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At least 19 recordsLinked to original sources
PubMed2026

MACS3: A Peak-calling Platform for Bulk and Single-cell Regulatory Genomics.

Since the original publication of Model-based Analysis for ChIP-Seq (MACS), the software has been widely used to identify enriched genomic regions in ChIP-seq, ATAC-seq, CUT&RUN, DNase-seq, and related regulatory genomics assays. Over the years, MACS has evolved substantially, with MACS version 3 (MACS3) now serving as the actively maintained implementation. MACS3 preserves the core MACS framework for fragment pileup, dynamic local background noise, statistical enrichment testing, and peak refinement, while adding functionality needed for contemporary bulk and single-cell workflows. It supports conventional bulk peak calling, paired-end and fragment-based file formats, modular signal processing, direct analysis of single-cell ATAC-seq fragment files, barcode-restricted pseudobulk and cluster-level peak calling, specialized ATAC-seq and variant-calling modules, as well as command-line and programmatic interfaces. MACS3 is distributed through standard software channels and supported by continuous testing across operating systems, Python versions, and CPU architectures. Here we describe the architecture, current capabilities, and recommended use of MACS3, providing an updated reference for applying the MACS framework in contemporary bulk and single-cell regulatory genomics workflows. MACS3 is open-source software available at https://github.com/macs3-project/MACS.

Bioinformatics software↗
PubMed2025

Chrom-Sig: de-noising 1D genomic profiles by signal processing methods.

MOTIVATION: Modern genomic research is driven by next-generation sequencing experiments such as ChIP-seq, CUT&Tag, and CUT&RUN that generate coverage files for transcription factor binding, as well as ATAC-seq that yield coverage files for chromatin accessibility. Due to the inherent technical noise present in the experimental protocols, researchers need statistically rigorous and computationally efficient methods to extract true biological signal from a mixture of signal and noise. However, existing approaches are often computationally demanding or require input or spike-in controls. RESULTS: We developed Chrom-Sig, a Python package to quickly de-noise 1D genomic coverage tracks by computing the empirical null distribution without prior assumptions or experimental controls. When tested on 19 ChIP-seq, CUT&RUN, ATAC-seq, and snATAC-seq datasets, Chrom-Sig can effectively decompose the data into signal and noise components. Notably, Chrom-Sig performs de-noising and peak calling in 1-2 h using around 20 GB of memory. The de-noised signal corroborates with biologically meaningful results: CTCF CUT&RUN data retained a high percentage of peaks overlapping CTCF binding motifs, while ATAC-seq and RNA Polymerase II data were enriched in enhancers and promoters. We envision Chrom-Sig to be a versatile and general tool for current and future genomic technologies. AVAILABILITY AND IMPLEMENTATION: Chrom-Sig is publicly available on GitHub (https://github.com/minjikimlab/chromsig) and Zenodo (doi: 10.5281/zenodo.17488772) under the MIT licence.

Genomics↗
PubMed2025

Defining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes.

BACKGROUND/PURPOSE: Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D). METHODS: We isolated B cells from four healthy individuals, ages 9-17. HiChIP was performed using a CTCF antibody, and CTCF peaks were called within each sample separately. Peaks observed in all four samples were identified. CTCF loops were called within the pediatric samples using three CTCF peak datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIP-seq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets. RESULTS: The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed&#x2009;<&#x2009;1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks. Significant looping differences were even fewer when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets. CONCLUSION: The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBV-transformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

Humans↗
PubMed1978

Antilipolytic nature of gut GLI, and mode of action of two highly potent intestinal lipolytic species in birds.

Three major lipolytic factors, termed peaks 1, 2 and 3, according to their elution sequence from Biogel P6 columns, have been identified in duck intestinal extracts. The small molecular weight peaks 2 and 3, were even more lipolytically potent on chick adipocytes than pancreatic glucagon; peak 1, called gut GLI, because of its cross-reactivity in a radioimmunoassay for glucagon, modified the lipolytic activity of peak 2 and pancreatic glucagon. It did so by modifying their capacity to stimulate cyclic AMP production. Peaks 2 and 3 exert their lipolytic effects via different intermediary pathways: only peak 2 induced the formation of cyclic AMP. Insulin in birds is devoid of any antilipolytic activity; this fundamental role may be assumed by gut GLI.

Adipose Tissue↗
PubMed1976

Dynamic changes in regional CBF, intraventricular pressure, CSF pH and lactate levels during the acute phase of head injury.

