Search

Purpose: The aim of our study is to evaluate local tumour control rates, radiation side-effects, visual preservation and disease-free survival (DFS) of uveal melanoma (UM) patients treated with fractionated stereotactic radiotherapy (fSRT). Methods: A retrospective study of UM patients, who were treated with fSRT (N = 189), was performed by the Rotterdam Ocular Melanoma Study group (ROMS), the Netherlands, between 1999 and 2014 with a follow-up of at least 5 years. Results: The 1-, 3-, 5-, 10- and 15-year local tumour control rates were as follows: 99.4%, 92.8%, 92.2%, 89.3% and 89.3%, respectively. Cataract (67.8%) was the most common side-effect of fSRT followed by retinopathy (35.1%), maculopathy (23.8%), vitreous haemorrhage (20.1%), neovascular glaucoma (NVG) (20.0%) and optic neuropathy (12.4%). Patients with anterior located UMs developed cataract more frequently (p = 0.047, multivariable analysis). By multivariable analysis, significant factors for secondary enucleation were tumour recurrence (p

6 pags. 5 figs., For the first time, the FRagment Separator (FRS) and the Multiple-Reflection Time-Of-Flight Mass-Spectrometer (MR-TOF-MS) particle identification (PID) systems at GSI have been coupled. This new approach adds to the standard FRS PID an additional unambiguous identification of the fragments and the possibility to identify and count long-lived isomeric states (>ms). For this purpose, single-event timestamp information given by a common clock was used to correlate both systems. Two methods were implemented to improve the signal-to-background ratio by more than a factor 2 in the high resolution mass spectrum obtained with the MR-TOF-MS for the 109In isotope. Moreover, the coupling of the systems allows an improvement in the on-line monitoring of the FRS-Ion Catcher (IC) efficiency and extraction time. In addition, range calculations were implemented in the on-line monitoring; a powerful tool for real-time optimization of stopped beam experiments., The ELI-NP group was supported by Extreme Light Infrastructure Nuclear Physics (ELI-NP), Germany Phase II, a project co-financed by the Romanian Government and the European Union through the European Regional Development Fund the Competitiveness Operational Programme (1/07.07.2016, COP,ID 1334) and by the Romanian Ministry of Research and Innovation under contract PN 19 06 01 05. This work was supported by the German Federal Ministry for Education and Research (BMBF) under contracts No. 05P19RGFN1, 05P12RGFN8 and 05P15RGFN1, by Justus Liebig University Gießen, Germany and GSI, Germany under the JLU-GSI strategic Helmholtz partnership agreement, by HGS-HIRe, and by theHessian Ministry for Science and Art (HMWK), Germany. O. Hall was supported by UKRI STFC, United Kingdom grant ST/P004008/1.

Although typically possessing four limbs and short bodies, lizards have evolved diverse morphologies, including elongate trunks with tiny limbs. Such forms are hypothesized to aid locomotion in cluttered/fossorial environments but propulsion mechanisms (e.g., the use of body and/or limbs to interact with substrates) and potential body/limb coordination remain unstudied. Here, we use biological experiments, a geometric theory of locomotion, and robophysical models to investigate body–limb coordination in diverse lizards. Locomotor field studies in short-limbed, elongate lizards ( Brachymeles and Lerista ) and laboratory studies of fully limbed lizards ( Uma scoparia and Sceloporus olivaceus ) and a snake ( Chionactis occipitalis ) reveal that body-wave dynamics can be described by a combination of standing and traveling waves; the ratio of the amplitudes of these components is inversely related to the degree of limb reduction and body elongation. The geometric theory (which replaces laborious calculation with diagrams) helps explain our observations, predicting that the advantage of traveling-wave body undulations (compared with a standing wave) emerges when the dominant thrust-generation mechanism arises from the body rather than the limbs and reveals that such soil-dwelling lizards propel via “terrestrial swimming” like sand-swimming lizards and snakes. We test our hypothesis by inducing the use of traveling waves in stereotyped lizards via modulating the ground-penetration resistance. Study of a limbed/undulatory robophysical model demonstrates that a traveling wave is beneficial when propulsion is generated by body–environment interaction. Our models could be valuable in understanding functional constraints on the evolutionary processes of elongation and limb reduction as well as advancing robot designs.

