Computational frameworks integrating deep learning and statistical models in mining multimodal omics data

BACKGROUND

In health research, multimodal omics data analysis is widely used to address important clinical and biological questions. Traditional statistical methods rely on the strong assumptions of distribution. Statistical methods such as testing and differential expression are commonly used in omics analysis. Deep learning, on the other hand, is an advanced computer science technique that is powerful in mining high-dimensional omics data for prediction tasks. Recently, integrative frameworks or methods have been developed for omics studies that combine statistical models and deep learning algorithms.

METHODS AND RESULTS

The aim of these integrative frameworks is to combine the strengths of both statistical methods and deep learning algorithms to improve prediction accuracy while also providing interpretability and explainability. This review report discusses the current state-of-the-art integrative frameworks, their limitations, and potential future directions in survival and time-to-event longitudinal analysis, dimension reduction and clustering, regression and classification, feature selection, and causal and transfer learning.

iNGNN-DTI: prediction of drug-target interaction with interpretable nested graph neural network and pretrained molecule models

MOTIVATION

Drug-target interaction (DTI) prediction aims to identify interactions between drugs and protein targets. Deep learning can automatically learn discriminative features from drug and protein target representations for DTI prediction, but challenges remain, making it an open question. Existing approaches encode drugs and targets into features using deep learning models, but they often lack explanations for underlying interactions. Moreover, limited labeled DTIs in the chemical space can hinder model generalization.

RESULTS

We propose an interpretable nested graph neural network for DTI prediction (iNGNN-DTI) using pre-trained molecule and protein models. The analysis is conducted on graph data representing drugs and targets by using a specific type of nested graph neural network, in which the target graphs are created based on 3D structures using Alphafold2. This architecture is highly expressive in capturing substructures of the graph data. We use a cross-attention module to capture interaction information between the substructures of drugs and targets. To improve feature representations, we integrate features learned by models that are pre-trained on large unlabeled small molecule and protein datasets, respectively. We evaluate our model on three benchmark datasets, and it shows a consistent improvement on all baseline models in all datasets. We also run an experiment with previously unseen drugs or targets in the test set, and our model outperforms all of the baselines. Furthermore, the iNGNN-DTI can provide more insights into the interaction by visualizing the weights learned by the cross-attention module.

AVAILABILITY AND IMPLEMENTATION

The source code of the algorithm is available at https://github.com/syan1992/iNGNN-DTI.

A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data

Motivation

Human microbiome is complex and highly dynamic in nature. Dynamic patterns of the microbiome can capture more information than single point inference as it contains the temporal changes information. However, dynamic information of the human microbiome can be hard to be captured due to the complexity of obtaining the longitudinal data with a large volume of missing data that in conjunction with heterogeneity may provide a challenge for the data analysis.

Results

We propose using an efficient hybrid deep learning architecture convolutional neural network-long short-term memory, which combines with self-knowledge distillation to create highly accurate models to analyze the longitudinal microbiome profiles to predict disease outcomes. Using our proposed models, we analyzed the datasets from Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) study and DIABIMMUNE study. We showed the significant improvement in the area under the receiver operating characteristic curve scores, achieving 0.889 and 0.798 on PROTECT study and DIABIMMUNE study, respectively, compared with state-of-the-art temporal deep learning models. Our findings provide an effective artificial intelligence-based tool to predict disease outcomes using longitudinal microbiome profiles from collected patients.

Availability and implementation

The data and source code can be accessed at https://github.com/darylfung96/UC-disease-TL.

A scoping review of preprocessing methods for unstructured text data to assess data quality

Introduction

Unstructured text data (UTD) are increasingly found in many databases that were never intended to be used for research, including electronic medical record (EMR) databases. Data quality can impact the usefulness of UTD for research. UTD are typically prepared for analysis (i.e., preprocessed) and analyzed using natural language processing (NLP) techniques. Different NLP methods are used to preprocess UTD and may affect data quality.

Objective

Our objective was to systematically document current research and practices about NLP preprocessing methods to describe or improve the quality of UTD, including UTD found in EMR databases.

Methods

A scoping review was undertaken of peer-reviewed studies published between December 2002 and January 2021. Scopus, Web of Science, ProQuest, and EBSCOhost were searched for literature relevant to the study objective. Information extracted from the studies included article characteristics (i.e., year of publication, journal discipline), data characteristics, types of preprocessing methods, and data quality topics. Study data were presented using a narrative synthesis.

Results

A total of 41 articles were included in the scoping review; over 50% were published between 2016 and 2021. Almost 20% of the articles were published in health science journals. Common preprocessing methods included removal of extraneous text elements such as stop words, punctuation, and numbers, word tokenization, and parts of speech tagging. Data quality topics for articles about EMR data included misspelled words, security (i.e., de-identification), word variability, sources of noise, quality of annotations, and ambiguity of abbreviations.

Conclusions

Multiple NLP techniques have been proposed to preprocess UTD, with some differences in techniques applied to EMR data. There are similarities in the data quality dimensions used to characterize structured data and UTD. While a few general-purpose measures of data quality that do not require external data; most of these focus on the measurement of noise.

The effect of disease co-occurrence measurement on multimorbidity networks: a population-based study

Background

Network analysis, a technique for describing relationships, can provide insights into patterns of co-occurring chronic health conditions. The effect that co-occurrence measurement has on disease network structure and resulting inferences has not been well studied. The purpose of the study was to compare structural differences among multimorbidity networks constructed using different co-occurrence measures.

Methods

A retrospective cohort study was conducted using four fiscal years of administrative health data (2015/16 – 2018/19) from the province of Manitoba, Canada (population 1.5 million). Chronic conditions were identified using diagnosis codes from electronic records of physician visits, surgeries, and inpatient hospitalizations, and grouped into categories using the Johns Hopkins Adjusted Clinical Group (ACG) System. Pairwise disease networks were separately constructed using each of seven co-occurrence measures: lift, relative risk, phi, Jaccard, cosine, Kulczynski, and joint prevalence. Centrality analysis was limited to the top 20 central nodes, with degree centrality used to identify potentially influential chronic conditions. Community detection was used to identify disease clusters. Similarities in community structure between networks was measured using the adjusted Rand index (ARI). Network edges were described using disease prevalence categorized as low (< 1%), moderate (1 to < 7%), and high (≥7%). Network complexity was measured using network density and frequencies of nodes and edges.