The authors measured regional cerebral 133xenon (133Xe) blood flow (rCBF), intraventricular pressure (IVP), cerebrospinal fluid (CSF) pH and lactate, systemic arterial blood pressure (SAP), and arterial blood gases during the acute phase in 23 comatose patients with severe head injuries. The IVP was kept below 45 mm Hg. The rCBF was measured repeatedly, and the response to induced hypertension and hyperventilation was tested. Most patients had reduced rCBF. No correlation was found between average CBF and clinical condition, and neither global nor regional ischemia contributed significantly to the reduced brain function. No correlation was found between CBF and IVP or CBF and cerebral perfusion pressure (CPP). The CSF lactate was elevated significantly in patients with brain-stem lesions, but not in patients with "pure" cortical lesiosn. The 133Xe clearance curves from areas of severe cortical lesions had very fast initial components called tissue peaks. The tissue peak areas correlated with areas of early veins in the angiograms, indicating a state of relative hyperemia, referred to as tissue-peak hyperemia. Tissue-peak hyperemia was found in all patients with cortical laceration or severe contusion but not in patients with brain-stem lesions without such cortical lesions. The peaks increased in number during clinical deterioration and disappeared during improvement. They could be provoked by induced hypertension and disappeared during hyperventilation. The changes in the tissue-peak areas appeared to be related to the clinical course of the cortical lesion.

Acid-Base Imbalance↗
PubMed1975

Alveolar lavage cytology in transplanted lungs. I. Staining methods and findings in dogs with autografts and allografts without immunosuppression.

Alveolar lavages were performed repetitively on the normal and transplanted lungs of dogs that had recieved autografts or allografts without immunosuppression. One half of the lavage returns was fixed as a cytologic smear; the other half was subjected to semi-thin section or electron microscopic examination. Of the staining methods was used, the periodic acid-Schiff (PAS) and Giemsa techniques were best for differentiating and counting cells. The Ladewig technique was best for evaluating the presence and location of fibrin. After autotransplantation, the proportion of so-called alveolar marcophages increased, reached a peak in 4 to 7 days, and then returned to normal. Phagocytized fibrin increased for the first postoperative week, but not extracellular fibrin was ever observed. After allotransplantation, a progressive decrease in the proportion, size, and vacuolization of so-called alveolar macrophages was noted along with an increase in extracellular fibrin. Intracellular fibrin could be detected only up to the third day. These findings define adequate methods for preparing and staining material obtained from diagnostic alveolar lavages, and they suggest that the procedure may serve as an index of lung allograft rejection.

Animals↗
PubMed1975

Existence in fetal and adult rat of several forms of material reacting with anti-insulin antibody (IRI).

The double antibody procedure detects 3 peaks in the elution fractions of adult or fetal rat sera, after passage on Sephadex G50 or G100 columns. Peak A (apparent MW 6000) contains insulin monomer; peak B (apparent MW 10-12000) is tentatively attributed to proinsulin (or proinsulin like substances); peak C (apparent MW 50-100000) is similar to the so called "big big" insulin. During intravenously induced hyperglycemia, the 3 peaks show parallel increases, but, after the disappearance of peaks A and B in streptozotocin treated rats, peak C remains unaltered. Pancreatic extracts and secreta present a very minor and inconstant peak C, the bulk of their immunoreactive material belonging to peaks A and B. A companion paper further discusses the nature of peaks B and C materials.

Animals↗
PubMed1975

A temporal component of the auditory evoked response.

We studied the 75-225 msec portion of the auditory evoked response (AER) in 32 normal adults at vertex (Cz) and temporal (T3 and T4) placements referred to a balanced, noncephalic reference electrode using a monaural 1 msec click stimulus delivered every 4.7 sec at 60 dB above threshold. The tape-recorded EEG was filtered at 1-25 c/sec, and 128 individual responses were summed, sampling every 0.5 msec for 250 msec post-stimulation. The Cz AERs showed the classic vertex response, a negative peak, N1, at 100 msec, followed by a positive peak, P2, at 160-200 msec. The T3 and T4 AERs were similar to the Cz AERs from 0 to 80 msec and from 200 to 250 msec. They differed significantly from the Cz AERs from 80 to 200 msec. The difference is best explained by the hypothesis that the Cz AERs consisted of N1P2, while the T3 and T4 AERs consisted of N1P2 plus an additional superimposed component, which we called the T complex, comprising a positive peak, Ta, at 105-110 msec, and a negative peak, Tb, at 150-160 msec. By computer, the corresponding Cz and T3 or T4 AERs were normalized to equalize their amplitudes, and the former was subtracted from the latter, thus isolating the T complex. The Ta peak was found to occur 1.5 +/- 1.6 msec earlier at the electrode contralateral to stimulation, and 2.2 +/- 4.0 msec earlier at the T4 (right) electrode. Both differences were statistically significant. The T complex amplitude was greater at the electrode contralateral to stimulation and at the T4 electrode. These findings appear to resolve current controversies concerning the form of the temporal AER. While N1P2 is apparently a product of widespread areas of cortex, we conclude that the T complex is probably a product of secondary auditory cortex.

