Incidence and sociodemographic, living environment and maternal health associations with stillbirth in a tertiary healthcare setting in Kano, Northern Nigeria

Background

Almost two million stillbirths occur annually, most occurring in low- and middle-income countries. Nigeria is reported to have one of the highest stillbirth rates on the African continent. The aim was to identify sociodemographic, living environment, and health status factors associated with stillbirth and determine the associations between pregnancy and birth factors and stillbirth in the Murtala Mohammed Specialist Hospital, Kano, Nigeria.

Methods

A three-month single-site prospective observational feasibility study. Demographic and clinical data were collected. We fitted bivariable and multivariable models for stillbirth (yes/no) and three-category livebirth/macerated stillbirth/non-macerated stillbirth outcomes to explore their association with demographic and clinical factors.

Findings

1,998 neonates and 1,926 mothers were enrolled. Higher odds of stillbirth were associated with low-levels of maternal education, a further distance to travel to the hospital, living in a shack, maternal hypertension, previous stillbirth, birthing complications, increased duration of labour, antepartum haemorrhage, prolonged or obstructed labour, vaginal breech delivery, emergency caesarean-section, and signs of trauma to the neonate following birth.

Interpretation

This work has obtained data on some factors influencing stillbirth. This in turn will facilitate the development of improved public health interventions to reduce preventable deaths and to progress maternal health within this site.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12884-022-04971-x.

Preterm Babies: Management and Challenges Associated with Survival in a Resource-Limited Setting

BACKGROUND

Preterm babies have constituted a major constraints on human and material resources due to early mortality and long term disability among survivors. Rates of disability among survivors have increased over the period, with high rates of broncho-pulmonary dysplasia.

OBJECTIVE

To determine the survival and management challenges of preterm babies in University of Maiduguri Teaching Hospital, Maiduguri Borno State REUSLTS: Of the 1129 preterm babies managed in the Special Care Baby Unit (SCBU), 714 cases notes were retrieved and analyzed giving a retrieval rate of 63%. There were 256 (35.9%) preterm babies as in-born, while 458 (64.1%) were out-born. Male preterm babies were 372 (52.1%), while female preterm babies were 342 (47.9%); with female to male ratio of 1.08:1. Extreme low birth weight (<1000grams) were 17 (2.3%), very low birth weight (1000-1499 grams) were 288 (40.3%) while low birth weight (1500-2499 grams) were 406 (56.9%). We also documented 3 preterm babies whose weights >2500 grams were large for gestational age weight. Duration of oxygen therapy (p = 0.620), duration of phototherapy (p = 0.474), and EBT (p = 0.466) showed no association with their survival while only duration of incubator care (p = 0.005) demonstrated significant association with outcome.

CONCLUSION

The population of preterm babies studied is 32.70% and their survival has remarkably improved. However, this improved survival of preterm babies especially the extreme and very low birth weight categories has posed a big challenge due to limited access to incubator care, use of caffeine and surfactant which might influence the outcome.

Afatinib versus methotrexate as second-line treatment in Asian patients with recurrent or metastatic squamous cell carcinoma of the head and neck progressing on or after platinum-based therapy (LUX-Head & Neck 3): an open-label, randomised phase III trial

BACKGROUND

Treatment options are limited for patients with recurrent or metastatic squamous cell carcinoma of the head and neck (HNSCC) following progression after first-line platinum-based therapy, particularly in Asian countries.

PATIENTS AND METHODS

In this randomised, open-label, phase III trial, we enrolled Asian patients aged ≥18 years, with histologically or cytologically confirmed recurrent/metastatic HNSCC following first-line platinum-based therapy who were not amenable for salvage surgery or radiotherapy, and had an Eastern Cooperative Oncology Group (ECOG) performance status of 0/1. Patients were randomised (2 : 1) to receive oral afatinib (40 mg/day) or intravenous methotrexate (40 mg/m2/week), stratified by ECOG performance status and prior EGFR-targeted antibody therapy. The primary end point was progression-free survival (PFS) assessed by an independent central review committee blinded to treatment allocation.

