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PubMed1979

A low temperature investigation of the intermediates of the photocycle of light-adapted bacteriorhodopsin. Optical absorption and fluorescence measurements.

Optical absorption and emission measurements have been made on samples of light-adapted purple membrane of Halobacterium halobium at temperatures ranging from 77 K to room temperature. As a result of these experiments a set of equations is given which described thermal and photochemical reactions interrelating various intermediates of the reaction cycle of the chromophore of light-adapted bacteriorhodopsin (BR). Further some specific problems connected to these intermediates have been investigated. Thus the room temperature emission spectrum of bacteriorhodopsin has been found to exhibit a Stokes shift of 3430 cm-1 only, if low excitation intensities are used. The recently detected intermiediate P-BR can be shown to convert thermally into bacteriorhodopsin following a first-order decay with the activation energy delta E = 2.4 +/- 0.2 kcal/mol. The thermal decay of K-BR consists of two exponentials if measured on purple membrane suspensions in a mixture of H2O and glycerol (1 : 1, v/v). A simple procedure is given for trapping the intermediate L-BR at 170 K in a very pure form. M-BR is shown to consist of two species, MI-BR and MII-BR. They are characterized by similar optical absorption spectra but different thermal stability. Further the oscillator strengths corresponding to the long wavelength absorption bands of the intermediates bacteriorhodopsin, K-, L, MI- and MII-BR have been calculated. They have been discussed with respect to the question which of the corresponding absorption spectra show the characteristics of isomerism of the chromophore or simply solvatochromism.

Bacteriorhodopsins↗
PubMed2026

Research on the genome of microorganisms: ethical considerations and recommendations regarding the incidental bystander sequencing of human genetic material.

In genomic research primarily targeting microorganisms (or pathogens), a substantial risk exists that the presence of human genetic bycatch is not sufficiently recognised, and that the potential harm of unwarranted analysis, access, or sharing of human genetic bystander data is also insufficiently acknowledged or mitigated. In this Personal View, we contend that mandatory risk mitigation measures are necessary, more so in view of the likely increase of sharing of materials and pathogen sequence information under the WHO Pandemic Agreement and the related Pathogen Access and Benefit Sharing framework. Based on a joint reflection of the Institutional Review Board and individual researchers at the Institute of Tropical Medicine in Antwerp, Belgium, we propose a four-step approach to mitigate such risks: prevention or early removal of human genetic sequences, secure storage of samples and data, adaptation of informed consent, and targeted ethics review. This approach should contribute to maintaining ethical integrity, protect the rights of individuals and communities, and bolster public trust in the expanding use of untargeted sequencing in global health research.

Humans↗
PubMed1978

Comparison of WI-38, MRC-5, and IMR-90 cell strains for isolation of viruses from clinical specimens.

With the diminishing supply of the human fetal lung WI-38 cell strain, a replacement for viral isolation is needed. Two candidates are the human fetal lung strains MRC-5 and IMR-90. A comparison of WI-38, MRC-5, and IMR-90 was performed to evaluate efficiency and speed of viral isolation, clarity of cytophatic effect, and ease of growing the cells. The inocula were clinical specimens rather than tissue culture-adapted isolates. Frozen samples of 46 specimens that had previously yielded an isolate on WI-38 were thawed and inoculated onto WI-38, MRC-5, and IMR-90 cells. In addition, 95 freshly taken clinical specimens uf undetermined infectivity were inoculated onto the cell strains. Viral recovery rates were similar on all three strains, as were the appearance and speed of onset of the cytophatic effect. MRC-5 and WI-38 cells remained healthy until generation 36, whereas IMR-90 cells went into crisis by generation 20. The longer life span of the MRC-5 cells makes them more suitable than IMR-90 cells to replace the WI-38 strain for routine use in viral diagnosis.

Cell Line↗
PubMed1979

Social adaptation in juvenile diabetes.

A sample of 36 juvenile diabetics, age 19--28 years, and with a duration of diabetes of 14--17 years were interviewed with regard to their social adaptation. Five patients could not be traced and six patients did not want to participate. Educational and professional careers were normal. However, none had received individual diabetes-oriented vocational guidance. A majority of patients was unsatisfied with the information given at the diabetic clinics, and a negative attitude towards society and its institutions was common. Patients often felt that as children they had been neglected by the diabetic team, while their parents received all information. It is concluded that diabetic children and adolescents require continuous socio-psychological support, that psychologists and/or social workers should be permanent members of the diabetic teams, and that paediatricians should follow diabetic patients until they are fully grown up.