Results

Relative risk and lift highlighted co-occurrences between pairs of low prevalence health conditions. Kulczynski emphasized relationships between high and low prevalence conditions. Joint prevalence focused on highly-prevalent conditions. Phi, Jaccard, and cosine emphasized associations involving moderately prevalent conditions. Co-occurrence measurement differences significantly affected the number and structure of identified disease clusters. When limiting the number of edges to produce visually interpretable graphs, networks had significant dissimilarity in the percentage of co-occurrence relationships in common, and in their selection of the highest-degree nodes.

Conclusions

Multimorbidity network analyses are sensitive to disease co-occurrence measurement. Co-occurrence measures should be selected considering their intrinsic properties, research objectives, and the health condition prevalence relationships of greatest interest. Researchers should consider conducting sensitivity analyses using different co-occurrence measures.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12874-022-01607-8.

A New Approach for Mining Correlated Frequent Subgraphs

Nowadays graphical datasets are having a vast amount of applications. As a result, graph mining—mining graph datasets to extract frequent subgraphs—has proven to be crucial in numerous aspects. It is important to perform correlation analysis among the subparts (i.e., elements) of the frequent subgraphs generated using graph mining to observe interesting information. However, the majority of existing works focuses on complexities in dealing with graphical structures, and not much work aims to perform correlation analysis. For instance, a previous work realized in this regard, operated with a very naive raw approach to fulfill the objective, but dealt only on a small subset of the problem. Hence, in this article, a new measure is proposed to aid in the analysis for large subgraphs, mined from various types of graph transactions in the dataset. These subgraphs are immense in terms of their structural composition, and thus parallel the entire set of graphs in real-world. A complete framework for discovering the relations among parts of a frequent subgraph is proposed using our new method. Evaluation results show the usefulness and accuracy of the newly defined measure on real-life graphical datasets.

Predictive analytics on open big data for supporting smart transportation services

In the current era of big data, huge quantities of valuable data, which may be of different levels of veracity, are being generated at a rapid rate. Embedded into these big data are implicit, previously unknown and potentially useful information and valuable knowledge that can be discovered by data science solutions, which apply techniques like data mining. There has been a trend that more and more collections of these big data have been made openly available in science, government and non-profit organizations so that people could collaboratively study and analysis these open big data. In this article, we focus on open big data for public transit because public transit (e.g., bus) as a means of transportation is a vital part of many people’s lives. As time is a precious resource, bus delays could negatively affect commuters’ plans. Unfortunately, they are inevitable. Hence, many existing works focused on predicting bus delays. However, predicting on-time or early buses is also important. For instance, commuters who come to a bus stop on time may still miss their buses if the buses leave early. So, in this article, we examine open big data about bus performance (e.g., early, on-time, and late stops). We analyze the data with frequent pattern mining and make predictions with decision-tree based classification. For illustration, we perform predictive analytics on real-life open big data available on Winnipeg Open Data Portal, about bus performance from Winnipeg Transit. It shows the benefits of predictive analytics on open big data for supporting smart transportation services.

Operon-based approach for the inference of rRNA and tRNA evolutionary histories in bacteria

Background

In bacterial genomes, rRNA and tRNA genes are often organized into operons, i.e. segments of closely located genes that share a single promoter and are transcribed as a single unit. Analyzing how these genes and operons evolve can help us understand what are the most common evolutionary events affecting them and give us a better picture of ancestral codon usage and protein synthesis.

Results

We introduce BOPAL, a new approach for the inference of evolutionary histories of rRNA and tRNA genes in bacteria, which is based on the identification of orthologous operons. Since operons can move around in the genome but are rarely transformed (e.g. rarely broken into different parts), this approach allows for a better inference of orthologous genes in genomes that have been affected by many rearrangements, which in turn helps with the inference of more realistic evolutionary scenarios and ancestors.

Conclusions

From our comparisons of BOPAL with other gene order alignment programs using simulated data, we have found that BOPAL infers evolutionary events and ancestral gene orders more accurately than other methods based on alignments. An analysis of 12 Bacillus genomes also showed that BOPAL performs just as well as other programs at building ancestral histories in a minimal amount of events.

Evolution of the haemagglutinin gene of the influenza A(H1N1)2009 virus isolated in Hong Kong, 2009–2011

Phylogenetic analysis of the haemagglutinin (HA) gene shows that the influenza A(H1N1)2009 viruses collected in Hong Kong clustered in two main branches characterised by the E391E and E391K amino acids. The main branch E391K evolved in two sub-branches with N142D and S202T mutations that first appeared in March and July 2010, respectively, with the latter becoming the predominant strain. These genetic variants that emerged display similar antigenic characteristics. Concurrent with genetic surveillance, laboratories should continue monitoring the circulating viruses antigenically.

Evolution of the haemagglutinin gene of the influenza A(H1N1)2009 virus isolated in Hong Kong, 2009-2011

Phylogenetic analysis of the haemagglutinin (HA) gene shows that the influenza A(H1N1)2009 viruses collected in Hong Kong clustered in two main branches characterised by the E391E and E391K amino acids. The main branch E391K evolved in two sub-branches with N142D and S202T mutations that first appeared in March and July 2010, respectively, with the latter becoming the predominant strain. These genetic variants that emerged display similar antigenic characteristics.Concurrent with genetic surveillance, laboratories should continue monitoring the circulating viruses antigenically.

Assessment of rates of structural change in glaucoma using imaging technologies

PURPOSE

To review the ability of current imaging technologies to provide estimates of rates of structural change in glaucoma patients.

PATIENTS AND METHODS

Review of literature.

RESULTS

Imaging technologies, such as confocal scanning laser ophthalmoscopy (CSLO), scanning laser polarimetry (SLP), and optical coherence tomography (OCT), provide quantifiable and reproducible measurements of the optic disc and parapapillary retinal nerve fibre layer (RNFL). Rates of change as quantified by the rim area (RA) (for CSLO) and RNFL thickness (for SLP and OCT) are related to glaucoma progression as detected by conventional methods (eg, visual fields and optic disc photography). Evidence shows that rates of RNFL and RA loss are significantly faster in progressing compared with non-progressing glaucoma patients.

