Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity.

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Perceptual Speech Outcomes After Early Primary Palatal Repair in Ugandan Patients With Cleft Palate.

OBJECTIVE: To provide speech outcomes of English-speaking Ugandan patients with a cleft palate with or without cleft lip (CP±L). DESIGN: Prospective case-control study. SETTING: Referral hospital for patients with cleft lip and palate in Uganda. PARTICIPANTS: Twenty-four English-speaking Ugandan children with a CP±L (15 boys, 9 girls, mean 8.4 years) who received palatal closure prior to 6 months of age and an age- and gender-matched control group of Ugandan children without cleft palate. INTERVENTIONS: Comparison of speech outcomes of the patient and control group. MAIN OUTCOME MEASURES: Perceptual speech outcomes including articulation, resonance, speech understandability and acceptability, and velopharyngeal composite score (VPC-sum). Information regarding speech therapy, fistula rate, and secondary surgery. RESULTS: Normal speech understandability was observed in 42% of the patients, and 38% were judged with normal speech acceptability. Only 16% showed compensatory articulation. Acceptable resonance was found in 71%, and 75% of the patients were judged perceptually to present with competent velopharyngeal function based on the VPC-sum. Additional speech intervention was recommended in 25% of the patients. Statistically significant differences for all these variables were still observed with the control children (P < .05). CONCLUSIONS: Overall, acceptable speech outcomes were found after early primary palatal closure. Comparable or even better results were found in comparison with international benchmarks, especially regarding the presence of compensatory articulation. Whether this approach is transferable to Western countries is the subject for further research.

Endurance training remodels skeletal muscle phospholipid composition and increases intrinsic mitochondrial respiration in men with Type 2 diabetes.

The effects of exercise training on the skeletal muscle (SKM) lipidome and mitochondrial function have not been thoroughly explored in individuals with Type 2 diabetes (T2D). We hypothesize that 10 wk of supervised endurance training improves SKM mitochondrial function and insulin sensitivity that are related to alterations in lipid signatures within SKM of T2D (males n = 8). We employed integrated multi-omics data analyses including ex vivo lipidomics (MS/MS-shotgun) and transcriptomics (RNA-Seq). From biopsies of SKM, tissue and primary myotubes mitochondrial respiration were quantified by high-resolution respirometry. We also performed hyperinsulinemic-euglycemic clamps and blood draws before and after the training. The lipidomics analysis revealed that endurance training (>95% compliance) increased monolysocardiolipin by 68.2% (P ≤ 0.03), a putative marker of mitochondrial remodeling, and reduced total sphingomyelin by 44.8% (P ≤ 0.05) and phosphatidylserine by 39.7% (P ≤ 0.04) and tended to reduce ceramide lipid content by 19.8%. Endurance training also improved intrinsic mitochondrial respiration in SKM of T2D without alterations in mitochondrial DNA copy number or cardiolipin content. RNA-Seq revealed 71 transcripts in SKM of T2D that were differentially regulated. Insulin sensitivity was unaffected, and HbA1c levels moderately increased by 7.3% despite an improvement in cardiorespiratory fitness (V̇o2peak) following the training intervention. In summary, endurance training improves intrinsic and cell-autonomous SKM mitochondrial function and modifies lipid composition in men with T2D independently of alterations in insulin sensitivity and glycemic control.

The prevalence and factors associated with malnutrition among infants with cleft palate and/or lip at a hospital in Uganda: a cross-sectional study.