Nuclear properties across the chart of nuclides are key to improving and validating our understanding of the strong interaction in nuclear physics. We present high-precision mass measurements of neutron-rich Fe isotopes performed at the TITAN facility. The multiple-reflection time-of-flight mass spectrometer (MR-ToF-MS), achieving a resolving power greater than $600\,000$ for the first time, enabled the measurement of $^{63-70}$Fe, including first-time high-precision direct measurements ($\delta m/m \sim 10^{-7}$) of $^{68-70}$Fe, as well as the discovery of a long-lived isomeric state in $^{69}$Fe. These measurements are accompanied by both mean-field and ab initio calculations using the most recent realizations which enable theoretical assignment of the spin-parities of the $^{69}$Fe ground and isomeric states. Together with mean-field calculations of quadrupole deformation parameters for the Fe isotope chain, these results benchmark a maximum of deformation in the $N = 40$ island of inversion in Fe, and shed light on trends in level densities indicated in the newly-refined mass surface., Comment: 9 pages, 6 figures

BackgroundDiverse architectures of nervous systems (NSs) such as a plexus in cnidarians or a more centralized nervous system (CNS) in insects and vertebrates are present across Metazoa, but it is unclear what selection pressures drove evolution and diversification of NSs. One underlying aspect of this diversity lies in the cellular and molecular mechanisms driving neurogenesis, i.e. generation of neurons from neural precursor cells (NPCs). In cnidarians, vertebrates, and arthropods, homologs of SoxB and bHLH proneural genes control different steps of neurogenesis, suggesting that some neurogenic mechanisms may be conserved. However, data are lacking for spiralian taxa.ResultsTo that end, we characterized NPCs and their daughters at different stages of neurogenesis in the spiralian annelidCapitella teleta. We assessed cellular division patterns in the neuroectoderm using static and pulse-chase labeling with thymidine analogs (EdU and BrdU), which enabled identification of NPCs that underwent multiple rounds of division. Actively-dividing brain NPCs were found to be apically-localized, whereas actively-dividing NPCs for the ventral nerve cord (VNC) were found apically, basally, and closer to the ventral midline. We used lineage tracing to characterize the changing boundary of the trunk neuroectoderm. Finally, to start to generate a genetic hierarchy, we performed double-fluorescent in-situ hybridization (FISH) and single-FISH plus EdU labeling for neurogenic gene homologs. In the brain and VNC,Ct-soxB1andCt-neurogeninwere expressed in a large proportion of apically-localized, EdU+NPCs. In contrast,Ct-ash1was expressed in a small subset of apically-localized, EdU+NPCs and subsurface, EdU−cells, but not inCt-neuroD+orCt-elav1+cells, which also were subsurface.ConclusionsOur data suggest a putative genetic hierarchy withCt-soxB1andCt-neurogeninat the top, followed byCt-ash1, thenCt-neuroD, and finallyCt-elav1. Comparison of our data with that fromPlatynereis dumeriliirevealed expression ofneurogeninhomologs in proliferating NPCs in annelids, which appears different than the expression of vertebrateneurogeninhomologs in cells that are exiting the cell cycle. Furthermore, differences between neurogenesis in the head versus trunk ofC. teletasuggest that these two tissues may be independent developmental modules, possibly with differing evolutionary trajectories.

Synopsis Elongate, snake- or eel-like, body forms have evolved convergently many times in most major lineages of vertebrates. Despite studies of various clades with elongate species, we still lack an understanding of their evolutionary dynamics and distribution on the vertebrate tree of life. We also do not know whether this convergence in body form coincides with convergence at other biological levels. Here, we present the first craniate-wide analysis of how many times elongate body forms have evolved, as well as rates of its evolution and reversion to a non-elongate form. We then focus on five convergently elongate squamate species and test if they converged in vertebral number and shape, as well as their locomotor performance and kinematics. We compared each elongate species to closely related quadrupedal species and determined whether the direction of vertebral or locomotor change matched in each case. The five lineages examined are obscure species from remote locations, providing a valuable glimpse into their biology. They are the skink lizards Brachymeles lukbani, Lerista praepedita, and Isopachys anguinoides, the basal squamate Dibamus novaeguineae, and the basal snake Malayotyphlops cf. ruficaudus. Our results support convergence among these species in the number of trunk and caudal vertebrae, but not vertebral shape. We also find that the elongate species are relatively slower than their limbed counterparts and move with lower frequency and higher amplitude body undulations, with the exception of Isopachys. This is among the first evidence of locomotor convergence across distantly related, elongate species.

