Why Has the Number of Scientific Retractions Increased?

Background

The number of retracted scientific publications has risen sharply, but it is unclear whether this reflects an increase in publication of flawed articles or an increase in the rate at which flawed articles are withdrawn.

Methods and Findings

We examined the interval between publication and retraction for 2,047 retracted articles indexed in PubMed. Time-to-retraction (from publication of article to publication of retraction) averaged 32.91 months. Among 714 retracted articles published in or before 2002, retraction required 49.82 months; among 1,333 retracted articles published after 2002, retraction required 23.82 months (p<0.0001). This suggests that journals are retracting papers more quickly than in the past, although recent articles requiring retraction may not have been recognized yet. To test the hypothesis that time-to-retraction is shorter for articles that receive careful scrutiny, time-to-retraction was correlated with journal impact factor (IF). Time-to-retraction was significantly shorter for high-IF journals, but only ∼1% of the variance in time-to-retraction was explained by increased scrutiny. The first article retracted for plagiarism was published in 1979 and the first for duplicate publication in 1990, showing that articles are now retracted for reasons not cited in the past. The proportional impact of authors with multiple retractions was greater in 1972–1992 than in the current era (p<0.001). From 1972–1992, 46.0% of retracted papers were written by authors with a single retraction; from 1993 to 2012, 63.1% of retracted papers were written by single-retraction authors (p<0.001).

Conclusions

The increase in retracted articles appears to reflect changes in the behavior of both authors and institutions. Lower barriers to publication of flawed articles are seen in the increase in number and proportion of retractions by authors with a single retraction. Lower barriers to retraction are apparent in an increase in retraction for “new” offenses such as plagiarism and a decrease in the time-to-retraction of flawed work.     

Repair of laser-severed stress fibers in myocardial non-muscle cells

Phase-dense stress fibers in cultured non-muscle cells from neonatal rat ventricles were severed using the 532 nm wavelength of a Q-switched Nd Yag laser microbeam. The breaks were confirmed using anti-actin antibodies and Coomassie blue staining. SEM showed that no visible membrane damage resulted from the laser. Following irradiation, severed stress fiber ends quickly retracted 3–5 μm apart and repaired, averaging 12.2 min, in 84% of the control cells. Most fibers not repairing had much longer, > 10 μm, retraction distances. Disruption of microfilaments by cytochalasin B (CB) or chlorpromazine (CPZ) resulted in increased retraction distances and a dose-dependent decrease in the ability of stress fibers to repair. Fibers not repairing in CB or CPZ consistently displayed directional depolymerizations of fiber segments on the proximal side of the cut relative to the cell center and, at the extreme, condensations of stress fiber material into ‘knob-like’ structures. It appears to us that increased retraction distances might reflect CB or CPZ disruption of stress fiber-membrane attachments. Directional depolymerization suggests that stress fibers are unipolar structures, yet we failed to see any directional repair. Microtubule removal by colcemid, vinblastine, or podophyllotoxin resulted in a doubling of stress fiber repair rates. This in vivo evidence suggests that a relationship does exist between stress fibers and microtubules. Finally, inhibition of protein synthesis by 95% had little effect upon fiber repair, therefore indicating that protein synthesis is not necessary for stress fiber repair.     

Mechanical Properties of the Red Cell Membrane: I. Membrane Stiffness and Intracellular Pressure

The technique of Mitchison and Swann (1954) was modified for determining the resistance to deformation, or “stiffness,” of the red cell membrane and the pressure gradient across the cell wall. It requires a measure of the pressure needed to suck a portion of the cell into a micropipette. Stiffness of hypertonically crenated cells was less than that of biconcave discs or hypotonically swollen cells. Crenated cells showed zero pressure gradient and a stiffness, probably due to pure bending, equivalent to 0.007 ± 0.001 (SE) dynes/cm. Normal and swollen cells showed a pressure gradient of 2.3 ± 0.8 (SE) mm H₂O and a stiffness, due to bending and tension in the membrane, equivalent to 0.019 ± 0.002 (SE) dynes/cm. No difference in stiffness was found between the rim and the biconcavity of the cell or between biconcave discs and hypotonically swollen cells. Micromanipulation showed that the membrane can withstand large bending strains but limited tangential strains (stretching). These results have significant implications in any theory explaining the cell shape. For example, the data give no indication that the physical properties of the membrane are different at the rim from those of the biconcavities, and the existence of a positive pressure in the normal cell is established.     