Adolescent↗
PubMed1978

[Chronic vascular catheterization in the rat. Adaptation to injections and semi-continous blood sampling for hormonal studies].

A method for frequent sampling of blood and injections of fluids in undisturbed rats is described. The right external jugular vein and the left carotid artery are cannulated without completely blood stream interruption in the vessel. Injection or perfusion can be performed during several weeks. Blood was collected for at least 15 post-operative days. The technique appears suitable for pituitary kinetics studies which can be carried out several times in rats bearing indwelling catheters.

Acclimatization↗
PubMedDate not supplied

[Neonatal screening of congenital hypothyroidism with TSH measurement in dried blood spots on filter paper. A two years experience (author's transl)].

Systematic screening for congenital hypothyroidism was started in Lyon in september 1976. This screening was coupled with PKU, using the same dried blood samples on filter paper obtained on the 5th day of life. TSH levels were determined by radioimmunoassay adapted for dried blood samples (Kit Abbott). In 24 months, 56 176 samples were analyzed. The critical level calling for control was successively raised from from 20 to 30, now 40 microUI/ml of serum. A high level of TSH was found in 307 children (0,55%). Pathological deliveries were found in most of these infants (neonatal injury, cesarean, section forceps or ocytocic perfusion, neonatal icterus) and a second or a third measurement showed normal TSH level. Congenital hypothyroidism, was found detected in 18 infants: 12 ectopic gland, 5 athyreosis and 1 dyshormonogenesis. Treatment was begun at a mean age of 38 days (29 to 50 days).

Congenital Hypothyroidism↗
PubMedDate not supplied

[Neonatal screening for congenital hypothyroidism by measuring TSH in dried blood samples. Two years experience in the method (author's transl)].

Systematic screening for congenital hypothyroidism was started in Lyon in September 1976. This screening was coupled with PKU screening, using the same dried blood samples in filter paper obtained on the 5 th day of life. TSH levels were determined by radioimmunoassay adapted for dried blood samples (Kit Abbott). In 24 months, 56 176 samples were analyzed. The critical level calling for control was successively raised from 20 to 30 now 40 muUl/ml of serum. A high level of TSH was found in 307 children (0.55 p. 100). Pathological deliveries were found in most of these infants (neonatal injury, cesarean section, forceps or ocytocic perfusion, neonatal icterus) and a second or a third measurement showed normal TSH level. Congenital hypothyroidism, was detected in 18 infants: 12 ectopic gland, 5 athyreosis and 1 dyshormonogenesis. Treatment was begun at a mean age of 38 days (29 to 50 days). Despite a short follow-up the psychomotor development of the infants seems to be normal in all cases but one (one athyreosis with a neonatal injury and a malformative syndrome).

Blood Specimen Collection↗
PubMed1978

Relationship between dimensions of adaptive behavior and sheltered workshop productivity.

A factor analysis was performed on the 24 domains of the AAMD Adaptive Behavior Scale using a sample of 217 adult retarded workshop clients. Of the seven dimensions found to describe adaptive behavior, Personal Independence, Social Maladaptation, and Personal Maladaptation accounted for the majority of variance in the factor matrix. Scores on each of the seven factors were obtained for all clients and used to predict productivity in a workshop setting as defined by average hourly salary for the time period in which the scale was administered. A stepwise regression analysis yielded a highly significant regression effect in which the factors of Personal Independence and Social Maladaptation accounted for 25% of the variance in salary and had a multiple correlation coefficient of .50 with the predicted variable. We concluded that adaptive behavior is a multidimensional variable, significantly affecting productivity in sheltered workshop settings.

Adaptation, Psychological↗
PubMed2015

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Adaptation, Biological↗
PubMed1978

Method for the simultaneous establishment of many axenic cultures of Paramecium.

A method is described for the simultaneous treatment of 42 (or more) stocks of Paramecium, and their adaptation to growth in axenic culture. Samples of dense cultures of these ciliates growing with Enterobacter aerogenes are rendered bacteria-free by migration through 2 sets of tubes containing Adaptation Medium (Peters' salts solution, stigmaterol, vitamins, and autoclaved E. aerogenes). The 2nd set of tubes contains Adaptation Medium plus antibiotics. Bacteria-free samples containing approximately 100 animals are then transferred to test tubes containing Adaptation Medium without antibiotics. This medium also serves as a growth medium. It supports indefinite growth of all Paramecium stocks tested. After adaptation to this medium, the ciliattes can be grown in the axenic medium developed by Soldo, Godoy & van Wagtendonk. On a single trial at least half of the stocks can be expected to produce axenic cultures within 5 to 10 days by these procedures. The method has been applied successfully to several of the species of the Paramecium aurelia complex, to all syngens of Paramecium multimicronucleatum, to several stocks of Paramecium jenningsi, and to 1 stock of Paramecium caudatum and Paramecium calkinsi. A modification of the method also works for Didinium nasutum.