Endolysosomal compartments maintain cellular fitness by clearing dysfunctional organelles and proteins from cells. Modulation of their activity offers therapeutic opportunities. Quantification of cargo delivery to and/or accumulation within endolysosomes is instrumental for characterizing lysosome-driven pathways at the molecular level and monitoring consequences of genetic or environmental modifications. Here we introduce LysoQuant, a deep learning approach for segmentation and classification of fluorescence images capturing cargo delivery within endolysosomes for clearance. LysoQuant is trained for unbiased and rapid recognition with human-level accuracy, and the pipeline informs on a series of quantitative parameters such as endolysosome number, size, shape, position within cells, and occupancy, which report on activity of lysosome-driven pathways. In our selected examples, LysoQuant successfully determines the magnitude of mechanistically distinct catabolic pathways that ensure lysosomal clearance of a model organelle, the endoplasmic reticulum, and of a model protein, polymerogenic ATZ. It does so with accuracy and velocity compatible with those of high-throughput analyses.

Many animals frequently transition between different media while navigating their heterogeneous environments. These media vary in compliance, moisture content, and other characteristics that affect their physical properties. As a result, animals may need to alter their kinematics to adapt to potential changes in media while maintaining performance during predator escape and foraging. Due to its fluid nature, water is highly compliant, and although usually associated with swimming, water running has evolved in a variety of animals ranging from insects to mammals. While the best studied large water runners are the bipedal basilisk lizards (Basiliscus spp.), other lizards have also been observed to run across the surface of water, namely, Hemidactylus platyurus, a house gecko, and in this study, Anolis sagrei, the brown anole. Unlike the basilisk lizard, the primarily arboreal Anolis sagrei is not adapted for water running. Moreover, water running in A. sagrei, similar to that of the house gecko, was primarily quadrupedal. Here, we tested for performance and kinematic differences between aquatic and terrestrial running and if the variance in performance and kinematic variables differed between the two media. We found no difference in average and maximum velocity between running on land and water. We also found that Anolis sagrei had higher hindlimb stride frequencies, decreased duty factor, and shorter stride lengths on water, as well as more erect postures. Finally, we found that most kinematics did not differ in variance between the two media, but of those that were different, almost all were more variable during terrestrial running. Our findings show that animals may be capable of specialized modes of locomotion, even if they are not obviously adapted for them, and that they may do this by modulating their kinematics to facilitate locomotion through novel environments.

We present first preliminary results of a novel method for measuring independent isotopic fission yields (IIFYs) of spontaneous fission (SF) via direct mass measurements, at the FRS Ion Catcher (FRS-IC) at GSI. Fission products were generated from a 252Cf source installed in a cryogenic stopping cell, and were identified and counted with the multiple-reflection time-of-flight mass spectrometer (MR-TOF-MS) of the FRS-IC, utilizing well-established measurement and data analysis methods. The MR-TOF-MS resolves isobars unambiguously, even with limited statistics, and its non-scanning nature ensures minimal relative systematic uncertainties amongst fission products. The analysis for extracting IIFYs includes isotope-dependent efficiency corrections for all components of the FRS-IC. In particular, we applied a self-consistent technique that takes into account the element-dependent survival efficiencies in the CSC, due to chemical reactions with the buffer gas. Our IIFY results, which cover several tens of fission products in the less-accessible high-mass peak (Z = 56 to 63) down to fission yields at the level of 10−5, are generally similar to those of the nuclear database ENDF/B-VII.0. Nevertheless, they reveal some structures that are not observed in the database smooth trends. These are the first results of a planned campaign to investigate IIFY distributions of spontaneous fission at the FRS-IC. Upcoming experiments will extend our results to wider Z and N ranges, lower fission yields, and other spontaneously-fissioning actinides.