CONCLUSION

Measurements of rates of optic disc and RNFL change are becoming increasingly precise and individualized. Currently available imaging technologies have the ability to detect and quantify progression in glaucoma, and their measurements may be suitable end points in glaucoma clinical trials.

Comparisons of anterior segment biometry between Chinese and Caucasians using anterior segment optical coherence tomography

PURPOSE

To compare anterior segment parameters between eyes of Chinese and Caucasians using anterior segment optical coherence tomography and to evaluate the association between these parameters and anterior chamber angle width between the two ethnic groups.

METHODS

60 Chinese and 60 Caucasians, 30 with open angles and 30 with narrow angles (defined as Shaffer grade < or =2 in > or =3 quadrants during dark room gonioscopy) in each group, were consecutively enrolled. One eye of each subject was randomly selected for imaging in a completely darkened room. Measurements, including anterior chamber depth (ACD), scleral spur-to-scleral spur distance (anterior chamber width (ACW)), anterior chamber angle width, iris convexity and iris thickness, were compared between the groups. The associations between angle opening distance and biometric measurements were evaluated with univariate and multivariate regression analyses.

RESULTS

There were no differences in age, axial length, anterior chamber angle measurements, pupil diameter and iris convexity between Chinese and Caucasians in both open-angle and narrow-angle groups. However, the ACD and ACW were smaller and the iris was thicker in Chinese. In the multivariate analysis, the ACD was the most influential biometric parameter for angle opening distance in both Chinese and Caucasians. After adjusting the effects of axial length, age and sex, ACD and ACW were significantly smaller in Chinese.

CONCLUSIONS

Chinese eyes had smaller ACD, smaller ACW and greater iris thickness than Caucasians. ACD was the most influential parameter in determining the angle width in both ethnic groups.

Intermittency of velocity fluctuations in turbulent thermal convection

We analyze velocity fluctuations in turbulent Rayleigh-Bénard convection. The velocity measurements were taken at the center of an aspect-ratio-one convection cell filled with water. The measured probability density functions of the velocity difference over a time interval tau are found to change with tau, indicating that the velocity fluctuations are intermittent. The velocity intermittency can be well characterized by the She-Leveque hierarchical structure. Our analyses further show that the vertical velocity component has distinct statistical features from the horizontal components. This result indicates that the vertical direction is special and buoyancy is important even at the center of the convection cell.

Removal and recovery of copper (II) ions by bacterial biosorption

Studies were conducted to investigate the removal and recovery of copper (II) ions from aqueous solutions by Micrococcus sp., which was isolated from a local activated sludge process. The equilibrium of copper biosorption followed the Langmuir isotherm model very well with a maximum biosorption capacity (q(max)) of 36.5 mg of Cu2+/g of dry cell at pH 5.0 and 52.1 mg of Cu2+/g of dry cell at pH 6.0. Cells harvested at exponential growth phase and stationary phase showed similar biosorption characteristics for copper. Copper uptake by cells was negligible at pH 2.0 and then increased rapidly with increasing pH until 6.0. In multimetal systems, Micrococcus sp. exhibited a preferential biosorption order: Cu approximate to Pb > Ni approximate to Zn. There is virtually no interference with copper uptake by Micrococcus sp. from solutions bearing high concentrations of Cl-, SO4(2-), and NO3- (0-500 mg/L). Sulfuric acid (0.05 M) was the most efficient desorption medium, recovering >90% of the initial copper sorbed. The copper capacity of Micrococcus sp. remained unchanged after five successive sorption and desorption cycles. Immobilization of Micrococcus sp. in 2% calcium alginate and 10% polyacrylamide gel beads increased copper uptake by 61%. Biomass of Micrococcus sp. may be applicable to the development of potentially cost-effective biosorbent for removing and recovering copper from effluents.

Effects of heavy metals on the survival and feeding behaviour of the sandy shore scavenging gastropod Nassarius festivus (Powys)

The effects of Cu, Cd, Zn and Cr on the survival and feeding behaviour of the sandy shore scavenging gastropod Nassarius festivus were compared. The 96-h LC50 for Cu, Cd, Zn and Cr were 0.36, 1.52, 1.76 and 36.9 mg l(-1), respectively. Four sublethal concentrations of each metal plus a control were prepared and the snails were exposed to experimental solutions for 96 h. Feeding behaviour was studied after the snails were starved for five days. As compared with the control, the number of individuals feeding was significantly reduced by exposure to 0.05 mg l(-1) Cu, 0.2 mg l(-1) Zn, 0.5 mg l(-1) Cd and 5 mg l(-1) Cr. The time spent feeding was greater for individuals exposed to greater concentrations of Zn and Cd but no effect was found for Cu and Cr. Chemoreception of food was studied by placing the snails at a fixed distance of 15 cm from the bait. The success rate of reaching the bait was less for individuals exposed to Cr but no effect was found for Zn, Cu or Cd. The time required for an individual to reach the bait decreased as the concentration of Zn increased. In contrast, a longer time was required for individuals exposed to Cr whereas the effect of Cd and Cu was insignificant. The potential of using feeding behaviour and chemoreception in contaminant evaluations is discussed.

Recent advances in clinical aspects of in vitro fertilisation

While early success rates using in vitro fertilisation ranged from 10% to 15%, improved technology has more than doubled that rate, owing to the availability of recombinant follicle-stimulating hormone, improved ovarian stimulation protocols, and assisted fertilisation technology. This latter technology has already revolutionised the management of male-factor infertility. The future goal is to further increase the overall pregnancy rate and to reduce the risk of multiple gestation by using pre-implantation genetic diagnosis and blastocyst transfer.

Serum pharmacokinetics of antimycobacterial drugs in patients with multidrug-resistant tuberculosis during therapy

Serum samples of 13 patients with multidrug-resistant tuberculosis were taken 0, 1, 2, 4, 8 h after administration of antimycobacterial drugs for assay of levels in order to gain further insight into their basic pharmacokinetics. The drugs assessed were amikacin, kanamycin, ofloxacin, levofloxacin, para-aminosalicylic acid, prothionamide, cycloserine, pyrazinamide and ethambutol. Techniques used for assay were reversephase high-performance liquid chromatography, gas liquid chromatography and fluorescent polarization immunoassay. The results from 12 patients were evaluated. These provided new pharmacokinetic data on high-dose levofloxacin, cycloserine and prothionamide given once daily, and could be useful in guiding the scheduling of drugs. The data obtained might also lead to insights into the development of therapeutic drug monitoring in multidrug-resistant tuberculosis.