Acoustic Stimulation↗
PubMed1979

Complement response after experimental bacterial infection in various nutritional states.

In malnourished rats, nutritionally rehabilitated rats at various stages, and in well nourished rats, levels of serum complement after bacterial infection caused by Staphylococcus aureus, as well as tuberculin reactivity, were examined. The elevation of complement showed a peak 2--3 days after infection, herein called the first complement response. A reelevation occurred at a later stage, 7--14 days after infection, and is referred to as the second complement response. The first complement response was observed in all the rats after Staphylococcus aureus infection but it was greater in well nourished rats. In malnourished rats, only the first complement response was observed and the tuberculin reaction and second complement response were lacking. After 1 week of nutritional rehabilitation, 40% of the rats showed recovery of tuberculin responses and both the first and second complement responses were observed. Nutritionally rehabilitated rats treated longer than 2 weeks, together with the well nourished control rats, showed positive tuberculin reactivity. The second complement response was also observed in such rats when bacterial infection was severe but not with mild infection.

Animals↗
PubMed1975

[Metachromasia, double refraction and dichroism caused by Toluidine Blue reaction (author's transl)].

The present paper is concerned with those optical phenomena which may be caused in histological structures by the toluidine blue reaction. They relate to absorption as well as refraction properties. The paper gives a detailed description of how the toluidine blue reaction is carried out on histological preparations. The analysis of absorption results leads, in connection with physicochemical considerations, to a new explanation of the cause of toluidine blue metachromasia. In this, the assumption is made that the conditions of attachment of protons to the hydrogen-bearing nitrogen of dye molecules are largely responsible for the occurrence of metachromasia, the way in which the attachment of the proton to this quaternary nitrogen is influenced being of no consequence in this particular connection. It may result from both a combination of homogeneous toluidine blue molecules into associates and a shift to the alkaline region of the pH value of the dye solution. However, the term metachromasia is used to describe only that shift of the absorption spectrum which is produced by associates. The thus produced metachromasia ("concentration metachromasia") involves the development of a so-call "gamma-band" (with an absorption peak of gamma = 546 nm), there being a causal rather than a fundamental difference between the latter band and the normal metachromatic mu-band (with an absorption peak of gamma = 540 nm). Whereas in the case of concentration metachromasia and for an aqueous solution there may be observed an association of dye molecules having a maximum intermolecular distances of less than 5 angström units, which is due to the large number of toluidine blue molecules per unit volume, mu-metachromasia is usually observed in connection with chromotropic structures. This association results in the lone-pair electrons of the hydrogen-bearing nitrogen atom being included in the intermolecular resonance system, which in turn results in the attachment of a proton to this nitrogen being weakened, which leads to the assumption of a red color. The difference to gamma-metachromasia lies in the fact that even by treatment with dilute solutions, in which the dye is present in a monomeric form, such a metachromasia may be produced on account of the sufficiently dense charge pattern of the chromotropic structure. This particular pattern tends to induce an association of dye molecules which in turn are associated, through hydrogen bridges, with the anionic groups. The orthochromatic toluidine blue reaction was found to be a possible method of detecting bridge-bond-active hydrogen in histological structures. The cause of the assumption of a blue color, which is observed in this connection, is a monomeric attachment of the dye. Additional factors leading to ortho-chromatism are also discussed...

Birefringence↗
PubMed1979

Human visual acuity assessment through linear extrapolation to threshold of bar grating VERs.