People of different racial/ethnic backgrounds, demographics, health, and socioeconomic characteristics have experienced disproportionate rates of infection and death due to COVID-19. This study tests if and how county-level rates of infection and death have changed in relation to societal county characteristics through time as the pandemic progressed. This longitudinal study sampled monthly county-level COVID-19 case and death data per 100,000 residents from April 2020 to March 2022, and studied the relationships of these variables with racial/ethnic, demographic, health, and socioeconomic characteristics for 3125 or 97.0% of U.S. counties, accounting for 96.4% of the U.S. population. The association of all county-level characteristics with COVID-19 case and death rates changed significantly through time, and showed different patterns. For example, counties with higher population proportions of Black, Native American, foreign-born non-citizen, elderly residents, households in poverty, or higher income inequality suffered disproportionately higher COVID-19 case and death rates at the beginning of the pandemic, followed by reversed, attenuated or fluctuating patterns, depending on the variable. Patterns for counties with higher White versus Black population proportions showed somewhat inverse patterns. Counties with higher female population proportions initially had lower case rates but higher death rates, and case and death rates become more coupled and fluctuated later in the pandemic. Counties with higher population densities had fluctuating case and death rates, with peaks coinciding with new variants of COVID-19. Counties with a greater proportion of university-educated residents had lower case and death rates throughout the pandemic, although the strength of this relationship fluctuated through time. This research clearly shows that how different segments of society are affected by a pandemic changes through time. Therefore, targeted policies and interventions that change as a pandemic unfolds are necessary to mitigate its disproportionate effects on vulnerable populations, particularly during the first six months of a pandemic.

Segmentation gives rise to the anterior-posterior axis in many animals, and in vertebrates this axis comprises serially arranged vertebrae. Modifications to the vertebral column abound, and a recurring, but functionally understudied, change is the elongation of the body through the addition and/or elongation of vertebrae. Here, we compared the vertebral and axial kinematics of the robustly limbed Fire skink (Riopa fernandi) representing the ancestral form, the limbless European glass lizard (Ophisaurus apodus), and the Northern water snake (Nerodia sipedon). We induced these animals to traverse through channels and peg arrays of varied widths and densities, respectively, using high-speed X-ray and light video. We found that even though the snake had substantially more and shorter vertebrae than either lizard, intervertebral joint angles did not differ between species in most treatment levels. All three species decreased the amplitude and wavelength of their undulations as channels narrowed and the lizard species increased wave frequency in narrower channels. In peg arrays, both lizard species decreased wave amplitude, while the snake showed no differences. All three species maintained similar wavelengths and frequencies as peg density increased in most cases. Our results suggest that amplitude is decoupled from wavelength and frequency in all three focal taxa. The combination of musculoskeletal differences and the decoupling of axial kinematic traits likely facilitates the formation of different undulatory waves, thereby allowing limbless species to adopt different modes of locomotion.

Summary Retropulsion represents a severe disorder of postural control in the sagittal plane. It is characterized by a posterior displacement of the center of mass with respect to the base of support and active resistance to passive correction of this posture.Although retropulsion seems quite frequent and relevant for neurorehabilitation, research on this postural behavior is limited. One major problem is that there is no established tool available to assess and quantify the behavior. Thus the objective of this Delphi study was to develop a clinical scale to assess retropulsion in neurological disorders. The Delphi method was applied to gather opinions from experts and build consensus on the validity of the content of theScale for Retropulsion. Twelve experts from different countries and disciplines participated in the Delphi study. The Delphi process comprised three rounds. All items of the scale reached consensus in the second round. The final version of the Scale for Retropulsion includes four subtests: A) static postural control, B) reactive postural control, C) resistance, and D) dynamic postural control which are tested in a sitting and a standing (initial) position. High level of international, multidisciplinary overall expert agreement was achieved for the scale (median 9, IQR 1). This bed side test will help clinicians, therapists and researchers to evaluate postural instability in the sagittal plane and to study the epidemiology, the etiology, and the rehabilitation process of patients with retropulsion. The next stage is to evaluate the clinimetric properties of the scale.

Granular substrates ranging from silt to gravel cover much of the Earth's land area, providing an important habitat for fossorial animals. Many of these animals use their heads to penetrate the substrate. Although there is considerable variation in head shape, how head shape affects fossorial locomotor performance in different granular substrates is poorly understood. Here, head shape variation for 152 species of fossorial lizards was quantified for head diameter, slope and pointiness of the snout. The force needed to penetrate different substrates was measured using 28 physical models spanning this evolved variation. Ten substrates were considered, ranging in particle size from 0.025 to 4 mm in diameter and consisting of spherical or angular particles. Head shape evolved in a weakly correlated manner, with snouts that were gently sloped being blunter. There were also significant clade differences in head shape among fossorial lizards. Experiments with physical models showed that as head diameter increased, absolute penetration force increased but force normalized by cross-sectional area decreased. Penetration force decreased for snouts that tapered more gradually and were pointier. Larger and angular particles required higher penetration forces, although intermediate size spherical particles, consistent with coarse sand, required the lowest force. Particle size and head diameter effect were largest, indicating that fossorial burrowers should evolve narrow heads and bodies, and select relatively fine particles. However, variation in evolved head shapes and recorded penetration forces suggests that kinematics of fossorial movement are likely an important factor in explaining evolved diversity.