Troponin-I, myoglobin, and mass concentration of creatine kinase-MB in acute myocardial infarction

Myoglobin, creatine kinase-MB (CKMB) mass concentration and troponin-I are newer biochemical markers for the diagnosis of acute myocardial infarction (AMI). We conducted a prospective study to formulate a model for the collective interpretation of these three markers in the diagnosis of AMI. Eighty-seven patients with AMI had serial serum samples taken to establish the time-frame sensitivity of individual markers. None of the markers had a good sensitivity within the first 4 h of infarction. Myoglobin and CKMB (mass) had sensitivities of 92.3% and 96.2%, respectively, at 4-8 h post infarct. CKMB (mass) and troponin-I had sensitivities >92% at 8-24 h. Troponin-I maintained sensitivity >93% until 72 h. A guideline was formulated based on the results. Our data suggest that troponin-I, myoglobin and CKMB (mass) yield satisfactory diagnostic sensitivity when used with reference to specific time frames. The combined use of these markers can provide valuable information for clinicians in managing AMI patients.

Is inhaled corticosteroid useful as adjunctive management in tuberculous pyrexia?

Systemic corticosteroid is currently the standard adjunctive therapy for tuberculous pyrexia. A preliminary prospective open study to examine the efficacy of inhaled budesonide at a dose of 2,400 micrograms daily in the management of this condition was performed. Out of nine non-HIV infected patients with tuberculous pyrexia studied, four patients succeeded to achieve defervescence at a mean of 3.25 days (range = 2 to 5 days), while the rest of the patients failed to do so within 7 days. None of the patients had unwanted side effects of systemic corticosteroid and patients' acceptance of such therapy was high. The potential usefulness of inhaled corticosteroid in some patients with tuberculous pyrexia might warrant further evaluation.

Hong Kong male subfertility links to mercury in human hair and fish

The focus of the present study was on the relationship between Hong Kong male subfertility and fish consumption. Mercury concentrations found in the hair of 159 Hong Kong males aged 25-72 (mean age = 37 years) was positively correlated with age and was significantly higher in Hong Kong subjects than in European and Finnish subjects (1.2 and 2.1 ppm, respectively). Mercury in the hair of 117 subfertile Hong Kong males (4.5 ppm, P < 0.05) was significantly higher than mercury levels found in hair collected from 42 fertile Hong Kong males (3.9 ppm). Subfertile males had approx. 40% more mercury in their hair than fertile males of similar age. Although there were only 35 female subjects, they had significantly lower levels of hair mercury than males in similar age groups. Overall, males had mercury levels that were 60% higher than females. Hair samples collected from 16 vegetarians living in Hong Kong (vegans that had consumed no fish, shellfish or meat for at least the last 5 years) had very low levels of mercury. Their mean hair mercury concentration was only 0.38 ppm.

Differential expression of pre- and postsynaptic GABA(B) receptors in rat substantia nigra pars reticulata neurones

Whole-cell recordings were made from substantia nigra pars reticulata in rat midbrain slices to study the functional expression of pre- and postsynaptic GABA(B) receptors in GABA output neurones. Baclofen (up to 300 microM) dose-dependently activated a weak current which was insensitive to tetrodotoxin and Ca2+-free solution but blocked by Ba2+ and 2-OH-saclofen. The maximum current activated by baclofen (30 microM) was 43.0 +/- 4.5 pA (n = 27), representing only 23% of that in dopamine neurones. Baclofen (1-30 microM) also reduced the frequency of the GABA(A) receptor-mediated miniature inhibitory postsynaptic currents while the distribution of their amplitudes was unaffected. This presynaptic effect of baclofen, prominent at a concentration as low as 1 microM, was sensitive to 2-OH-saclofen and occluded by Cd2+, but was unaffected by Ba2+. The results suggest a predominant role of the presynaptic GABA(B) receptors in substantia nigra pars reticulata. The relative abundance of pre- and postsynaptic GABA(B) receptor subtypes in this brain region may also be important in mediating the anticonvulsant effect of baclofen in rats.

Fifteen years' review of advanced childhood neuroblastoma from a single institution in Hong Kong

OBJECTIVE

To assess the progress in the treatment of advanced childhood neuroblastoma.

METHODS

From 1981 to 1996, there were 32 children with neuroblastoma (NB) diagnosed, staged and treated in our institution. There were 4 patients with stage II NB (12%), 5 stage III (16%), 21 stage IV (66%) and 2 stage IV s (6%). The NBs were excised if CT scan indicated that the tumors were operable. For advanced NB, stages III and IV, multiple drug chemotherapy was started first and operability was assessed with serial CT scan examinations. Once the X-ray imaging indicated the tumors were operable, surgical interventions were done. The medical records of the advanced NB were reviewed.

RESULTS

In the initial period of the study, 9 patients were treated using the VAC protocol [vincristine (vcr), adriamycin (adria) and cyclophosphamide (cyc)]. No patient was convertible to operable and all died with a mean survival of 10 months. OPEC [vcr, cyc, VM26, cisplatin (cis)], Rapid COJEC (carboplatin, VP16, vcr, cis and cyc) and more recently N6 protocol (cyc, adria, vcr, VP16, cis) was used for 17 patients. 80% of them were converted to operable. In 4 patients, surgical specimens showed only necrotic tissue without viable tumor tissue and 6 (35%) tumors were converted to ganglioneuroma or ganglioneuroblastoma. Although 2 (12%) patients died of fungal septicemia and 1 (6%) developed Fanconi's syndrome after chemotherapy, the mean survival period increased to 27 months. In the 10 survivors (60%), 4 had megatherapy with melphalan followed by autologous peripheral blood stem cell (PBSC) transplantation and 2 were waiting for transplantation.