Visual evoked responses (VERs) were obtained from seven normal eyes, using high contrast square-wave gratings of varying bar size on an 8 degrees or 24 degrees stimulus field. VER amplitude was plotted as a function of bar size. These plots, called square wave transfer functions (SWTFs), have one or more peaks when generated by a 24 degree field. In some individuals, the small bar size extreme of the function can be fitted well with a straight line for purposes of extrapolation to the visual acuity bar size. However, interindividual differences in the shape of the 24 degree field SWTF invalidates any a priori assumption of what bar sizes may be included in the extrapolation. Results from three subjects, using an 8 degree field, suggest that a more uniform single-peaked triangular SWTF with a peak near 5 min arc may be assumed for extrapolation purposes. The interindividual SWTF differences obtained with the 24 degree field were not random, the subjects falling into one of two groups on the basis of SWTF shape. This SWTF shape dichotomy may be correlated with the presence or absence of strabismus.

Adult↗
PubMed1976

[Electronmicroscopic characterisation of human plasma lipoproteins after isolation by zonal ultracentrifugation (author's transl)].

Human plasma proteins were isolated by zonal ultracentrifugation and the fractions obtained examined under the electron microscope. HDL2 had a high degree of uniformity in normal persons, characterised by numerous two-dimensional, hexagonal arrangements. Optical diffraction analysis of HDL2 gave a centre distance of 11.3 nm, individual HDL2 particles being spherical with a diameter of 9.8 nm. HDL3 represented a somewhat less uniform lipoprotein population with a particle diameter between 6.5 and 9.5 nm. LDL had a diameter of 20-25 nm. In patients with hyperlipoproteinaemia type III a third peak was isolated, in addition to the two normal lipoprotein peaks VLDL and LDL. It lies between them and has been called Lp III. VLDL from type III plasma consisted of spherical particles, diameter 31-81 nm, morphologically indistinguishable from normal VLDL. Lp III consisted of a relatively homogeneous spherical lipoprotein population with a diameter of 25-30 nm. LDL consisted of spherical particles whose size was highly homogeneous (18-23 nm diameter), indistinguishable from normal LDL.

Adult↗
PubMed1975

The action of ether and methoxyflurane on synaptic transmission in isolated preparations of the mammalian cortex.

1. The actions of ether and methoxyflurane on the evoked potentials of in vitro preparations of the guinea-pig olfactory cortex were studied. Following stimulation of the lateral olfactory tract (l.o.t.) evoked potentials could be recorded from the cortical surface; these potentials consisted of an initial wave (the compound action potential of the l.o.t.) followed by a negative field potential which was associated with the synchronous excitation of many superficial excitatory synapses (population e.p.s.p.). Superimposed on the population e.p.s.p. was a number of positive peaks. These positive peaks reflect the synchronous discharge of many neurones and so have been called population spikes. 2. When ether or methoxyflurane was added to the gas stream that superfused the surface of the preparations, the population e.p.s.p.s. and population spikes were depressed at lower concentrations than those required to depress the compound action potential of the afferent fibres. 3. The evoked activity of individual cells in the cortex was depressed by ether and methoxyflurane. However, five of the twelve cells tested in ether showed an increase in their evoked activity at concentrations below 4-5%, but at higher concentrations these cells also became depressed. 4. Both ether and methoxyflurane depressed the sensitivity of cortical neurones to iontophoretically applied L-glutamate and may similarly depress the sensitivity of the post-synaptic membrane to the released transmitter substance. 5. Neither anaesthetic appeared to increase the threshold depolarization required for nerve impulse generation. Thus, the decrease of the discharge of the post-synaptic cells was primarily caused by a depression of chemical transmission. 6. Ether caused some cells in the cortex to alter their normal pattern of synaptically evoked discharge and both anaesthetics induced similar changes during excitation by glutamate.

Animals↗
PubMed1979

Species-specific perceptual processing of vocal sounds by monkeys.

Monkeys of four species were trained to discriminate between sets of natural tonal calls of Japanese macaques (Macaca fuscata) by the position of a frequency-inflection peak or by initial pitch. The Japanese macaques consistently performed best on peak position and the other species on pitch. The results imply special strategies for perceptional processing of vocal sounds and suggest parallels with human speech perception.

Animals↗
PubMed2025

The impact of the live broadcast of Stromae's song L'enfer on social media publications, calls to the national helpline, and suicide attempt rates in France.