Evolutionary reversals, including re-evolution of lost structures, are commonly found in phylogenetic studies. However, we lack an understanding of how these reversals happen mechanistically. A snake-like body form has evolved many times in vertebrates, and occasionally a quadrupedal form has re-evolved, including in Brachymeles lizards. We use body form and locomotion data for species ranging from snake-like to quadrupedal to address how a quadrupedal form could re-evolve. We show that large, quadrupedal species are faster at burying and surface locomotion than snake-like species, indicating a lack of expected performance trade-off between these modes of locomotion. Species with limbs use them while burying, suggesting that limbs are useful for burying in wet, packed substrates. Palaeoclimatological data suggest that Brachymeles originally evolved a snake-like form under a drier climate probably with looser soil in which it was easier to dig. The quadrupedal clade evolved as the climate became humid, where limbs and large size facilitated fossorial locomotion in packed soils.

Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This 'ecomechanical approach' integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, we identify key factors needed for mass data collection, analysis, and the dissemination of models relevant to this framework.

Ibrutinib has now been approved for treatment of chronic lymphocytic leukemia (CLL) in both front-line setting and as later-line treatment. However, knowledge about the outcomes and adverse events (AE) among patients at a population-based level is still limited. Objectives: To report outcomes and AEs in a population-based cohort treated with ibrutinib outside clinical trials. Methods: We conducted a multicenter, retrospective cohort study including all patients with CLL treated with ibrutinib. Results: In total, 205 patients were included of whom 39 (19%) were treatment-naïve. The median follow-up was 21.4 months (interquartile range (IQR), 11.9,32.8), the estimated overall survival at 12 months was 88.8% (95% confidence interval (CI); 84.3%, 93.3%), and the estimated progression-free survival at 12 months was 86.3% (95% CI; 81.3%, 91.2%). During follow-up, 200 (97.6%) patients had at least one AE and 100 (48.8%) patients had at least one grade ≥3 AE. Eighty-six patients (42.0%) discontinued ibrutinib, hereof 47 (54.7%) due to AEs and 19 (22.1%) had progression of CLL or Richter transformation. Conclusions: In our study, we find comparable, though slightly inferior, overall, and progression-free survival, and discontinuation due to toxicity was higher compared with clinical trials. Patient training and information may improve treatment adherence outside clinical trials.

Dramatic evolutionary transitions in morphology are often assumed to be adaptive in a new habitat. However, these assumptions are rarely tested because such tests require intermediate forms, which are often extinct. In vertebrates, the evolution of an elongate, limbless body is generally hypothesized to facilitate locomotion in fossorial and/or cluttered habitats. However, these hypotheses remain untested because few studies examine the locomotion of species ranging in body form from tetrapod to snake-like. Here, we address these functional hypotheses by testing whether trade-offs exist between locomotion in surface, fossorial and cluttered habitats in Australian Lerista lizards, which include multiple intermediate forms. We found that snake-like species penetrated sand substrates faster than more lizard-like species, representing the first direct support of the adaptation to fossoriality hypothesis. By contrast, body form did not affect surface locomotion or locomotion through cluttered leaf litter. Furthermore, all species with hindlimbs used them during both fossorial and surface locomotion. We found no evidence of a trade-off between fossorial and surface locomotion. This may be either because Lerista employed kinematic strategies that took advantage of both axial- and limb-based propulsion. This may have led to the differential occupation of their habitat, facilitating diversification of intermediate forms.