The Tail Movement of Bull Spermatozoa: Observations and Model Calculations

Detailed observations of the tail movement of non-rotating and rotating bull spermatozoa have been carried out. For rotating sperm a helical tail wave was found with a ratio of the amplitudes of the two perpendicular components of approximately 3 to 1. For both types of cells the variation of the amplitude and the phase shift of the wave as it travels from the proximal to the distal part are reported. Model calculations indicate that the stiffness of the tail originates in the fibrous sheath, which has a Young's modulus of 3 × 10⁷ dynes/cm². Active contractile elements distributed continuously along the tail are found necessary to maintain the amplitude of the tail wave against damping by the fluid drag. If the longitudinal fibers are identified with the contractile elements the maximum tension to be developed by these fibers is 4 × 10⁶ dynes/cm². The energy dissipated by the “active” part of the tail wave is at least approximately 70 percent of the total dissipation.     

Rheological properties and wall structures of large veins

The static and dynamic viscoelastic properties were studied of longitudinal and circumferential strips excised from various large veins of dogs. The mechanical behavior in longitudinal direction could be regarded as elastic, while that in circumferential direction was highly viscoelastic. No distinct regionality was observed in either of the longitudinal and the circumferential groups. Noradrenaline and papaverine did not alter the elastic behavior of the longitudinal strips. In circumferential strips, however, noradrenaline caused a considerable decrease in stress relaxation and some steepening in the slope of the upper limb of hysteresis loop. Papaverine did not affect the circumferential characteristics. These findings suggest the dominant contribution of smooth muscle tone to the circumferential characteristics of venous walls. Pretreatment with formic acid abolished the occurrence of stress relaxation in circumferential direction but produced no change in the longitudinal behavior. This indicates that elastin fibers may be a principal determinant of the elastic behavior in longitudinal direction and that a residual tension observed in stress-relaxation tests of circumferential strips may be due to stretched elastin fibers. The elastic moduli of elastase pretreated venous walls were in the order of 10(8) dynes/cm2, about 1000 times higher than those of the control. Accordingly, collagen fibers seemed not to play any appreciable role in the rheological behavior of venous walls under physiological conditions. This inference was supported by histological observations of venous walls under unstretched and stretched states. Models were proposed in regard to the architecture of the fibrous elements in the venous walls.     

Mechanical Properties of the Sarcolemma and Myoplasm in Frog Muscle as a Function of Sarcomere Length

The elastimeter method was applied to the single muscle fiber of the frog semitendinosus to obtain the elastic moduli of the sarcolemma and myoplasm, as well as their relative contributions to resting fiber tension at different extensions. A bleb which was sucked into a flat-mouthed pipette at the fiber surface separated into an external sarcolemmal membrane and a thick inner myoplasmic region. Measurements showed that the sarcolemma does not contribute to intact fiber tension at sarcomere lengths below 3 µ. It was estimated that the sarcolemma contributed on the order of 10% to intact fiber tension at sarcomere lengths between 3 and 3.75 µ, and more so with further extension. Between these sarcomere lengths, the sarcolemma can be linearly extended and has a longitudinal elastic modulus of 5 x 10⁶ dyne/cm² (assuming a thickness of 0.1 µ). Resistance to deformation of the inner bleb region is due to myoplasmic elasticity. The myoplasmic elastic modulus was estimated by use of a model and was used to predict a fiber length-tension curve which agreed approximately with observations.     