Animals↗
PubMed1977

Psychological changes accompanying pregnancy and motherhood.

This study was an attempt to investigate some of the psychological changes that occur during first pregnancy and the early postpartum months. The major theoretical assumption was that pregnancy and early motherhood may be viewed as a series of developmental tasks, and that the way in which these are coped with will be predictive of adaptation to the maternal role. The aims of the study were (a) to identify the affective changes that occur in women during first pregnancy and to assess the extent to which pregnancy and motherhood are experienced as a period of psychological crisis; (b) to trace the development of maternal feeling; and (c) to assess the extent to which characteristics measured early in pregnancy are predictive of attitudes and adjustment to later stages of pregnancy and the degree to which these factors are themselves predictive of adaptation to parenthood. The sample consisted of 19 white, middle class primigravidas, with an age range of 22-33 years. Only women who had no previous gynecological or psychiatric difficulties and who were currently living with their husbands were accepted as Ss. Each woman was interviewed at each trimester of pregnancy, on the third postpartum day, and at 2 months postpartum. A follow up questionnaire was mailed at 7 months postpartum, The data obtained were derived from ratings of extensive interview schedules and a number of personality measures. Results indicated that although emotional upheaval and rapid change were characteristic of pregnancy, for some women a growing sense of adulthood, of fulfillment, and integration of a new maturational stage clearly co-existed with the emotional disequilibrium. Analysis of the interrelationship among characteristics shown in early pregnancy, adjustment to the pregnancy overall, and adaptation to parenthood indicated that the degree of personality integration achieved by early pregnancy was predictive of the extent to which psychological growth was experienced throughout pregnancy and early parenthood.

Adaptation, Psychological↗
PubMed2026

PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.

MOTIVATION: Accurate detection of copy number variations (CNVs) from targeted panel sequencing remains challenging due to limited genomic coverage and pronounced sample-specific biases. Existing normalization strategies, including baseline-cohort, matched-control, and single-sample approaches, often struggle to balance noise suppression with adaptability, leading to inconsistent performance across heterogeneous samples. RESULTS: We present PScnv, a personalized self-normalizing framework for robust CNV detection from panel sequencing data. PScnv integrates a pre-built panel-of-normals (PoN) with sample-intrinsic stable chromosomes through ridge-regression normalization to generate individualized log2 ratio profiles with reduced systematic variation. CNVs are then identified using a hierarchical multi-phase segmentation pipeline incorporating z-score pre-partitioning, kernel-based correction, and circular binary segmentation. In 139 clinical tumor samples with orthogonal FISH validation at MET, ERBB2, and MTAP, PScnv showed improved accuracy and robustness over existing methods that do not require patient-matched normal samples, provided that a pre-built PoN cohort is available. AVAILABILITY: Source code is available for academic use at https://github.com/lvws/PScnv.

DNA Copy Number Variations↗
PubMed2024

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality.

Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus-host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.

Nipah Virus↗
PubMed1976

[Isoelectric focusing of complex protein mixtures in the nanogram range in microgels (author's transl)].

A method is described for isolectric focusing of complex protein mixtures in 2, 5 or 10 mul capillaries. For one separation only 15- 50 ng of a protein mixture is needed. Isoelectric focusing is finished after 10 min, staining takes 20 min and destaining approximately 30 min. Using defined mixtures of Servalyt from different pH ranges, isoelectric focusing can be adapted to the protein sample to be fractionated. Protein peaks separated by isoelectric focusing can be electrophoretically eluted and for further analysis refractionated directly in a microgradient gel. The resolution power of microisoelectric focusing is as good as that of the wellknown macroprocedure, as is demonstrated by isoelectric focusing of the water soluble proteins from cerebellum and heart, of rat and human serum and of a human oncocytoma of the thyroid gland.

Animals↗
PubMed2025

MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples.