Additional file 4: Figure S3. Fates of subclones derived from the 2d sub-lineage. (A–L’) Apotome micrographs of C. teleta at different stages of neurogenesis (0–72 h post injection (hpi)) labeled with DiI (red) and Hoescht33322 (cyan) derived from 2d11 (A–D’), 2d1 (E–H′) and 2d2 (I–L’). Closed and open arrowheads in H show cell intercalation between DiI+ cells from the right side and Hoescht labeled nuclei from the left side. Closed arrowheads indicate a DiI+ cell whereas an open arrowhead indicates an intercalated non-DiI+. Asterisk in panels A, A’, E, E’, I and I′ indicates the blastopore while in all other panels asterisk denotes the mouth opening. A, A’, E, E’, I and I′ panels indicate vegetal views of blastopore stage 3 while all other panels are ventral views. In each panel, anterior is to the left and posterior the right. The number of animals examined and showing the staining pattern is indicted on the top right-hand corner of each panel. Bottom rows indicate DiI labeled patches in black and white. Prototroch (pt) and telotroch (tt) are indicated by dashes. The length of time each animal is grown is indicated at the lower left corner. Vnc: ventral nerve cord, nt: neurotroch, nec: neuroectoderm, pt.: prototroch, tt: telotroch, pg: pygidium, veg: vegetal. Scale bar: 50 μm.

Additional file 10: Figure S5. Gene expression in trunk EdU+ cells at later developmental stages. (A–E”) 30-min EdU pulse (cyan) at different stages of neurogenesis was combined with FISH (red). Ventral views of the trunk neuroectoderm (A, B, C, D, E) and transverse sections through the anterior (A’, B′, C′, D’, E’), and posterior (A”, B″, C″, D”, E”) trunk neuroectoderm are shown. Overlap of EdU+ cells with Ct-soxB1 (A–A”), Ct-ngn (B–B″), Ct-ash1 (C–C″), Ct-neuroD (D–D”), and Ct-elav1 (E–E”) at later stages are shown. In panels A–E”, closed arrowheads indicate EdU+/gene+ cells while open arrowheads show EdU−/gene+ cells. In ventral view panels A–E, orientation of the animal is indicated in the bottom right corner, and developmental stage is indicated in the top right corner. (F–H) The number of EdU+ cells expressing a Ct-soxB1 (F), Ct-ngn (G), and Ct-ash1 (H) counted within ROI 1, 2 and 3 in segments 2–4, 5–7, and 8–10 in the VNC were scored at stages 4–6 as shown in Fig. S4H. In F–H, capital letters on top of the boxplots (e.g. A, B etc.) indicate statistical significance computed using mixed effects model analysis for comparison of individual ROIs across stages, e.g., comparison of EdU+/gene+ numbers in ROI 1 at stage 4 to that at stage 5 and 6 and so on for ROI 2. Black dots represent outliers (±3 S.D.). In orthogonal views, apical is up, basal is down and yellow dot shows the position of the ventral midline. White dotted line marks the apical boundaries of the neuroectoderm. In ventral views, anterior is to the left and posterior to the right. An asterisk denotes the mouth. Scale bar is 50 μm. ant, anterior; vent, ventral. ST4mid: Stage 4 middle, ST4tt: Stage 4 telotroch, ST5: Stage 5, ST6: Stage 6.

Additional file 2: Figure S2. (A) EdU pulse-chase experiments involving 30-min EdU pulses at stage 4 once a telotroch is present followed by 3-h thymidine chase and incubation in seawater for different lengths of time as indicated. (B) Images showing apical to basal migration of initially labeled NPCs and their daughters in the head with time. Length of time post-EdU pulse indicated on the upper-left corner of each panel (C) Method for counting EdU+ cells using ROIs across different depths of the head. Differentially colored boxes indicate the ROIs at different depths where counts were conducted. The solid double-head arrow indicates distance between each ROI. The dotted double-head arrow indicates the distance of the lateral edges of the ROIs from the nearest apical surface showing that cells lying in those regions can misleadingly represent basally-localized cells when they are actually apical. (D–F) Graphs indicate the dynamics and behavior of initially labeled NPCs and their daughters across different lengths of time. The x-axis represents the times post EdU pulse while the panels indicate depths for ROI 1 and 4. Boxplots within each depth (ROI 1 versus 4) indicate the lengths of the seawater chase in ascending order beginning from left to right – 0 h (red) and 48 h (blue). Capital letters above the boxplots compare chase within a particular ROI and hence are comparisons across each set of eight adjacent box plots. The lowercase letters below the boxplots indicate comparison of apical versus basal depths (ROI 1 versus ROI 4) at a particular time point e.g. comparison between the first boxplot of the two different depths and so on (for example, 0–10 μm depth at t = 0 versus 30–40 μm depth at t = 0). In all cases, “a” or “A” corresponds to treatments that have the lowest values and then the letters advance in alphabetical order as the y-axis variable increases. Boxplots with the same letter are not significantly different. Those with different letters are significantly different, with p