Ventral stress fibers induce plasma membrane deformation in human fibroblasts

Interactions between the actin cytoskeleton and the plasma membrane are important in many eukaryotic cellular processes. During these processes, actin structures deform the cell membrane outward by applying forces parallel to the fiber’s major axis (as in migration) or they deform the membrane inward by applying forces perpendicular to the fiber’s major axis (as in the contractile ring during cytokinesis). Here we describe a novel actin–membrane interaction in human dermal myofibroblasts. When labeled with a cytosolic fluorophore, the myofibroblasts displayed prominent fluorescent structures on the ventral side of the cell. These structures are present in the cell membrane and colocalize with ventral actin stress fibers, suggesting that the stress fibers bend the membrane to form a “cytosolic pocket” that the fluorophores diffuse into, creating the observed structures. The existence of this pocket was confirmed by transmission electron microscopy. While dissolving the stress fibers, inhibiting fiber protein binding, or inhibiting myosin II binding of actin removed the observed pockets, modulating cellular contractility did not remove them. Taken together, our results illustrate a novel actin–membrane bending topology where the membrane is deformed outward rather than being pinched inward, resembling the topological inverse of the contractile ring found in cytokinesis.     

Theoretical estimates of mechanical properties of the endothelial cell cytoskeleton.

Current modeling of endothelial cell mechanics does not account for the network of F-actin that permeates the cytoplasm. This network, the distributed cytoplasmic structural actin (DCSA), extends from apical to basal membranes, with frequent attachments. Stress fibers are intercalated within the network, with similar frequent attachments. The microscopic structure of the DCSA resembles a foam, so that the mechanical properties can be estimated with analogy to these well-studied systems. The moduli of shear and elastic deformations are estimated to be on the order of 10(5) dynes/cm2. This prediction agrees with experimental measurements of the properties of cytoplasm and endothelial cells reported elsewhere. Stress fibers can potentially increase the modulus by a factor of 2-10, depending on whether they act in series or parallel to the network in transmitting surface forces. The deformations produced by physiological flow fields are of insufficient magnitude to disrupt cell-to-cell or DCSA cross-linkages. The questions raised by this paradox, and the ramifications of implicating the previously unreported DCSA as the primary force transmission element are discussed.     

New Membrane Concept Applied to the Analysis of Fluid Shear- and Micropipette-Deformed Red Blood Cells

A two-dimensional elastomer material concept of the red cell membrane is applied to the analysis of fluid shear-deformed, point-attached red cells and micropipette aspiration of red cell disks. The elastic constant (corresponding to the “shear” modulus multiplied by the membrane thickness) is of the order 10^-2 dyn/cm for both cases. Additional experimental observations are in agreement with the membrane model, e.g. teardrop and “tether” formation of the sheared disks, pressure difference vs. aspirated length of the cell for micropipette experiments, etc     

Mechanical properties of the tracheal mucosal membrane in the rabbit. II. Morphometric analysis.

Folding of the airway mucosal membrane provides a mechanical load that impedes airway smooth muscle contraction. Mechanical testing of rabbit tracheal mucosal membrane showed that the membrane is stiffer in the longitudinal than in the circumferential direction of the airway. To explain this difference in the mechanical properties, we studied the morphological structure of the rabbit tracheal mucosal membrane in both longitudinal and circumferential directions. The collagen fibers were found to form a random meshwork, which would not account for differences in stiffness in the longitudinal and circumferential directions. The volume fraction of the elastic fibers was measured using a point-counting technique. The orientation of the elastic fibers in the tissue samples was measured using a new method based on simple geometry and probability. The results showed that the volume fraction of the elastic fibers in the rabbit tracheal mucosal membrane was approximately 5% and that the elastic fibers were mainly oriented in the longitudinal direction. Age had no statistically significant effect on either the volume fraction or the orientation of the elastic fibers. Linear correlations were found between the steady-state stiffness and the quantity of the elastic fibers oriented in the direction of testing.     

Discovery of the migrasome,an organelle mediating release of cytoplasmic contents during cell migration

Cells communicate with each other through secreting and releasing proteins and vesicles. Many cells can migrate. In this study, we report the discovery of migracytosis, a cell migration-dependent mechanism for releasing cellular contents, and migrasomes, the vesicular structures that mediate migracytosis. As migrating cells move, they leave long tubular strands, called retraction fibers, behind them. Large vesicles, which contain numerous smaller vesicles, grow on the tips and intersections of retraction fibers. These fibers, which connect the vesicles with the main cell body, eventually break, and the vesicles are released into the extracellular space or directly taken up by surrounding cells. Since the formation of these vesicles is migration-dependent, we named them “migrasomes”. We also found that cytosolic contents can be transported into migrasomes and released from the cell through migrasomes. We named this migration-dependent release mechanism “migracytosis”.     