CONCLUSIONS

There is a high percentage of advanced NB on presentation in Hong Kong. With more potent multiple drug chemotherapy for advanced stage NB there are (1) improvement in the survival of these patients, (2) opportunities for more operations for tumor excision and (3) opportunities for autologous PBSC transplantation for better tumor eradication.

Pre-synaptic effect of the ATP-sensitive potassium channel opener diazoxide on rat substantia nigra pars reticulata neurons

Spontaneous synaptic currents were recorded from visually identified substantia nigra pars reticulata (SNR) neurons in the rat brain slice preparation by whole-cell patch clamp technique. GABA neurons were distinguished from dopamine neurons by their electrophysiological characteristics. In the presence of 20 microM AP5 and CNQX, the spontaneous synaptic currents recorded from GABA neurons were sensitive to bicuculline and reversed polarity at a potential close to the equilibrium potential of Cl-, indicating that they were mediated by GABA(A) receptors. TTX at 1 microM eliminated action potential-dependent release of GABA from nerve terminals, revealing the miniature inhibitory post-synaptic currents (mIPSCs). The ATP-sensitive potassium channel (K(ATP) channel) opener diazoxide (30-300 microM) significantly reduced the frequency of the mIPSCs in a dose-dependent manner. However, diazoxide did not affect the average value and the distribution of the mIPSC amplitudes. Thus, this effect of diazoxide was pre-synaptic in nature. The K(ATP) channel blocker glibenclamide (300 microM) was able to restore the frequency of the mIPSCs. These data suggest that the striatonigral projection, which represents the major inhibitory input controlling SNR GABA neuron activities, possesses presynaptic K(ATP) channels on the nerve terminals.

Sulphonylureas reverse hypoxia induced K(+)-conductance increase in substantia nigra pars reticulata neurones

Membrane potentials were recorded from neuronal somata in the substantia nigra pars reticulata of the rat midbrain slice using the whole-cell patch-clamp technique. Hypoxia induced a consistent decrease in input resistance often accompanied by membrane hyperpolarization and cessation of firing. The membrane hyperpolarization was mediated by K+ as indicated by its reversal potential at -88 +/- 9 mV, which is close to the equilibrium potential of K+. The hypoxic response was not sensitive to 1 microM tetrodotoxin or superfusion with Ca2(+)-free medium. While glibenclamide at 30 microM and tolbutamide at 300 microM had no effect on the resting membrane properties of the neurones, these sulphonylureas reversed the hypoxia-induced membrane hyperpolarization and restored firing. Inclusion of 2 mM of ATP in the recording pipette also prevented the hyperpolarization. These observations suggest that post-synaptic ATP-sensitive potassium channels exist on the GABA neurones of SNR and that these channels are activated in energy-depleting conditions exemplified by hypoxia.

Cisplatin neuropathy: a prospective clinical and electrophysiological study in Chinese patients with ovarian carcinoma

Nineteen Chinese patients with stage III or IV epithelial ovarian carcinoma by the criteria established by the International Federation of Gynaecology and Obstetrics, treated with cisplatin, 120 mg/m2, every 4 weeks for a maximum of twelve courses if possible, were studied prospectively with clinical and electrophysiological evaluation before and 3, 6, 9 and 12 months during cisplatin administration. Neuropathy occurred in 12 of the 19 patients at the cumulative dose of 360 mg/m2. Up to 89% of the patients assessed in their final examination developed neuropathy. Decreased vibration sensation at the ankles and depressed ankle reflexes were the early manifestations. Electrophysiological findings consisted of low amplitude sensory action potentials of median, ulnar and sural nerves, and slowing of their sensory nerve conduction velocities. Despite substantial involvement of sensory nerves, there was little change in motor nerve conduction velocities or motor unit action potentials. The progression of the neuropathy was unpredictable and could be delayed. As cisplatin is highly effective in the treatment of the tumour which is invariably fatal, if inadequately treated, patient selection with regard to neurotoxicity is unnecessary.

Association between human in vitro fertilization rate and pregnancy outcome: a possible involvement of spermatozoal quality in subsequent embryonic viability

A conventional view of mammalian fertilization is that the active component of the process: the spermatozoon, by virtue of its progressive motility and acrosomal enzymes, penetrates an otherwise passive oocyte. This concept has placed bias on spermatozoal normality as largely determining the outcome of fertilization; once this has been achieved then the contribution of the spermatozoon is often forgotten, and attention switches to the maternally derived "blue-print" for early embryonic development. Paternal genomic contribution is known to start at the eight-cell stage in the human, but this is usually after the time when early cleavage stage (2 to 8-cell stage) embryos are replaced in human assisted reproductive technologies (ART) procedures such as in vitro fertilization and embryo transfer (IVF-ET). Hence, fundamental abnormal contributions to embryogenesis derived from the fertilizing spermatozoon have often been ignored. Human IVF-ET has permitted far greater powers of analysis of the fertilization event, and fertilization success appears to be determined in such a system by three main factors: spermatozoal quality, oocyte quality, and quality of in vitro culture conditions (the gamete environment). If the second two factors are more carefully controlled than the first, as is the usual emphasis in routine human IVF practice, then any large variation in fertilization rates that are also significantly related to embryonic viability and ultimately pregnancy outcome, may be thought to be more directly associated with original quality of the fertilizing spermatozoon. An analysis of results of 758 IVF cases provides preliminary evidence to show that there is a close association between human in vitro fertilization rate and subsequent embryo viability following replacement. In accepting this hypothesis as a possibility, we should drastically change our attitude from one of the spermatozoon as a robust, simple initiator of embryonic development, and embrace the idea of the vulnerability of such germ cells both during and after their production, and how detrimental influences on this might profoundly affect embryogenesis after successful fertilization.

