enriched transcription factor CREB-H. LZIP and CREB-H represent a new subfamily of bZIP factors. CREB-H activates transcription by binding to cAMP responsive element, box B, and ATF6-binding element. Interestingly, CREB-H has a putative transmembrane (TM) domain and it localizes ambiently to the endoplasmic reticulum. Proteolytic cleavage that removes the TM domain leads to nuclear translocation and activation of CREB-H. CREB-H activates the promoter of hepatic gluconeogenic enzyme phosphoenolpyruvate carboxykinase. This activation can be further stimulated by cAMP and protein kinase A. CREB-H transcript is exclusively abundant in adult liver. In contrast, the expression of CREB-H mRNA is aberrantly reduced in hepatoma tissues and cells. The enforced expression of CREB-H suppresses the proliferation of cultured hepatoma cells. Taken together, our findings suggest that the liver-enriched bZIP transcription factor CREB-H is a growth suppressor that plays a role in hepatic physiology and pathology

Impact of regulatory variation across human iPSCs and differentiated cells.

Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility, and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell-type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell-type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell-type-specific chromatin accessibility

Genome-Wide Association Study of Hepatocellular Carcinoma in Southern Chinese Patients with Chronic Hepatitis B Virus Infection

One of the most relevant risk factors for hepatocellular carcinoma (HCC) development is chronic hepatitis B virus (HBV) infection, but only a fraction of chronic HBV carriers develop HCC, indicating that complex interactions among viral, environmental and genetic factors lead to HCC in HBV-infected patients. So far, host genetic factors have incompletely been characterized. Therefore, we performed a genome-wide association (GWA) study in a Southern Chinese cohort consisting of 95 HBV-infected HCC patients (cases) and 97 HBV-infected patients without HCC (controls) using the Illumina Human610-Quad BeadChips. The top single nucleotide polymorphisms (SNPs) were then validated in an independent cohort of 500 cases and 728 controls. 4 SNPs (rs12682266, rs7821974, rs2275959, rs1573266) at chromosome 8p12 showed consistent association in both the GWA and replication phases (ORcombined = 1.31–1.39; pcombined = 2.71×10−5–5.19×10−4; PARcombined = 26–31%). We found a 2.3-kb expressed sequence tag (EST) in the region using in-silico data mining and verified the existence of the full-length EST experimentally. The expression level of the EST was significantly reduced in human HCC tumors in comparison to the corresponding non-tumorous liver tissues (P<0.001). Results from sequence analysis and in-vitro protein translation study suggest that the transcript might function as a long non-coding RNA. In summary, our study suggests that variations at chromosome 8p12 may promote HCC in patients with HBV. Further functional studies of this region may help understand HBV-associated hepatocarcinogenesis