BACKGROUND: To determine the prevalence and factors associated with malnutrition among infants with Cleft palate and/or cleft lip (CP+/-L) at Comprehensive Rehabilitation for Uganda Hospital (CoRSU) in Uganda. METHODS: This was a cross-sectional study done on infants with CP+/-L and their caretakers admitted between November 2013 and October 2014 at CoRSU hospital which was the study setting. A questionnaire was answered by the infants' caretakers. The main outcome measure, malnutrition was defined and classified based on Z-scores obtained using the W.H.O Z-calculator in which weights of the infants in kilograms and lengths in centimeters respectively were placed. The values obtained were expressed as a proportion using all enrolled infants with CP+/-L as denominator. Multivariable analysis was used to determine the risk factors. RESULTS: A total of 44 infants with CP+/-L were enrolled. Of these, 77% were below 4 months of age and 97.7% were immunized. The male-to-female ratio was 1.06:1. About 59% had unilateral CP+/-L. A total of 93.2% were delivered at term with 69.4% having a birth weight greater than 3 kg. Generally, 68% were malnourished, with the highest burden among females (71.4%), infants below 4 months (73.5%) and those with unilateral CP+/-L (77%). About 57% had moderate-to-severe malnutrition. There was delayed supplementation to breast milk, with cow-milk as the main supplemental feed for all the infants. In the multivariable analysis, factors associated with malnutrition included, having caretakers lacking nutritional information post-delivery (OR = 3.8, p = 0.17), low birth weight (OR = 3.4, p = 0.20), and having less than 10 feeds/day (OR = 4.9, p = 0.09). CONCLUSION: CP+/-L infants born in Uganda suffer a high-burden of malnutrition. Preventional strategies are needed with focus on proper feeding information. Research on cost-effective feeds, feeding methods and reasons behind gender disparities in these infants is also required.

Twistors and amplitudes.

A brief review is given of why twistor geometry has taken a central place in the theory of scattering amplitudes for fundamental particles. The emphasis is on the twistor diagram formalism as originally proposed by Penrose, the development of which has now led to the definition by Arkani-Hamed et al. of the 'amplituhedron'.

Reconstruction of Punitive Ear Amputations in Uganda: A Unique Surgical Burden of Disease.

Over the course of 12 months, a plastic surgical team from Paris, France, undertook 2 intensive ear reconstruction missions with plastic surgeons from the CoRSU Rehabilitation Hospital in Uganda. A cohort of over 30 adult women was assessed having been subjected to ear amputations by members of the Lords Resistance Army in Northern Uganda in the 1990s. The patients were identified, mobilized, and transferred to Kampala for surgery by a charitable arm of the Watoto Church, known as Living Hope. The surgical team performed 15 ear reconstruction cases during the first 1-week mission and 16 ear reconstruction cases during the second 1-week mission. All cases were reconstructed successfully using the 2-stage autologous auricular reconstruction method advocated by the senior author (FF). Local skin was used to cover the costal cartilage framework in the first stage without need for temporo-parietal fascial flaps. Technical challenges included the older age of patients and ossified costal cartilage, high prevalence of HIV positivity, bilateral amputation, and difficulty of surgical follow-up. The main modifications to standard practice were routine pre-op testing of the costal cartilage, pre-op viral load and CD4 count screening in HIV-positive patients, simultaneous bilateral first-stage ear reconstruction, prolonged hospital stay, and implementation of routine surgical counting procedures.

Global variation in cleft palate repairs: an analysis of 352,191 primary cleft repairs in low- to higher-middle-income countries.

Objectives : Resources for repair of cleft lip and palate may be lacking in low- and middle-income countries. The Smile Train is a registered charity that supports cleft repair in resource-poor settings. In the global health care challenge, it has been suggested that many babies born with cleft palates are not repaired. This study aims to determine whether any variation exists in the proportion of cleft lip and cleft palate repairs undertaken in low- and middle-income countries. Methods : Data were obtained from the Smile Train database of 352,191 consecutive cleft operations performed between 2008 and 2011 in low- to higher-middle-income countries. The ratio of cleft lip to palate repair was analyzed as a function of geographic region and by country income (gross national income). Results : A significant correlation exists between both the income of a country and its geographical region to the ratio of lip and palate repair procedures undertaken. Higher-income countries had a higher ratio of cleft palate repairs. Countries in sub-Saharan Africa have the lowest proportion of cleft palate repairs. Conclusion : This study emphasizes that many babies born with cleft palates in resource-poor regions do not have their palates repaired. This finding may be explained by an increased neonatal mortality in cleft palate babies. Furthermore, fewer isolated palatal clefts may present to an appropriate health care facility or there may be a reluctance to treat cleft palate due to concerns regarding higher perioperative risks or the lack of available surgical and anesthetic expertise.

Impact of early synchronous lip and palatal repair on speech.