Routine intrauterine insemination and the effect of spermatozoal washing as assessed by computer-assisted semen analyzer

We present the results from 283 cycles of intrauterine insemination (IUI) performed on 237 patients. Their indications for treatment included cervical factor infertility, spermatozoal antibodies, idiopathy, poor postcoital test, and oligozoospermia. Pregnancies arose in all groups, with 28 pregnancies from natural cycles, and 17 from clomiphene citrate-supplemented cycles. A live birth rate per cycle of 12.7% (36/283) was achieved following nine miscarriages. A further 133 patients, with only cervical factor or idiopathic infertility, underwent 144 cycles of IUI in natural cycles; this more homogeneous group had their spermatozoal performance monitored by a computer-assisted semen analyzer (CASA) before and after spermatozoal washing for IUI. All factors in the spermatozoal profile changed significantly after washing. Twelve clinical pregnancies resulted from these 144 cycles of IUI, and a comparison was made between the spermatozoal profiles, as assessed by CASA, of conceptual and nonconceptual cycles. Post-wash spermatozoal concentration was slightly greater (P less than .1) in the conceptual cycles, whilst spermatozoal velocity was significantly less (P less than .005). The relevance of these findings to the definition of a "hyperactivational" state for human spermatozoa is discussed, and the general applicability of IUI as a "frontline" treatment for nontubal infertility is proposed.

The diagnostic value of seminal adenosine triphosphate (ATP) in an in vitro fertilization (IVF) program

The level of adenosine triphosphate (ATP) was quantitated in semen samples used for in vitro fertilization of human oocytes. Seminal ATP level correlated with the concentration and percentage motility of spermatozoa but not with the in vitro fertilization rate of human oocytes. Seminal ATP measurement appears to have little diagnostic value in predicting the fertilizing capacity of spermatozoa as evaluated by the multivariate stepwise discriminant analysis.

Successful pregnancies resulting from the use of prolonged-incubation human spermatozoa in gamete intrafallopian transfer

Human spermatozoa that were incubated overnight at room temperature before intrafallopian transfer with freshly collected oocytes gave rise to successful pregnancies and normal live births. The resulting pregnancy rate per transfer of 50% (4 of 8) compared favorably with the average pregnancy rate of 41.8% (38 of 91), achieved by our standard spermatozoal preparation procedure that prepared the spermatozoa approximately 2 hours before the GIFT operation. This new approach for the preparation of human spermatozoa would be applicable to oligospermic patients and some GIFT patients whose partners may have difficulties in producing a semen specimen immediately before the GIFT operation.

The hypoosmotic swelling test and cryosurvival of human spermatozoa

The hypoosmotic swelling test is a simple laboratory test to evaluate the functional integrity of the membrane of human spermatozoa. This test was performed on 83 samples of human semen before cryopreservation to determine whether it has any predictive value for the cryosurvival of human spermatozoa. Stepwise regression analysis demonstrated that conventional sperm characteristics, including the concentration, motility, normal morphology and viability, of pre-freeze semen samples were of limited value in predicting the cryosurvival of human spermatozoa. Further, the hypoosmotic swelling test results from pre-freeze semen samples did not correlate with the post-thaw motility or the survival rate of spermatozoa after cryopreservation.

Intrauterine insemination as front-line treatment for non-tubal infertility

Eighty-one clinical pregnancies occurred from 508 cycles of intrauterine insemination (IUI) in 242 patients. Following 20 miscarriages 30 pregnancies have been delivered, and 31 remain ongoing at 16 weeks and beyond. This represents a 12% delivered/ongoing pregnancy outcome per cycle of IUI, in women of average age 30.9 years who with their partners had suffered on average 3.65 years of infertility. All forms of non-tubal infertility were treated with pregnancies occurring in all primary categories. No pregnancies occurred in 5 women who underwent IUI in 18 natural cycles. All pregnancies arose in the 237 women who received clomiphene citrate, human menopausal gonadotropin, or a combination of both with ovulation triggered by human chorionic gonadotropin. Dependent upon patient age and duration of infertility, we implement IUI as a frontline treatment for all cases of non-tubal infertility prior to subjecting patients to the more costly and invasive tubal transfer techniques.

Pancreatic cholesterol esterases. 1. Pancreatic cholesterol esterase induction during maturation

The activities of pancreatic cholesterol esterase from calf and cow pancreas were examined in detail. A 1300-fold enhancement of enzymatic activity was found after maturation, even though cholesterol esterase activity levels in other organs did not change from the juvenile to the adult species. Radioimmunoassays also showed that the calf pancreas contained at least 100-fold less cholesterol esterase protein. Decreased amounts of protein were not due to enhanced proteolysis, since cytosol from cow pancreas degrades exogenously added cholesterol esterase faster than that from calf pancreas. Rather, enhancement of pancreatic cholesterol esterase activity associated with bovine maturation was the result of specific, increased synthesis of a 72-kDa enzyme. This labile 72-kDa cholesterol esterase species was purified to homogeneity by a two-step process in 75% yield and is the major form of bovine pancreatic cholesterol esterase (99%). A much less abundant 67-kDa species, accounting for less than 1% of total pancreatic cholesterol esterase activity, was also purified to homogeneity in a similar two-step process. These results demonstrate that a specific form of pancreatic cholesterol esterase is induced during maturation, and they bear importantly on understanding juvenile cholesterol metabolism as related to dietary absorption of this sterol.

Effects of dibutyryl cyclic guanosine monophosphate on human spermatozoal motility and penetration of zona-free hamster oocytes

The possible effects of N2,2'-O-dibutyryl 3'-5'-cyclic guanosine monophosphate (dbcGMP), imidazole (IM) or their combination on human spermatozoal motility and penetration of zona-free hamster oocytes were investigated. Motility of human spermatozoa was assessed at 0, 0.5, 2, 3, 5 and 8 h over an 8-h incubation period with various concentrations of dbcGMP, IM or dbcGMP plus IM. Both percentage motile spermatozoa and progression of human spermatozoa decreased with increasing concentrations of dbcGMP (12-96 mM) and IM (10-80 mM). This inhibitory effect on motility was more pronounced when dbcGMP was added with IM. For assessment of human spermatozoal penetration into zona-free hamster oocytes, spermatozoa were treated for 30 min with either dbcGMP, IM or both after 5 h of capacitation pre-incubation at 37 degrees C. Alternatively, the compounds were only added during the capacitation preincubation period. At concentrations of dbcGMP less than or equal to 24 mM, neither of the treatments had a significant effect on the penetration rate of zona-free hamster oocytes in comparison with the controls. However, a higher concentration of dbcGMP (48 mM) inhibited the penetration rate. A similar trend was observed when dbcGMP plus IM were added. IM alone had no significant effect on the penetration rate at the concentrations tested (10-40 mM). Our data indicated an inhibitory effect of dbcGMP on both human spermatozoal motility and penetration into zona-free hamster oocytes.