RESULTS

A total of 340 patients were randomised (228 afatinib; 112 methotrexate). After a median follow-up of 6.4 months, afatinib significantly decreased the risk of progression/death by 37% versus methotrexate (hazard ratio 0.63; 95% confidence interval 0.48-0.82; P = 0.0005; median 2.9 versus 2.6 months; landmark analysis at 12 and 24 weeks, 58% versus 41%, 21% versus 9%). Improved PFS was complemented by quality of life benefits. Objective response rate was 28% with afatinib and 13% with methotrexate. There was no significant difference in overall survival. The most common grade ≥3 drug-related adverse events were rash/acne (4% with afatinib versus 0% with methotrexate), diarrhoea (4% versus 0%), fatigue (1% versus 5%), anaemia (<1% versus 5%) and leukopenia (0% versus 5%).

CONCLUSIONS

Consistent with the phase III LUX-Head & Neck 1 trial, afatinib significantly improved PFS versus methotrexate, with a manageable safety profile. These results demonstrate the efficacy and feasibility of afatinib as a second-line treatment option for certain patients with recurrent or metastatic HNSCC.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT01856478.

In vitro and in silico evaluation of fucosterol from Sargassum horridum as potential human acetylcholinesterase inhibitor

The fucosterol has been reported numerous biological activities. In this study, the activity in vitro of the fucosterol from Sargassum horridum as potential human acetylcholinesterase inhibitor was evaluated. The structural identification was obtained by nuclear magnetic resonance (NMR) spectroscopy and based on experimental data, we combined docking and molecular dynamics simulations coupled to the molecular-mechanics-generalized-born-surface-area approach to evaluating the structural and energetic basis for the molecular recognition of fucosterol and neostigmine at the binding site of acetylcholinesterase (AChE). In addition, the Lineweaver-Burk plot showed the nature of a non-competitive inhibition. The maximum velocity (Vmax) and the constant of Michaelis-Menten (Km) estimated for fucosterol (0.006 µM) were 0.015 1/Vo (ΔA/h and 6.399 1/[ACh] mM-1, respectively. While, for neostigmine (0.14 µM), the Vmax was 0.022 1/Vo (ΔA/h) and Km of 6.726 1/[ACh] mM-1, these results showed a more effective inhibition by fucosterol respect to neostigmine. Structural analysis revealed that neostigmine reaches the AChE binding site reported elsewhere, whereas fucosterol can act as a no-competitive and competitive acetylcholinesterase inhibitor, in agree with kinetic enzymatic experiments. Binding free energy calculations revealed that fucosterol reaches the acetylcholinesterase binding site with higher affinity than neostigmine, which is according to experimental results. Whereas the per-residue decomposition free energy analysis let us identify crucial residues involved in the molecular recognition of ligands by AChE. Results corroborate the ability of theoretical methods to provide crucial information at the atomic level about energetic and structural differences in the binding interaction and affinity from fucosterol with AChE. Communicated by Ramaswamy H. Sarma.

Vitrification treatment of municipal solid waste bottom ash

This study involves the chemical characterization of municipal solid waste (MSW) bottom ash (BA) produced at a combustor facility in Rimini (Italy), and vitrification experiments, performed at lab scale under atmospheric conditions, maximum temperature of 1100 °C, for different durations (2-16 h). LA-ICP-MS analyses of the glasses obtained revealed that the overall volatility of metal elements increases with the time but it cannot be simply predicted by element boiling point. Elements have been here categorized into three different groups depending on their volatility comparing the glass product with the BA starting sample- high, medium or low, respectively- (1) Cu, W, Cl; (2) Pb, Zn, Sr; (3) Mo, Cr, V, Ni. The behavior of Cs, Rb, Ag, Ba, Ga, Co, U, Zr, Hf and Ta in the glassy slag is not defined because we did not observe statistically significant changes in their volatility behavior. Vitrification allows us to produce chemically stable glassy materials and immobilize potentially harmful elements, thus producing from waste new vitreous materials that are relatively inert and suitable for potential re-utilization in new products and/or applications for building and construction industries. Moreover, the samples show REE chondrite-normalized patterns indicating relative enrichments in Light-Rare Earth Elements (LREE), in particular La and Nd which may be interesting from an economic point of view in terms of waste recovery. Thus, the results obtained show how to treat bottom ashes from incinerator in order to provide more chemically inert and economically useful resources for recycle and reuse of solid waste BA.