Additional file 7: Figure S4. Assessment of cell proliferation and contribution of EdU+ NPCs at stage 4 to the VNC. (A) Schematic showing EdU pulse chase experiment with EdU pulse at stage 4 telotroch followed by 3 h of 10 μm thymidine chase and subsequent incubation in sea-water for respective time lengths. (B–G.2) Panels show the cell proliferation profiles and the behavior of their progeny from 0 h till 72 h. Ventral views (B, C, D, E, F, G) and orthogonal views (B.1, B.2, C.1, C.2, D.1, D.2, E.1, E.2, F.1, F.2, G.1, G.2) of larval trunk neuroectoderm at six different time intervals (0 h, 6 h, 9 h, 20 h, 36 h and 72 h) shown labeled with EdU (green) and Hoescht 33,322 (magenta). B.1, C.1, D.1. E.1, F.1, G.1 indicate orthogonal views along the dashed line labeled “1” and B.2, C.2, D.2. E.2, F.2, G.2 represent orthogonal views along the dashed line labeled “2” in B, C, D, E, F, G, respectively. Arrows in D.2, E.1, E.2, F.1, F.2 indicate stippled labeled EdU+ cells localized on the surface trunk ectoderm. In each panel showing ventral views (B, C, D, E, F, G), anterior is to the left and posterior the right. Prototroch (pt) and telotroch (tt) are indicated by dashes. Asterisk denotes the position of the mouth in all ventral views. The length of thymidine chase and sea-water incubation is indicated at the upper right-hand corner. In the orthogonal views, the yellow dot denotes the position of the ventral midline. Apical is upwards while basal is down in all orthogonal views (B.1, B.2, C.1, C.2, D.1, D.2, E.1, E.2, F.1, F.2, G.1, G.2). (H) Counting method for EdU+ cells and Hoescht+ cells in the trunk. For stage 4, the distance of the presumptive neuroectoderm was measured to be ~ 22 μm from the ventral midline (dotted line segment). Square boxes represent 30 μm × 30 μm ROIs where cells were counted using Fiji Cell-Counter plugin (ImageJ, NIH). In each animal ROIs 1 and 2 were counted on the left and right sides of the animal for stages 4 and 5. For stage 6, ROIs 1, 2 and 3 were counted on either side of the midline. ST4tt: stage 4 telotroch, ST5e: stage 5 early, ST5mid: stage 5 middle, ST5l: stage 5 late, ST6e: stage 6 early, ST6mid: stage 6 middle. mo: mouth, ms: mesoderm, nec: neuroectoderm. Scale bar: 50 μm.

Iron deficiency is a common cause of reactive thrombocytosis resulting in usually mild to moderately increased but sometimes even in extreme thrombocytosis (ie, >1000×109/L). We report a case of a 34-year-old woman who developed an increased platelet count of 1953×109/L. Upon admission, cytoreductive therapy was initiated until an underlying chronic myeloproliferative neoplasia was ruled out. The patient had undergone bariatric surgery 5 years previously, and surprisingly, a diagnosis of reactive thrombocytosis due to iron deficiency secondary to iron malabsorption was made. It is concluded that the degree of extreme thrombocytosis may be even fourfold to fivefold increased in patients with severe iron deficiency. Our finding emphasises the importance of regular control of possible need for iron supplementation following bariatric surgery.

Additional file 8. Supplementary Material Supplementary Information with Supplementary Methods and Tables S1–S6.

Convergent evolution of phenotypes is considered evidence that evolution is deterministic. Establishing if such convergent phenotypes arose through convergent evolutionary pathways is a stronger test of determinism. We studied the evolution of snake-like body shapes in six clades of lizards, each containing species ranging from short-bodied and pentadactyl to long-bodied and limbless. We tested whether body shapes that evolved in each clade were convergent, and whether clades evolved snake-like body shapes following convergent evolutionary pathways. Our analyses showed that indeed species with the same numbers of digits in each clade evolved convergent body shapes. We then compared evolutionary pathways among clades by considering patterns of evolutionary integration and shape of relationship among body parts, patterns of vertebral evolution, and models of digit evolution. We found that all clades elongated their bodies through the addition, not elongation, of vertebrae, and had similar patterns of integration. However, patterns of integration, the body parts that were related by a linear or a threshold model, and patterns of digit evolution differed among clades. These results showed that clades followed different evolutionary pathways. This suggests an important role of historical contingency as opposed to determinism in the convergent evolution of snake-like body shapes.