Post-operative artificial insemination--does it improve GIFT outcome?

Based on a retrospective study of our gamete intra-Fallopian transfer (GIFT) programme we have analysed 102 cycles where a standard GIFT procedure was implemented and 92 cycles where a post-operative intrauterine and intracervical insemination (post-operative IUI/ICI) was performed, in addition to GIFT. Our comparison suggests that the pregnancy outcome has been significantly improved (P less than 0.05) by this additional post-operative IUI/ICI. The standard GIFT group (102 cycles) yielded 38 clinical pregnancies and, ultimately, 29 delivered pregnancies (37.2/28.4%), whilst the post-operative IUI/ICI group (92 cycles) gave 48 clinical pregnancies initially and, currently, 38 pregnancies are ongoing or delivered (52.2/41.3%). The possible implications of the 'normal' presence of spermatozoa in the human female tract as an explanation for this improvement is discussed, and the adoption of IUI/ICI after GIFT is proposed, following a prospective controlled study.

The use of human follicular fluid in gamete intra-fallopian transfer

We undertook a prospective study to compare our gamete intra-Fallopian transfer (GIFT) procedure with or without the use of human follicular fluid (FF) as a constituent for the final spermatozoal suspension and as the tubal transfer medium for both eggs and spermatozoa. We routinely perform an intrauterine and intracervical insemination (IUI and ICI) following GIFT, and FF or culture medium was used accordingly as a constituent in this spermatozoal suspension also. When FF was used (26 cycles), clear FF taken from the first egg-bearing follicle was sterilized by micropore filtration, gassed with 5% CO2 in air and warmed to 37 degrees C. This FF was then used to dilute the spermatozoal suspension (50:50, v/v) for both tubal, uterine and cervical inseminations at least 30 min before transfer, and all transferable eggs were placed into this FF before transfer. Alternatively (30 control cycles), eggs and spermatozoa were prepared and transferred in Earle's medium supplemented with 10% pooled fetal cord serum. The FF and control patient groups were relatively homogeneous, with no statistically significant differences in ovarian response, oocyte retrieval or transfer or seminal profiles. The outcome of the GIFT procedures using FF or culture medium showed no significant advantage of the use of FF. The clinical pregnancy rate was similar in both groups: 50% (15/30) control; 46.2% (12/26) FF.

Routine gamete intrafallopian transfer (GIFT): a highly successful option for treatment of non-tubal infertility

Gamete intrafallopian transfer (GIFT) is increasingly accepted as a realistic alternative to in vitro fertilization (IVF), or intrauterine insemination (IUI) for treatment of non-tubal infertility. The lack of information on fertilization capacity of the gametes, the greater cost relative to IUI, and the partly unsubstantiated claims of higher success rates, caused us some concern with the readiness with which GIFT had been accepted as a standard infertility treatment. So we undertook a provisional GIFT programme with these considerations in mind, and we report on the first 91 GIFT cycles performed in our clinic. Sixty of the patients (62 cycles) treated suffered from idiopathic infertility, 12 from minimal endometriosis, 9 from male factor infertility, and 8 from ovulatory dysfunction. An initial clinical pregnancy rate of 41% (38/91) was achieved; pregnancy loss was 23% (9/38), giving a continuing pregnancy rate of 32% (29/91). Given this undeniably encouraging result, and the potential for diagnostic IVF, embryo freezing, and ovum donation with surplus oocytes collected from this GIFT programme, we now have adopted GIFT permanently as a treatment to complement our IVF and IUI programmes.

Fallopian replacement of eggs with delayed intrauterine insemination (FREDI): an alternative to gamete intrafallopian transfer (GIFT)

This report contains details of what is the first group of patients with nontubal infertility to undergo fallopian replacement of eggs with delayed intrauterine insemination (FREDI). Twenty-three patients suffering from idiopathic or immune infertility, polycystic ovarian disease (PCOD), or mild endometriosis underwent follicular stimulation with human menopausal gonadotropin and/or pure follicle-stimulating hormone plus human chorionic gonadotropin prior to laparoscopic pickup of eggs of varying maturity. Eggs without spermatozoa were transferred at the time of laparoscopy. Subsequent high intrauterine insemination (IUI) of washed spermatozoa at a time when egg maturation within the tubes was judged to be complete enabled a cohort of fully capacitated spermatozoa to meet fully mature eggs in a totally physiological manner. Eight clinical pregnancies arose from this group, one healthy, male infant has been delivered, and four pregnancies remain ongoing. Although based on a small population of patients, it does seem that in vivo egg maturation following replacement in the fallopian tube is an effective alternative to in vitro maturation and, with the increased control over timing of egg insemination, leads us to propose FREDI as a flexible new therapeutic approach for the treatment of nontubal infertility.

Pregnancies from fallopian replacement of immature eggs with delayed intrauterine insemination

Gamete intrafallopian transfer requires that a woman should not only have patent tubes but should also have had mature eggs collected for replacement. Eggs must be collected as close to ovulation as possible, to give them a good chance of fertilizing upon replacing them directly into the tubes with the spermatozoa. Preliminary results from three patients who received Fallopian replacement of immature eggs followed by delayed intrauterine insemination indicate that maturation of eggs can occur in vivo in the Fallopian tubes. Intrauterine insemination at a later time when the eggs were judged to be mature has given rise to two pregnancies from the three patients with whom this procedure was adopted.

Comparative study of combined GIFT and IVF-ET with GIFT alone

Twenty-eight couples with unexplained infertility, or with suboptimal spermatozoa were divided into two groups. One group underwent gamete intra-Fallopian transfer (GIFT), and the other had combined GIFT and in-vitro fertilization--embryo transfer (IVF-ET) (GET). There was a marked difference in pregnancy rates between the two groups, with the pregnancy rate surprisingly being less in the combined GET group; 10% for GET, as compared with 39% for GIFT alone. The results suggest that GIFT and IVF-ET are incompatible. Differences in the pregnancy rates may be explained by limitations in implantation, whereby the embryo-endometrium interaction that allows for implantation and continued embryonic development has a 'single event capacity', and once this interaction is initiated, the 'implantation window' is closed to other embryos that may arrive later in the uterus.