The Anisotropic Elastic Properties of the Sarcolemma of the Frog Semitendinosus Muscle Fiber

Tension and curvature of the sarcolemmal tube of the frog muscle fiber were measured at different extensions and were used to calculate the anisotropic elastic properties of the sarcolemma. A model was derived to obtain the four parameters of the elasticity matrix of the sarcolemma. Sarcolemmal thickness was taken as 0.1 μm. Over the range of reversible sarcolemmal tube extension, the longitudinal elastic modulus E_L = 6.3 × 10⁷ dyn/cm², the circumferential modulus E_c = 0.88 × 10⁷ dyn/cm², the longitudinal Poisson's ratio σ_L = 1.2, and the circumferential Poisson's ratio σ_c = 0.18. At tubular rest length E_L = 1.2 × 10⁷ dyn/cm². The sarcolemma is less extensible in the longitudinal direction along the fiber axis than in the circumferential direction. It can be extended reversibly to 48% of its rest length, equivalent to extending the intact fiber from a sarcomere length of 3 μm to about 4.5 μm. The sarcolemma does not contribute to intact fiber tension at fiber sarcomere lengths <3 μm, and between 3 and 4 μm its contribution is about 20%. It also exerts a pressure on the myoplasm, which can be calculated by means of the model. The longitudinal elastic modulus of the whole fiber is 1 × 10⁵ dyn/cm² at a sarcomere length of 2.33 μm.     

Titin Extensibility In Situ: Entropic Elasticity of Permanently Folded and Permanently Unfolded Molecular Segments

Abstract. Titin (also known as connectin) is a giant protein that spans half of the striated muscle sarcomere. In the I-band titin extends as the sarcomere is stretched, developing what is known as passive force. The I-band region of titin contains tandem Ig segments (consisting of serially linked immunoglobulin-like domains) with the unique PEVK segment in between (Labeit, S., and B. Kolmerer. 1995. Science. 270:293–296). Although the tandem Ig and PEVK segments have been proposed to behave as stiff and compliant springs, respectively, precise experimental testing of the hypothesis is still needed. Here, sequence-specific antibodies were used to mark the ends of the tandem Ig and PEVK segments. By following the extension of the segments as a function of sarcomere length (SL), their respective contributions to titin's elastic behavior were established. In slack sarcomeres (~2.0 μm) the tandem Ig and PEVK segments were contracted. Upon stretching sarcomeres from ~2.0 to 2.7 μm, the “contracted” tandem Ig segments straightened while their individual Ig domains remained folded. When sarcomeres were stretched beyond ~2.7 μm, the tandem Ig segments did not further extend, instead PEVK extension was now dominant. Modeling tandem Ig and PEVK segments as entropic springs with different bending rigidities (Kellermayer, M., S. Smith, H. Granzier, and C. Bustamante. 1997. Science. 276:1112–1116) indicated that in the physiological SL range (a) the Ig-like domains of the tandem Ig segments remain folded and (b) the PEVK segment behaves as a permanently unfolded polypeptide. Our model provides a molecular basis for the sequential extension of titin's different segments. Initially, the tandem Ig segments extend at low forces due to their high bending rigidity. Subsequently, extension of the PEVK segment occurs only upon reaching sufficiently high external forces due to its low bending rigidity. The serial linking of tandem Ig and PEVK segments with different bending rigidities provides a unique passive force–SL relation that is not achievable with a single elastic segment.     

A light and electron microscopic study of the flagellate-to-ameba conversion in the MyxomyceteStemonitis pallida