Computational Study of the Binding Modes of Diverse DPN Analogues on Estrogen Receptors (ER) and the Biological Evaluation of a New Potential Antiestrogenic Ligand

Estrogen (17β-estradiol) is essential for normal growth and differentiation in the mammary gland. In the last three decades, previous investigations have revealed that Estrogen Receptor Alpha (ERα) plays a critical role in breast cancer. More recently, observations regarding the widespread expression of ERβ-like proteins in normal and neoplastic mammary tissues have suggested that ERβ is also involved in the mentioned pathology. Design of new drugs both steroidal and nonsteroidal that target any of these receptors represents a promise to treat breast cancer although it remains a challenge due to the sequence similarity between their catalytic domains. In this work, we propose a new set of compounds that could effectively target the estrogen receptors ERα and ERβ. These ligands were designed based on the chemical structure of the ERβ-selective agonist Diarylpropionitrile (DPN). The designed ligands were submitted to in silico ADMET studies, yielding in a filtered list of ligands that showed better drug-like properties. Molecular dynamics simulations of both estrogen receptors and docking analysis were carried-out employing the designed compounds, from which two were chosen due to their promising characteristics retrieved from theoretical results (docking analysis or targeting receptor predictions). They were chemically synthetized and during the process, two precursor ligands were also obtained. These four ligands were subjected to biological studies from which it could be detected that compound mol60b dislplayed inhibitory activity and its ability to activate the transcription via an estrogenic mechanism of action was also determined. Interestinly, this observation can be related to theoretical binding free energy calculations, where the complex: ERβ-mol60b showed the highest energy ΔGbind value in comparison to others.

Unconventional quantum optics in topological waveguide QED

The discovery of topological materials has motivated recent developments to export topological concepts into photonics to make light behave in exotic ways. Here, we predict several unconventional quantum optical phenomena that occur when quantum emitters interact with a topological waveguide quantum electrodynamics bath, namely, the photonic analog of the Su-Schrieffer-Heeger model. When the emitters' frequency lies within the topological bandgap, a chiral bound state emerges, which is located on just one side (right or left) of the emitter. In the presence of several emitters, this bound state mediates topological, tunable interactions between them, which can give rise to exotic many-body phases such as double Néel ordered states. Furthermore, when the emitters' optical transition is resonant with the bands, we find unconventional scattering properties and different super/subradiant states depending on the band topology. Last, we propose several implementations where these phenomena can be observed with state-of-the-art technology.

Long-range doublon transfer in a dimer chain induced by topology and ac fields

The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain’s end-points. This has the appealing feature that the transfer occurs only between the end-points – the particle does not pass through the intermediate sites–making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving.

Antimicrobial sensitivity pattern of organisms causing urinary tract infection in children with sickle cell anemia in Maiduguri, Nigeria

BACKGROUND

Patients with sickle cell disease have increased tendency to develop frequent and severe infections, especially of bones and urinary tract.

OBJECTIVE

The knowledge of antimicrobial sensitivity pattern of common etiological agents will serve as a guide to empiric treatment while results of urine culture and sensitivity are being awaited.

MATERIALS AND METHODS

Antimicrobial sensitivity test was carried out on bacterial isolates from the urine of febrile children with sickle cell anemia (SCA) and children with HbAA in Maiduguri. Urine specimens were collected and cultured by standard methods. Sensitivity to 15 antimicrobials (based on availability of sensitivity disc) was tested using the disc-diffusion technique of stokes.