Intrinsic and extrinsic factors in estrogen action in human breast cancer: role of polyamines and pituitary factors

Although polyamines are important in regulating proliferation of mammalian cells, their role in hormone induction of cell growth has not been delineated. In the estradiol-responsive human breast cancer cell line, T-47D clone 11, estradiol (10(-10) M) was able to stimulate cell proliferation and the activity of ornithine decarboxylase (ODC), the first and rate-limiting enzyme in the biosynthesis of polyamines. alpha-Difluoromethylornithine (DFMO), a specific inhibitor of ODC, blocked the estradiol-induced cell proliferation and ODC activity. Exogenous addition of putrescine, the natural product of ODC, rescued the inhibitory effect of DFMO. In addition, DFMO abolished the estradiol-induced growth of several other estrogen-responsive human breast cancer cell lines but did not affect the growth of hormone-independent cell lines. Further, a serum factor was found to be required for estradiol to exert its effect. To gain insight into the nature of this and possibly other extrinsic factors involved, the effect of estradiol on the proliferation of T-47D cells transplanted into athymic nude mouse was evaluated. In this in vivo system, estradiol alone produced only moderate growth of the human breast tumor. The simultaneous transplantation of a prolactin (PRL)- and growth hormone (GH)-secreting rat pituitary tumor or normal rat pituitary glands at a different site dramatically potentiated the effect of estradiol on the growth of the breast tumor xenograft. Purified PRL or GH were without effect, indicating that the active pituitary factor is neither PRL nor GH. Further, conditioned medium from rat pituitary tumor cells potentiated the mitogenic effect of estradiol on T-47D and several other estrogen receptor-positive human breast cancer cell lines in vitro under serum-free condition. In conclusion, we have identified both intrinsic (polyamines) and extrinsic (pituitary/serum) factors that are importance for estrogen to exert its mitogenic action. The next goal will be to elucidate the mechanisms of action of these molecules in the modulation of estrogen action.

Evidence for a novel pituitary factor that potentiates the mitogenic effect of estrogen in human breast cancer cells

Estrogen, prolactin, and other tissue-derived factors are implicated in the etiology and pathophysiology of human breast cancer (HBC). In a previous study, we demonstrated that a factor(s) secreted by rat pituitary tumor cells (GH3) synergizes with estrogen to induce growth of HBC cells (T-47D) transplanted into athymic nude mice. The present studies were carried out to characterize further this pituitary growth factor. Pituitary tumor cell lines (GH3, GH1, 235-1, and AtT-20) and normal rat pituitaries were transplanted s.c. into estrogen-treated (estradiol valerate injection, 500 micrograms/14 days) athymic nude mice which also received T-47D cells. The influence of the presence of these normal and tumorous pituitary cells on growth (size and weight) of T-47D tumors was monitored for 49 to 56 days. The results indicate that factor(s) from normal rat pituitary glands as well as from the GH1 and GH3 but not 235-1 and AtT-20 pituitary tumor cells were able to potentiate the growth of T-47D tumors in estrogenized mice. To ascertain whether or not prolactin and/or growth hormone are responsible for the growth-promoting activity, purified human and ovine growth hormone and ovine prolactin were administered to estrogenized athymic nude mice either by daily s.c. injection (100 micrograms/day) or by constant infusion using Alzat osmotic minipumps (1.25 and 5.0 micrograms/h) for 29 to 56 days. None of these treatments stimulated the growth of the T-47D tumors, suggesting that prolactin, growth hormone, and their intermediates may not be directly involved. We further determined whether the factor from pituitary tumor cells was present in serum-free conditioned medium and could stimulate the growth of HBC cells in vitro. Conditioned medium from GH3 and GH1 but not from 235-1 and AtT-20 pituitary cells significantly stimulated growth of T-47D cells in the presence of estradiol (10(-10) M) after 12 days of culture in a serum-free medium (Dulbecco's modified Eagle's medium containing bovine serum albumin, 0.5 mg/ml). Optimal serum-free growth of T-47D cells (2-fold above control) was observed in the presence of estradiol (10(-10) M) and conditioned medium (30% v/v) from 48-h cultures of GH3 cells. The bovine serum albumin concentration of the serum-free medium (Dulbecco's modified Eagle's medium) was also important: optimal T-47D cell proliferation was observed with BSA between 0.5 and 2.0 mg/ml. Conditioned medium preparations from serum-pretreated flasks (without cells) from GH3 cell monolayers for zero time and from actinomycin D plus cycloheximide-inhibited GH3 cells were inactive.(ABSTRACT TRUNCATED AT 400 WORDS)

Epidermal growth factor receptors and effect of epidermal growth factor on growth of human breast cancer cells in long-term tissue culture

Epidermal growth factor (EGF) may be important in regulating the proliferation of mammary epithelial cells. In the present study, we examined EGF binding and effect on growth in nine human mammary cell lines. The T-47D, MCF-7, SK-Br-3, AIAb 496, BT-20, and BT-474 tumor cell lines and a cell line (HBL-100) derived from milk exhibited EGF binding; both high (Ka 10(10) M-1)- and low (Ka 10(9) M-1)-affinity sites were detected. The total number of EGF receptors per cell of different cell lines varied from 1.6 X 10(3) sites/cell (for AIAb 496) to 1.5 X 10(6) sites/cell (for BT-20). The two floating cell lines, DU4475 and Lev III, had no detectable EGF binding. Effect of EGF on growth was studied by monitoring cell number and the incorporation of [3H]thymidine into DNA of cells maintained in Dulbecco's modified Eagle's medium supplemented with 0.1% fetal bovine serum. Using these procedures, only T-47D cells were stimulated by EGF at low concentrations (0.1 to 1 ng/ml). At concentrations higher than 10 ng/ml, EGF was inhibitory to varying degrees in most cell lines that contained EGF receptors. The growth of the two floating cell lines that had no detectable EGF binding was unaffected by EGF. Our results show that EGF receptors are not present in all human breast cancer cell lines. There is no apparent correlation between EGF binding and its mitogenic activity in cell lines with EGF receptors. EGF may have biological roles in human breast cancer other than growth regulation.