Summary The flagellate-to-ameba conversion process of the MyxomyceteStemonitis pallida was investigated with Nomarski optics and electron microscopy. The flagellate has two flagella, a long and a short one. When the water film containing the flagellates becomes very thin, they retract their flagella, usually the short one first and then the long one. The short flagellum is retracted by only one method, in which the sheath membrane of the flagellum fuses with the cell membrane, consequently causing the axoneme to be absorbed into the cytoplasm. Retraction of the long flagellum can be divided into four types. In all cases, fusion of the sheath membrane and the cell membrane takes place. The retracted axoneme of the long flagellum sometimes beats convulsively for about 10 minutes after retraction, and after 10–15 minutes it became indistinguishable as it was detached from the blepharoplast.Analysis of thin sections shows that the retracted axonemes disintegrate in the following squence: B-tubules, A-tubules, spokes, central microtubules. In almost all cells the degradation begins immediately after retraction and is completed within 90 minutes. Only on rare occasions, structures which seem to have been derived from retracted axonemes are observed in the ameba about 90 minutes after conversion. The basal bodies and cytoplasmic microtubules are a little more stable than the retracted axonemes. Some basal bodies of the short flagellum, whose C-tubules are affected, are present in the amebae more than 90 minutes after conversion. Cytoplasmic microtubules decrease in number and become shorter in the amebae after about 24 hours, when newly formed regions filled with flocculent material appear.     

Mechanical Forces Impeding Exocytotic Surfactant Release Revealed by Optical Tweezers

The release of surfactant from alveolar type II cells is essential to lower the surface tension in the lung and to facilitate inspiration. However, the factors controlling dispersal and diffusion of this hydrophobic material are still poorly understood. Here we report that release of surfactant from the fused vesicle, termed lamellar body (LB), resisted mechanical forces applied by optical tweezers: At constant trapping force, the probability to expand LB contents, i.e., to “pull” surfactant into the extracellular fluid, increased with time after LB fusion with the plasma membrane, consistent with slow fusion pore expansion in these cells. Elevations of the cytoplasmic Ca²⁺ concentration ([Ca²⁺]_c) had a similar effect. Inasmuch as surfactant did not disintegrate in the extracellular space, this method permitted for the first time the determination of elastic and recoil properties of the macromolecular complex, yielding a spring constant of ~12.5 pN/μm. This is the first functional evidence that release of hydrophobic material is mechanically impeded and occurs in an “all-or-none” fashion. This mode of release is most probably the result of cohesive forces of surfactant, combined with adhesive forces and/or retaining forces exerted by a constrictive fusion pore acting as a regulated mechanical barrier, withstanding forces up to 160 pN. In independent experiments equiaxial strain was exerted on cells without optical tweezers. Strain facilitated surfactant release from preexisting fused vesicles, consistent with the view of mechanical impediments during the release process, which can be overcome by cell strain.     

Local deformation of human red blood cells in high frequency electric field

A method of local and general deformation of single erythrocytes by external forces in high-frequency electric field is described. The method allows the avoidance of any mechanical contact of the cell with electrodes. Under the action of the forces applied human erythrocytes change their shape and produce various membrane structures: long filopodia-like processes, retraction fibers and lamella-like structures. These structures are never formed by erythrocytes under normal conditions, but are typical for fibroblasts, macrophages and epithelium cells. By the method developed the elastic properties of spicules on the membranes of echinocytes were also studied. Deformation of echinocyte in high-frequency electric field leads to the smoothing out of spicules. However, after the electric field is turned off, echinocyte restores its initial forms including the number and localization of all initial spicules on the cell surface.     

Electrically Induced Tentacle Retraction in the Suctorian Protozoon Discophrya collini (Root)1

Discophrya collini is a free-living suctorian with retractile tentacles covered by a thick fibrous cortex. The tentacles contain a microtubular central canal surrounded at the base by a fibrous collar. Electrical stimulation induces a reproducible tentacle retraction. With extracellular electrodes, the tentacles nearest the anode respond initially, contracting by up to 75% of their original length. There is an inverse relationship between voltage level and duration of stimulus in producing a threshold response, and at a set voltage, between duration and degree of retraction. With intracellular electrodes, the membrane potential has been measured as -30 mV, and tentacle retraction occurs in response to as little as 1.25 nA when the intracellular electrode is made the cathode of the circuit. SEM studies show that retracted tentacles have a wrinkled cortex, while TEM shows that the microtubular canal bends as it enters the cytoplasm. No consistent changes occur in the microtubule configuration of the canal on retraction, suggesting that the microtubules are not directly involved in the contractile mechanism.     