MOTIVATION: Minimal residual disease (MRD) as critical biomarker for cancer prognosis and management plays a crucial role in improving patient outcomes. However, detecting MRD via next-generation sequencing-based circulating tumor DNA variant calling remains unstable due to the extremely low variant allele frequency and significant inter- and intra-sample heterogeneity. Although parameter optimization can theoretically enhance the detection performance of variants, achieving stable MRD detection remains challenging due to three key factors: (i) the necessity for individualized parameter tuning across numerous heterogeneous genomic intervals within each sample, (ii) the tightly interdependent parameter requirements across different stages of variant detection workflows, and (iii) the limitations of current automated parameter optimization methods. RESULTS: In this study, we propose MRDagent, a novel variant detection tool designed specifically for MRD detection. MRDagent incorporates an iterative and self-adaptive optimization framework capable of handling unknown objectives, varying constraints, and highly coupled parameters across stages. A key innovation of MRDagent is the integration of a convolutional neural network-based meta-model, trained on historical data to enable rapid parameter prediction. This significantly enhances computational efficiency and generalization performance. Extensive evaluations on simulated and real-world datasets demonstrate MRDagent's superior and stable performance, providing an efficient, reliable solution for MRD detection in clinical and high-throughput research applications. AVAILABILITY AND IMPLEMENTATION: MRDagent is freely available at https://github.com/aAT0047/MRDagent.git. The corresponding dataset and software archive are available at Zenodo: https://doi.org/10.5281/zenodo.15458496.

Circulating Tumor DNA↗
PubMed1977

Subjective adaptation to loss of the work role: a longitudinal study.

Both social psychologists and social gerontologists have expressed considerable interest in adaptation to the loss of central life roles. The relationship between retirement and morale, where morale is viewed as an indicator of adaptation, is an example of research within this theoretical framework. In this study, longitudinal data for a select sample of 58 male subjects were used to examine intensively the process of adaptation to retirement. The strongest finding was evidence of high levels of adaptation in the sample as reflected in the overwhelming stability of morale over time. Multiple regression analysis indicated that social resources, particularly marital status and socioeconomic status, condition the relationship between adaptation and retirement. In summary, our analysis supports current suggestions that retirement be viewed as an event which occasions a complex social process of adaptation conditioned by a variety of resource and temporal variables.

Adaptation, Psychological↗
PubMed2025

LYCEUM: learning to call copy number variants on low-coverage ancient genomes.

MOTIVATION: Copy number variants (CNVs) are pivotal in driving phenotypic variation that facilitates species adaptation. They are significant contributors to various disorders, making ancient genomes crucial for uncovering the genetic origins of disease susceptibility across populations. However, detecting CNVs in ancient DNA (aDNA) samples poses substantial challenges due to several factors: (i) aDNA is often highly degraded; (ii) contamination from microbial DNA and DNA from closely related species introduces additional noise into sequencing data; and finally, (iii) the typically low-coverage of aDNA renders accurate CNV detection particularly difficult. Conventional CNV calling algorithms, which are optimized for high-coverage read-depth signals, underperform under such conditions. RESULTS: To address these limitations, we introduce LYCEUM, the first machine learning-based CNV caller for aDNA. To overcome challenges related to data quality and scarcity, we employ a two-step training strategy. First, the model is pre-trained on whole genome sequencing data from the 1000 Genomes Project, teaching it CNV-calling capabilities similar to conventional methods. Next, the model is fine-tuned using high-confidence CNV calls derived from only a few existing high-coverage aDNA samples. During this stage, the model adapts to making CNV calls based on the downsampled read depth signals of the same aDNA samples. LYCEUM achieves accurate detection of CNVs even in typically low-coverage ancient genomes. We also observe that the segmental deletion calls made by LYCEUM show correlation with the demographic history of the samples and exhibit patterns of negative selection inline with natural selection. AVAILABILITY AND IMPLEMENTATION: LYCEUM is available at https://github.com/ciceklab/LYCEUM.

DNA Copy Number Variations↗
PubMed1976

Rapid detection of bacterial endotoxins in drinking water and renovated wastewater.

A pilot study was conducted to determine the feasibility of using the Limulus endotoxin assay to detect endotoxins in potable waters and from reclaimed advanced waste treatment (AWT) plant effluents. Water samples were tested using both Limulus lysates prepared in our laboratory and a commercial product, Difco Pyrotest. The Limulus assay procedure was easily adapted to the testing of water samples for endotoxin. Measured endotoxin concentrations varied from 0.78 ng/ml to 1,250 ng/ml. Levels of endotoxin were not predictable based on whether the water was drinking water or AWT water, i.e., some AWT water samples had less endotoxin activity than some samples of drinking water, and some AWT waters had greater endotoxin activity than drinking water. Only three of the water samples tested were free of any detectable endotoxin. Breakpoint chlorination procedures seemed to reduce measurable endotoxin content, whereas passage through activated carbon columns was associated with greater final endotoxin concentrations in test waters.

Biological Assay↗