RESULTS

Significant bacteriuria was obtained from 65 (26%) of the 250 children with SCA and 51 (20.4%) of the 250 controls. The isolates were E. coli, Klebsiella, Coliforms, Proteus, Staph aureus and Salmonella. Sensitivity was highest to 3 rd generation cephalosporins, followed by the quinolones: ciprofloxacin (86.2%), ofloxacin (83.1%), and peflacine (73.8%). Sensitivity of the organisms to some of the commonly used antibiotics like ampicillin, cotrimoxazole, and nalidixic acid was generally low. In general, the pattern of bacteriuria and their sensitivity in the SCA group was similar to the pattern in the control group.

CONCLUSION

Etiological agents of childhood urinary tract infections (UTI) in this environment are resistant to most of the drugs commonly recommended for its treatment. Amoxicillin/clavulanic acid, cefuroxime, and gentamicin, are recommended as first-line drugs for treatment of UTI while awaiting results of culture and sensitivity. Ceftriaxone and ceftazidime should be reserved for case of non response to first-line drugs and severe infections.

Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells); cytokeratin 7 (ductal cells); and smooth muscle α-actin (myoepithelial cells) and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle α-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis.

Molecular abnormalities of chromosome-19 in malignant gliomas - preferential involvement of the 19q13.2-q13.4 region

A deletion mapping analysis of chromosome 19 was performed on a series of 101 samples derived from malignant gliomas. A total of 35 tumors displayed different deletions for the loci studied (D19S21, D19S11, D19S74, D19S7, D19S8, CKM, and D19S22). In most instances, losses involving the long arm markers of chromosome 19 were observed, and only four samples were characterized by losses on the short arm. No tumor was found displaying loss of both short and long arm markers. The higher frequency of deletions was detected in tumors with a major oligodendroglial component: 76% of samples included in this group displayed losses at 19q. Among the astrocytic tumors, the frequency of 19q alterations varied as follows: 11% in pilocytic astrocytomas, 17% in astrocytomas grade II, 10% in anaplastic astrocytomas and 21% in glioblastoma multiforme. No ependymoma was found displaying allele loss on chromosome 19. The common region of overlap for the 19q deletions observed involves primarily the distal portion of the long arm, 19q13.2-q13.4. In agreement with previous reports, these data suggest the non-random involvement of a tumor suppressor gene located at 19q13 in the genesis or progression of malignant gliomas.

Assessment of carcass contamination with E. coli O157 before and after washing with water at abattoirs in Nigeria

The study was carried out to assess the level of beef carcass contamination with Escherichia coli including O157 strains before and after washing with water. Samples of water used for washing carcasses were collected and thirty beef carcasses were swabbed within a period of one month in each of three abattoirs located in North-Western states of Nigeria. E. coli were enumerated as indicator organisms. Using conventional biochemical tests, the isolation rate of E. coli in the 120 swab samples collected in each abattoir from external and internal surfaces of the carcasses was 58.3% at Kano abattoir, 70.8% at Sokoto abattoir, while 76.7% was recorded at Zango abattoir. E. coli counts from external and internal surfaces of the carcasses were enumerated as mean log and ranged between 4.3 Log(10) and 4.6 Log(10) cfu/cm(2) before washing, while the values were 4.6 Log(10) and 4.9 Log(10) cfu/cm(2) after washing. Data analysis revealed that the increase in E. coli counts after washing carcasses with water was statistically significant (P<0.05) in all the abattoirs. However, there was no statistically significant difference (P>0.05) between the 3 abattoirs in mean log of E. coli counts from external surfaces of carcass after washing. E. coli O157 was identified from both the water and surfaces of carcasses using Latex agglutination kit. A prevalence of 2.8% of E. coli O157 was detected in 360 swab samples from 90 beef carcasses examined. E. coli counts from water used in washing carcasses were between 22 and 120 cfu/100 ml. Of the 72 water samples, 3(4.2%) were positive for E. coli O157. In conclusion, there was increased contamination of carcasses during processing and water used in washing carcasses might have contributed to carcass contamination in all the abattoirs studied due to use of non-potable water.