Measurement of Elastic Modulus of Collagen Type I Single Fiber

Collagen fibers are the main components of the extra cellular matrix and the primary contributors to the mechanical properties of tissues. Here we report a novel approach to measure the longitudinal component of the elastic moduli of biological fibers under conditions close to those found in vivo and apply it to type I collagen from rat tail tendon. This approach combines optical tweezers, atomic force microscopy, and exploits Euler-Bernoulli elasticity theory for data analysis. This approach also avoids drying for measurements or visualization, since samples are freshly extracted. Importantly, strains are kept below 0.5%, which appear consistent with the linear elastic regime. We find, surprisingly, that the longitudinal elastic modulus of type I collagen cannot be represented by a single quantity but rather is a distribution that is broader than the uncertainty of our experimental technique. The longitudinal component of the single-fiber elastic modulus is between 100 MPa and 360 MPa for samples extracted from different rats and/or different parts of a single tail. Variations are also observed in the fibril-bundle / fibril diameter with an average of 325±40 nm. Since bending forces depend on the diameter to the fourth power, this variation in diameter is important for estimating the range of elastic moduli. The remaining variations in the modulus may be due to differences in composition of the fibril-bundles, or the extent of the proteoglycans constituting fibril-bundles, or that some single fibrils may be of fibril-bundle size.     

Endothelial cell connecting filaments anchor endothelial cells to the subjacent elastic lamina in the developing aortic intima of the mouse

The ultrastructural association of endothelial cells with the subjacent elastic lamina was investigated in the developing mouse aorta by electron microscopy. In the 5-day postnatal aorta, extensive filament bundles extend along the subendothelial matrix connecting the endothelial cells to the underlying elastic lamina. The connecting filaments form lateral associations with the abluminal surface of the endothelial cells in regions of membrane occupied by membrane-associated dense plaques. On the intracellular face of each plaque, the termini of stress fibers penetrate and anchor to the cell membrane in alignment with the extracellular connecting filaments. Both the stress fibers and the connecting filaments are oriented parallel to the longitudinal axis of the vessel. High magnification electron micrographs of individual endothelial cell connecting filaments reveal features similar to those of elastin-associated microfibrils. Each connecting filament consists of a 9–10 nm linear core with an electron-lucent center and peripheral spike-like projections. From the filaments, small thread-like extensions span laterally, linking the filaments into a loose bundle and anchoring them to the endothelial cell membrane and the surface of the elastic lamina. The filaments also appear heavily coated with electron-dense material; often with some degree of periodicity along the filament length. During development, the number of endothelial cell connecting filaments decreases as the elastic lamina expands and the subendothelial matrix is reduced. In the aortic intima of mature mice, the elastic lamina is closely apposed to the abluminal surface of the endothelial cell and no connecting filaments are seen. These observations suggest that endothelial cell connecting filaments are developmental features of the aortic intima which, together with the intracellular stress fibers, aid to maintain the structural integrity of the endothelial cell layer during development by providing the cells with protection from intraluminal shear forces.     

Multiple Forms of Endocytosis In Bovine Adrenal Chromaffin Cells

We studied endocytosis in chromaffin cells with both perforated patch and whole cell configurations of the patch clamp technique using cell capacitance measurements in combination with amperometric catecholamine detection. We found that chromaffin cells exhibit two relatively rapid, kinetically distinct forms of stimulus-coupled endocytosis. A more prevalent “compensatory” retrieval occurs reproducibly after stimulation, recovering an approximately equivalent amount of membrane as added through the immediately preceding exocytosis. Membrane is retrieved through compensatory endocytosis at an initial rate of ~6 fF/s. Compensatory endocytotic activity vanishes within a few minutes in the whole cell configuration. A second form of triggered membrane retrieval, termed “excess” retrieval, occurs only above a certain stimulus threshold and proceeds at a faster initial rate of ~248 fF/s. It typically undershoots the capacitance value preceding the stimulus, and its magnitude has no clear relationship to the amount of membrane added through the immediately preceding exocytotic event. Excess endocytotic activity persists in the whole cell configuration. Thus, two kinetically distinct forms of endocytosis coexist in intact cells during perforated patch recording. Both are fast enough to retrieve membrane after exocytosis within a few seconds. We argue that the slower one, termed compensatory endocytosis, exhibits properties that make it the most likely mechanism for membrane recycling during normal secretory activity.