AIMS: The purpose of this study was to describe articulation and resonance characteristics of Ugandan English-speaking children with cleft lip and palate (CLP) after synchronous lip and palatal closure (Sommerlad technique) prior to the age of 6 months in comparison with an age- and gender-matched control group. METHODS: Eleven Ugandan patients with CLP (mean age 4;9 years), repaired during a synchronous lip and (soft and hard) palatal closure at a mean age of 3.4 months, were included as well as a control group (n = 22) consisting of 2 Ugandan age- and gender-matched noncleft children for each patient (mean age 4;10 years). Objective and perceptual speech assessment techniques were applied. RESULTS: Consonant inventories were significantly smaller in the CLP group. Moreover, phonetic disorders and phonological processes occurred in 91 and 100% of the CLP group, respectively. Perceptual consensus evaluation revealed absence of hyponasality and cul-de-sac resonance in all patients. Hypernasality and nasal emission/turbulence occurred in 18 and 27% of the patients, respectively. No significant group differences were observed regarding the mean nasalance values of oral speech samples. CONCLUSION: Various deviations from normal speech development seem to occur in patients with CLP following synchronous lip and palatal closure before 6 months of age.

Cleft lip and palate surgery carried out by one team in Uganda: where have all the palates gone?

OBJECTIVE: To determine the distribution of clefts in our operated population in comparison with data in the world literature. DESIGN: A retrospective review of hospital-based cleft procedures undertaken in Uganda over a 10-year period by one surgical team. PATIENTS: 1304 newly presenting cleft patients were identified and analyzed by sex, laterality, and type of cleft, and data were compared with the literature. RESULTS: We found male predominance in cleft lip (CL) and/or palate patients and female predominance in isolated cleft palate (CP) patients. Left-sided CLs presented more frequently than right-sided, bilateral, and midline cleft lips at a ratio of 50∶38∶11∶1. Patients presented most commonly with an isolated CL, followed by cleft lip and palate (CLP), with a small number presenting with isolated CP (966, 306, and 32, respectively). CONCLUSION: The distribution of sex and laterality broadly correlates with findings of other studies; however, a large discrepancy in the proportions of CL, CLP, and CP is apparent. Much higher numbers of CLs and much lower numbers of CLP and CP presented than would be expected in comparison with worldwide literature (2% of patients had an isolated CP). It is hypothesized that the low numbers of patients presenting with combined CLP and CP are due to high mortality among this cohort. If this hypothesis is correct, then in this series of 1304 cleft patients, as many as 3526 CP patients (91% of all CPs) are missing and probably died before undergoing surgical correction.

Metabolomic profiling of human pluripotent stem cell differentiation into lung progenitors.

Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation toward a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild-type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification toward lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.

Better speech outcomes after very early palatal repair?-A longitudinal case-control study in Ugandan children with cleft palate.

INTRODUCTION: Children born with cleft palate with or without cleft lip (CP±L) tend to use less oral pressure consonants and more glottal sounds in their babbling. The purpose of very early palatal repair (i.e., one-stage palatal closure prior to 6 months of age) is to make the palate functional before the onset of speech acquisition to reduce the anchoring of wrong patterns in the child's developing phonological system. As a result, less compensatory articulation errors are expected to be present. Currently, no detailed longitudinal speech outcomes after very early palatal closure are available. This study aimed to provide longitudinal speech outcomes in Ugandan children with CP±L who received palatal closure prior to the age of 6 months. METHODS: Ten children with CP±L were assessed at a mean age of 5 and 10 years old. Speech understandability, speech acceptability, resonance, nasal airflow and articulation were perceptually rated by two experienced speech-language pathologists. Velopharyngeal function was estimated using the velopharyngeal composite score (VPC-sum). Information regarding speech therapy, fistula rate, and secondary (speech) surgery was collected. The outcomes were compared with the longitudinal outcomes of an age- and gender-matched control group of 10 Ugandan children without CP±L. RESULTS: Speech understandability and acceptability improved significantly over time in the group with CP±L (all p's ≤ 0.05, all Z's > -2.43). At both test dates, significantly worse judgments were found for the group with CP±L compared to the control group for these variables and variables related to passive speech errors (all p's ≤ 0.05, all Z's > 2.49). A statistically significant difference with the control group was found for the presence of compensatory articulation errors at the age of 5 years but not at the age of 10 years, indicating a catch up by the children with CP±L. CONCLUSION: Whether a one-stage palatal closure prior to the age of 6 months is more favorable for speech outcomes compared to one-stage palatal closure at 12 months is still not clear. Speech of the children with CP±L improved over time, but significantly differed from the control group at the age of 5 and 10 years old. Limited access to health care facilities and possible influence of malnutrition on wound healing need to be considered when interpreting the results. Whether palatal closure prior to the age of 6 months is transferable to other countries is subject for further research, including both longitudinal and prospective designs with larger samples.