Urinary tract infection in febrile children with sickle cell anaemia

BACKGROUND

Sickle cell anaemia (SCA) is very common in Maiduguri, North-Eastern Nigeria. Children with this disease have increased tendency to develop frequent and severe infections especially of the urinary tract, bones and lungs. The prevalence of urinary tract infection (UTI) has however not been reported in this part of the Nigeria.

OBJECTIVE

To determine the prevalence of bacteriuria and bacterial isolates in the urine of febrile children with sickle cell anaemia.

METHODS

This was a prospective study carried out on 250 children with SCA and 250 controls with HbAA aged 6 months to 15 years. Following clinical assessment, midstream urine or urine obtained by suprapubic bladder aspiration was collected and subjected to microscopy and culture.

RESULTS

Bacteriuria was found in 65 (26%) of children with SCA and controls 514 (20.4%) of controls, p>0.05. Escherichia coli [16 (27.7%)] and Klebsiella species [16(24.6%)] were the predominant isolates in SCA group, while Escherichia coli [13(37.3%)] and Coliforms (25.4%) were predominant in the control group. Significant bacteruria occurred in patients with other clinical conditions such as pneumonia and septicaemia.

CONCLUSION

Urinary tract infection is common in children with SCA. Routine screening is therefore recommended during febrile illnesses.

Autofluorescence removal by non-negative matrix factorization

This paper describes a new, physically interpretable, fully automatic algorithm for removal of tissue autofluorescence (AF) from fluorescence microscopy images, by non-negative matrix factorization. Measurement of signal intensities from the concentration of certain fluorescent reporter molecules at each location within a sample of biological tissue is confounded by fluorescence produced by the tissue itself (autofluorescence). Spectral mixing models use mixing coefficients to specify how much fluorescence from each source is present and unmixing algorithms separate the two fluorescent sources. Current spectral unmixing methods for AF removal often require a priori knowledge of mixing coefficients. Those which do not, such as principal component analysis, generate negative mixing coefficients that are not physically meaningful. Non-negative matrix factorization constrains mixing coefficients to be non-negative, and has been used for spectral unmixing, but not AF removal. This paper describes a novel non-negative matrix factorization algorithm which separates fluorescent images into true signal and AF components utilizing an estimate of the dark current. We also present a test-bed, based on fluorescent beads, to compare the performance of different AF removal algorithms. Our algorithm out-performed previous state of the art on validation images.

Evaluation of the Nitrite Test in Screening for Urinary Tract Infection in Febrile Children with Sickle Cell Anaemia in Maiduguri- Nigeria

BACKGROUND: Urinary tract infection is a significant cause of morbidity in children with sickle cell anaemia (SCA). Individuals with SCA have increased risk of urinary tract infection (UTI). Facilities for urine culture may not be available in most rural and even some urban areas in most developing countries like Nigeria. It will therefore be useful to have a simple means of screening such children for UTI with the intent of prompt treatment. MATERIALS AND METHODS: The study will evaluate the usefulness of the nitrite test in detecting UTI in febrile SCA children. This study was carried out in the Department of Paediatrics University of Maiduguri Teaching Hospital and State Specialist Hospital Maiduguri. RESULTS: The study consisted of 250 children aged 6 months to 15 years with SCA presenting with fever (temperature ≥ 37. 5°C). Midstream urine specimen was collected from older children and suprapubic bladder aspiration of urine specimen was collected from infants. Samples were subjected to nitrite test, culture and sensitivity. There was significant bacteriuria in 65 (26+) children with SCA. A positive test for nitrite was obtained in 43 of the 65 (66.2+) children. The nitrite test has a specificity of 93.5+ in detecting bacteriuria, a sensitivity of 66.2+, a positive predictive value of 78.2+ and a negative predictive value of 93.5+. A positive nitrite test was significantly associated with bacteriuria, while a negative test was also significantly associated with an absence of bacteriuria. CONCLUSIONS: From this study, the nitrite test is useful as a screening test for UTI in SCA children. However in sick children with SCA, microscopy, culture and sensitivity should still be done in spite of a negative nitrite test.