On January 9, 2022, Belgian pop singer Stromae performed his new hit "L'enfer" live on French TV. The song addresses his personal struggles with suicidal ideation. To evaluate the impact of Stromae's performance, we modeled the evolution of hospital admission rates for suicide attempts (SAs) in France, calls to the national suicide prevention helpline (3114), and Twitter publications mentioning the singer or the helpline. We employed the Gombay test to identify change points within each time series. We identified a significant increase in mean SA rates among women aged 20-24&#xa0;years 6&#xa0;days after the singer's performance. No similar effect was observed in the general population or other young age groups. The show was immediately followed by a peak in tweets referring to the singer, while Twitter activity related to the 3114 remained modest. We did not observe any increase in calls to the helpline. Celebrity testimonies about suicidal experiences can help alleviate stigma but should be accompanied by prevention messages to reduce the risk of contagion.

Humans↗
PubMed1979

Medically equipped emergency ambulance units at "Hôpital Civil de Charleroi". Four years' activity.

In narrow collaboration with the so-called "900 Service", the civil Hospital of Charleroi provides, since 1971, medical attendance for two emergency medical aid flying squads. Five hospital doctors belonging to this "900 Service" alternately assume, night and day, such responsibilities. Their background is reanimation anesthesia. Medical attendance is assumed on the ground of gravity criterions which are appreciated by a switchboard operator working at the Telephone calls' Centre. The number of such emergency medical attendances is gradually increasing: 377 in 1974, 489 in 1975, 973 in 1976, 1661 in 1977, 2135 in 1978. The proportion of "flying" attendances assumed for sheer medical affections is also gradually increasing in regard to those assumed for traumatological causes. The daily average of such "flying interventions" reaches 5.8 with a daily peak record of 15, which unquestionably shows that such an organised medical service is definitely positive. One should concede that a better selection among such emergency telephone calls could make the good results now recorded even better. The way to improve this selection could be achieved if the operator were a physician as this is the case in France with the S.A.M.U. services. In theory, such an improvement could be reached through a Regional Centre for Emergency Medical Aid, such a Centre being activated by both local medical and hospital forces interdependent in the pursuit of the same goal i.e. "Cases of Emergency".

Ambulances↗
PubMed1979

Decision-making in repair of tetralogy of Fallot based on intraoperative measurements of pulmonary arterial outflow tract.

The equation that we proposed in this JOURNAL (1977), relating the postrepair ratio between peak right ventricular pressure and peak left ventricular pressure (PRV/LV) to the intraoperatively measured internal diameter of the narrowest point in the pulmonary arterial outflow tract (formerly called pulmonary "anulus"), performed well when prospectively tested in 25 patients undergoing repair of the tetralogy of Fallot. The observed PRV/LV in all 21 patients in whom no transannular patch was used fell within the 70 percent confidence limits (1 standard deviation) of that predicted from the measured diameter. A trivial difference (-0.03 +/- 0.069 PRV/LV units, P = 0.08) was found between predicted PRV/LV and that observed after repair, with body surface area (BSA) used for normalization. When the four additional patients who had secondary transannular patching are included, or where the normalization was with weight, the differences were not significant (p greater than 0.2). A slightly revised equation has been devised using the combined data from our original group and the patients used for prospective testing. This equation predicts with reasonable accuracy (r = -0.69, p less than 0.0001) postrepair PRV/LV without transannular patching from the intraoperatively measured diameter of the pulmonary arterial outflow tract. We believe it is therefore helpful in the operating room in making the important decision for or against using transannular patching.

Adolescent↗
PubMed1979

Epidemiology of nodular paragranuloma (Hodgkin's disease with lymphocytic predominance, nodular).

The age and sex distribution and the localization of excised lymph nodes from 206 patients with a nodular variant of Hodgkin's disease with lymphocytic predominance, called "nodular paragranuloma", are presented and compared with data on other types of Hodgkin's disease. The age curve of nodular paragranuloma showed a peak in the fourth decade, which was clearly separated from the peak in the third decade exhibited by the nodular sclerosis type of Hodgkin's disease and from the peak in the sixth and seventh decades of the mixed cellularity type. The peak in the age curve of nodular paragranuloma resulted from the high frequency in men in the fourth decade; the female age curve had no peaks. The overall male-to-female ratio was 2.4:1. The age and sex distribution of diffuse paragranuloma was nearly identical to that of nodular paragranuloma, whereas the age and sex distribution of cases of the lymphocytic predominance type other than paragranuloma resembled that of the mixed cellularity type. These data indicate that the lymphocytic predominance type of Hodgkin's disease is not a uniform group and support the view that paragranuloma is a separate entity.

Adolescent↗