Incidence of cleft lip and palate in Uganda.

OBJECTIVE: The purpose of the study was to estimate the need for resources for cleft repairs in Uganda by determining the overall incidence of oral-facial clefts and the ratio of isolated cleft lip to isolated cleft palate to cleft lip and palate. DESIGN: A 1-year prospective study was implemented in seven hospitals and health centers with maternity units in and around Kampala. All live babies were examined for cleft lip and/or palate at birth. The birth of a baby with a cleft was communicated to the research coordinator by maternity staff, and the babies were assessed within 24 hours of delivery. Maternity data (live births) for each center were collected monthly to determine the denominator. RESULTS: Over the course of 1 year (February 1, 2008 to January 31, 2009), 26,186 babies were delivered. Nineteen babies had a cleft lip and/or palate, giving an incidence of 0.73 in 1000; 12 of the 19 babies (63.2%) had a cleft lip and palate, six (31.2%) had an isolated cleft lip, and only one (5.3%) had an isolated cleft palate. The ratio of boys to girls was 1.1∶1. CONCLUSIONS: The incidence of clefts in this study was 0.73 in 1000. With an estimated 1100 babies born with a cleft per year, this would result in the need for 1800 cleft repairs for babies in Uganda (695 babies needing two repairs each). These data will be helpful to advocate for and plan the necessary resources to effectively treat this condition.

Vascularized fibula flap in the management of segmental bone loss following osteomyelitis in children at a Ugandan hospital.

Background: Hematogenous osteomyelitis is commonly observed in the pediatric population across sub-Saharan Africa. This retrospective case series was designed to evaluate the complications and outcomes of treatment using a vascularized fibula flap (VFF) to fill segmental bone defects secondary to osteomyelitis in children in a low-resource setting in CoRSU Rehabilitation Hospital, Uganda. Methods: Clinical notes and radiographs of children with a diagnosis of osteomyelitis that subsequently underwent a VFF procedure between October 2013 and December 2017 were reviewed. All patients were clinically and radiographically evaluated in 2019. Results: Forty-four children, with an average bone defect of 10.5 cm, were included. Eighty-four percent of children had successful VFF limb reconstruction. Integration of the graft was radiologically sound in 20.8 weeks on average. The postoperative phase was uneventful in 29 % of patients. Complications were observed in the remaining patients, including flap failure (6), donor leg neurapraxia (3), cutaneous paddle necrosis (11), graft fracture (2), skin graft loss (6), fixator failure (1) and non-union (2). Functional outcomes were rated as excellent in 13 patients, good in 14, fair in 9 and poor in 8. There was no recurrence of the bone infection in any of the enrolled children. Conclusion: Despite being a complex and demanding procedure, VFF is a good option for reconstructing post-osteomyelitis bone defects, particularly when associated with loss of soft tissue envelope. Considering the more than satisfactory functional and clinical outcomes, this procedure should be kept in mind for these complex pediatric cases of bone and soft tissue loss, even in a low-resource setting.

VIOLIN: vaccine investigation and online information network.

Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

"Reprogram Enablement" as an Assay for Identifying Early Oncogenic Pathways by Their Ability to Allow Neoplastic Cells to Reacquire an Epiblast State.

One approach to understanding how tissue-specific cancers emerge is to determine the requirements for "reprograming" such neoplastic cells back to their developmentally normal primordial pre-malignant epiblast-like pluripotent state and then scrutinizing their spontaneous reconversion to a neoplasm, perhaps rendering salient the earliest pivotal oncogenic pathway(s) (before other aberrations accumulate in the adult tumor). For the prototypical malignancy anaplastic thyroid carcinoma (ATC), we found that tonic RAS reduction was obligatory for reprogramming cancer cells to a normal epiblast-emulating cells, confirmed by changes in their transcriptomic and epigenetic profiles, loss of neoplastic behavior, and ability to derive normal somatic cells from their "epiblast organoids." Without such suppression, ATCs re-emerged from the clones. Hence, for ATC, RAS inhibition was its "reprogram enablement" (RE) factor. Each cancer likely has its own RE factor; identifying it may illuminate pre-malignant risk markers, better classifications, therapeutic targets, and tissue-specification of a previously pluripotent, now neoplastic, cell.