The use of highly active antiretroviral therapy for the prevention of mother-to-child transmission of the human immunodeficiency virus in Nigeria

Mother-to-child transmission of HIV accounts for 90% of paediatric HIV. The objective of this paper is to assess the outcome of preventing mother-to-child transmission of the human immunodeficiency virus (HIV), using highly active antiretroviral therapy (HAART). All pregnant women booking for antenatal care at the university of Maiduguri teaching hospital received voluntary counselling and testing for HIV. All HIV-positive mothers were placed on HAART for the prevention of mother-to-child transmission of HIV. All exposed babies received single dose nevirapine within 72 h of birth and zidovudine syrup for 6 weeks. The babies were then tested for viral DNA using the polymerase chain reaction (PCR) at 6 and 12 weeks of age. Among 5,461 mothers screened for HIV during the study period, 695 (12.7%) were confirmed HIV-positive. Out of 446 mother-baby pairs followed up to a minimum period of 6 months postpartum, only five (1.1%) babies were HIV-positive.

Automated pipeline for atlas-based annotation of gene expression patterns: application to postnatal day 7 mouse brain

Massive amounts of image data have been collected and continue to be generated for representing cellular gene expression throughout the mouse brain. Critical to exploiting this key effort of the post-genomic era is the ability to place these data into a common spatial reference that enables rapid interactive queries, analysis, data sharing, and visualization. In this paper, we present a set of automated protocols for generating and annotating gene expression patterns suitable for the establishment of a database. The steps include imaging tissue slices, detecting cellular gene expression levels, spatial registration with an atlas, and textual annotation. Using high-throughput in situ hybridization to generate serial sets of tissues displaying gene expression, this process was applied toward the establishment of a database representing over 200 genes in the postnatal day 7 mouse brain. These data using this protocol are now well-suited for interactive comparisons, analysis, queries, and visualization.

Liver Transplantation in Childhood With More Than 10 Years of Follow-up: Analysis of a Single-Center Experience

We pioneered pediatric liver transplantation (OLT) in Spain (June 1985). The aim of this study was to evaluate the current status of our OLT recipients with more than 10 years follow-up.

MATERIALS AND METHODS

The 50 patients with >10 years follow-up had a mean age at OLT of 5.6 years with 60% showing a main indication of biliary atresia. All but one (tacrolimus) received cyclosporine.

RESULTS

No patient loss occurred among these patients. Eighteen patients had follow-up >15 years and 12 >20 years. The incidence of acute rejection was 56%; chronic rejection, 16%; and lymphoproliferative disorders, 12%. Seven (14%) required retransplantation at a mean of 4.2 years after the first OLT due in four instances to chronic rejection. After 10 years of follow-up, one patient developed portal vein thrombosis and three biliary strictures. All patients remain on immunosuppression. In 64% cyclosporine was switched to tacrolimus or another agent. One patient developed acute rejection at 19.2 years. In 14% of patients the liver function test is abnormal with serum creatinine is >1.5 mg/dL in 10%; one requires insulin and three, antihypertensive drugs. Noncompliance with medications was detected in 10%. Three recipients had offspring.

CONCLUSIONS

OLT was an effective treatment with a good quality of life also on long-term follow-up.

Automated characterization of gene expression patterns with an atlas of the mouse brain

A spatio-temporal map of gene activity in the brain would be an important contribution to the understanding of brain development, disease, and function. Such a resource is now possible using high-throughput in situ hybridization, a method for transcriptome-wide acquisition of cellular resolution gene expression patterns in serial tissue sections. However, querying an enormous quantity of image data requires computational methods for describing and organizing gene expression patterns in a consistent manner. In addressing this, we have developed procedures for automated annotation of gene expression patterns in the postnatal mouse brain.

Learning-based segmentation framework for tissue images containing gene expression data

Associating specific gene activity with functional locations in the brain results in a greater understanding of the role of the gene. To perform such an association for the more than 20 000 genes in the mammalian genome, reliable automated methods that characterize the distribution of gene expression in relation to a standard anatomical model are required. In this paper, we propose a new automatic method that results in the segmentation of gene expression images into distinct anatomical regions in which the expression can be quantified and compared with other images. Our contribution is a novel hybrid atlas that utilizes a statistical shape model based on a subdivision mesh, texture differentiation at region boundaries, and features of anatomical landmarks to delineate boundaries of anatomical regions in gene expression images. This atlas, which provides a common coordinate system for internal brain data, is being used to create a searchable database of gene expression patterns in the adult mouse brain. Our framework annotates the images about four times faster and has achieved a median spatial overlap of up to 0.92 compared with expert segmentation in 64 images tested. This tool is intended to help scientists interpret large-scale gene expression patterns more efficiently.

Hybrid segmentation framework for tissue images containing gene expression data

Associating specific gene activity with functional locations in the brain results in a greater understanding of the role of the gene. To perform such an association for the over 20,000 genes in the mammalian genome, reliable automated methods that characterize the distribution of gene expression in relation to a standard anatomical model are required. In this work, we propose a new automatic method that results in the segmentation of gene expression images into distinct anatomical regions in which the expression can be quantified and compared with other images. Our method utilizes shape models from training images, texture differentiation at region boundaries, and features of anatomical landmarks, to deform a subdivision mesh-based atlas to fit gene expression images. The subdivision mesh provides a common coordinate system for internal brain data through which gene expression patterns can be compared across images. The automated large-scale annotation will help scientists interpret gene expression patterns at cellular resolution more efficiently.

Measuring the imaged-object distance with a stationary high-spatial-resolution scintillation camera

A method to measure the detector-to-object distance from the images obtained with stationary high-spatial-resolution gamma-ray cameras for in vivo studies has been developed. It exploits the shift of the imaged object in the image plane, obtained at a certain tilt of the parallel-hole collimator. A linear dependence of the image displacement on the distance to the object has been measured using a high-spatial-resolution scintillation camera employing an yttrium-aluminium perovskite (YAP) scintillator. It is shown that the modified YAP camera can be used to obtain three-dimensional information without moving the camera or the object. The method could be applied in scintimammography and radioguided surgery, in lymphoscintigraphy, as well as in the analysis of the biodistribution of radiopharmaceuticals.

3D volume reconstruction of a mouse brain from histological sections using warp filtering

Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

Performance measurements of a high-spatial-resolution YAP camera

Physical properties of a position-sensitive camera for the analysis of biodistributions of gamma- and beta-emitting radiopharmaceuticals in small animals have been studied, in order to achieve optimal operating conditions. The camera consisted of a highly segmented yttrium-aluminate perovskite (YAP) scintillator, coupled to a position-sensitive photomultiplier. The energy resolution, the detection efficiency, the spatial resolution, the spatial linearity and the count-rate linearity of the YAP camera have been determined. Images related to initial activity levels and successive biodistribution evolution in mice organs are presented as an illustration of the camera performance.

Scalp tumour as a sign of systemic B-cell lymphoma

An 86-year-old man presented with a painful reddish tumour on the scalp with a 3-month history, mental confusion with recent onset and lymphadenopathies. Histological examination of the lymph node and cutaneous lesion revealed a dense infiltrate of atypical and large B cells. There was no evidence of bone marrow invasion. According to REAL (Revised European-American Classification of Lymphoid Neoplasms), this lymphoma was considered as a diffuse large B-cell lymphoma with concurrent cutaneous and nodal involvement. Cerebral computerized tomography (CT) scan showed bone and dura mater invasion in the right parieto-occipital region with collapse of lateral ventricle. The patient was submitted to systemic chemotherapy with cyclophosphamide, vincristine and prednisolone (CVP). There was a good response with regression of the cutaneous lesion, but the patient died after the third cycle. We point out the unusual clinical presentation and aggressive behaviour of this lymphoma.