DNMT3B Oncogenic Activity in Human Intestinal Cancer Is Not Linked to CIMP or BRAFV600E Mutation.

Approximately 10% of human colorectal cancer (CRC) are associated with activated BRAFV600E mutation, typically in absence of APC mutation and often associated with a CpG island methylator (CIMP) phenotype. To protect from cancer, normal intestinal epithelial cells respond to oncogenic BRAFV600E by activation of intrinsic p53 and p16-dependent tumor suppressor mechanisms, such as cellular senescence. Conversely, CIMP is thought to contribute to bypass of these tumor suppressor mechanisms, e.g. via epigenetic silencing of tumor suppressor genes, such as p16. It has been repeatedly proposed that DNMT3B is responsible for BRAFV600E-induced CIMP in human CRC. Here we set out to test this by in silico, in vitro, and in vivo approaches. We conclude that although both BRAFV600E and DNMT3B harbor oncogenic potential in vitro and in vivo and show some evidence of cooperation in tumor promotion, they do not frequently cooperate to promote CIMP and human intestinal cancer.

An improvement in skeletal muscle mitochondrial capacity with short-term aerobic training is associated with changes in Tribbles 1 expression.

Exercise training and physical activity are known to be associated with high mitochondrial content and oxidative capacity in skeletal muscle. Metabolic diseases including obesity and insulin resistance are associated with low mitochondrial capacity in skeletal muscle. Certain transcriptional factors such as PGC-1α are known to mediate the exercise response; however, the precise molecular mechanisms involved in the adaptation to exercise are not completely understood. We performed multiple measurements of mitochondrial capacity both in vivo and ex vivo in lean or overweight individuals before and after an 18-day aerobic exercise training regimen. These results were compared to lean, active individuals. Aerobic training in these individuals resulted in a marked increase in mitochondrial oxidative respiratory capacity without an appreciable increase in mitochondrial content. These adaptations were associated with robust transcriptome changes. This work also identifies the Tribbles pseudokinase 1, TRIB1, as a potential mediator of the exercise response in human skeletal muscle.

Multi-omic comparison of Alzheimer's variants in human ESC-derived microglia reveals convergence at APOE.

Variations in many genes linked to sporadic Alzheimer's disease (AD) show abundant expression in microglia, but relationships among these genes remain largely elusive. Here, we establish isogenic human ESC-derived microglia-like cell lines (hMGLs) harboring AD variants in CD33, INPP5D, SORL1, and TREM2 loci and curate a comprehensive atlas comprising ATAC-seq, ChIP-seq, RNA-seq, and proteomics datasets. AD-like expression signatures are observed in AD mutant SORL1 and TREM2 hMGLs, while integrative multi-omic analysis of combined epigenetic and expression datasets indicates up-regulation of APOE as a convergent pathogenic node. We also observe cross-regulatory relationships between SORL1 and TREM2, in which SORL1R744X hMGLs induce TREM2 expression to enhance APOE expression. AD-associated SORL1 and TREM2 mutations also impaired hMGL Aß uptake in an APOE-dependent manner in vitro and attenuated Aß uptake/clearance in mouse AD brain xenotransplants. Using this modeling and analysis platform for human microglia, we provide new insight into epistatic interactions in AD genes and demonstrate convergence of microglial AD genes at the APOE locus.

Plastic and reconstructive surgery in Uganda--10 years experience.

We describe our experience of working in plastic and reconstructive surgery in Uganda over the last 10 years. There is a high burden of disease, a health system that is under resourced, and few qualified physicians to provide healthcare for a principally rural population. Training the physicians of the future is essential. Prevention and early wound management needs to be emphasized for traumatic injuries including burns. Subsidized up-country visits by trained specialists with the appropriate equipment are required to provide a service for the rural poor. There appears to be a high mortality rate in babies with unrepaired cleft palate, probably due to feeding difficulties in an environment where intercurrent illness is common. We now offer nutritional support with early combined cleft lip and palate repair in these babies, a practice that has a high success rate and may be suited to other specialist units in the developing world.