Venous thromboembolism (VTE) is associated with inferior survival in cancer patients. The risk of VTE and its effect on survival in chronic lymphocytic leukemia (CLL) patients remains unclear. The present study investigated the impact of patient-related factors, CLL prognostic markers, and CLL treatment on the risk of VTE and assessed overall survival relative to VTE. All patients in the Danish National CLL Registry (2008-2015) were followed from the date of CLL diagnosis to death, VTE, emigration, or administrative censoring. Hazard ratios (HRs) were estimated using Cox models, and second primary cancers and anticoagulation treatment were included as time-varying exposures. During a median follow-up of 2.6 years, 92 VTEs occurred among 3609 CLL patients, corresponding to a total incidence rate of 8.2 VTEs per 1000 person-years (95% confidence interval [CI], 6.7-10.1). A history of VTE or second primary cancer was associated with HRs of VTE of 5.09 (95% CI, 2.82-9.17) and 3.72 (95% CI, 2.15-6.34), respectively, while β2-microglobulin >4 mg/L, unmutated immunoglobulin HV and unfavorable cytogenetics had lower HRs. CLL patients with VTE had marginally higher mortality, which was most pronounced among patients

Study of the unfolded protein responses (UPR) is mainly addressed by challenging eukaryotic cells with chemical compounds that impair calcium, redox or glycan homeostasis. These dramatically alter the endoplasmic reticulum (ER) environment and function, but also trigger pleiotropic effects that may result in multi-organellar failure and cell death. Recent works showed that UPR induced by the accumulation of unfolded polypeptides in the ER lumen drastically differs from chemically induced UPR. Unfolded proteins are tolerated by cells, which activate a finely tuned UPR without entering apoptotic programs. How cells adapt the UPR to the burden of misfolded proteins, what structural features of the accumulating proteins determine UPR intensity and how these mechanisms translate into disease are crucial questions to be address in the future.

Evolutionary simplification of autopodial structures is a major theme in studies of body-form evolution. Previous studies on amniotes have supported Morse's law, that is, that the first digit reduced is Digit I, followed by Digit V. Furthermore, the question of reversibility for evolutionary digit loss and its implications for "Dollo's law" remains controversial. Here, we provide an analysis of limb and digit evolution for the skink genus Brachymeles. Employing phylogenetic, morphological, osteological, and myological data, we (a) test the hypothesis that digits have re-evolved, (b) describe patterns of morphological evolution, and (c) investigate whether patterns of digit loss are generalizable across taxa. We found strong statistical support for digit, but not limb re-evolution. The feet of pentadactyl species of Brachymeles are very similar to those of outgroup species, while the hands of these lineages are modified (2-3-3-3-2) and a have a reduced set of intrinsic hand muscles. Digit number variation suggests a more labile Digit V than Digit I, contrary to Morse's law. The observed pattern of digit variation is different from that of other scincid lizards (Lerista, Hemiergis, Carlia). Our results present the first evidence of clade-specific modes of digit reduction.

The stress sensors ATF6, IRE1, and PERK monitor deviations from homeostatic conditions in the endoplasmic reticulum (ER), a protein biogenesis compartment of eukaryotic cells. Their activation elicits unfolded protein responses (UPR) to re-establish proteostasis. UPR have been extensively investigated in cells exposed to chemicals that activate ER stress sensors by perturbing calcium, N-glycans, or redox homeostasis. Cell responses to variations in luminal load with unfolded proteins are, in contrast, poorly characterized. Here, we compared gene and protein expression profiles in HEK293 cells challenged with ER stress–inducing drugs or expressing model polypeptides. Drug titration to limit up-regulation of the endogenous ER stress reporters heat shock protein family A (Hsp70) member 5 (BiP/HSPA5) and homocysteine-inducible ER protein with ubiquitin-like domain 1 (HERP/HERPUD1) to levels comparable with luminal accumulation of unfolded proteins substantially reduced the amplitude of both transcriptional and translational responses. However, these drug-induced changes remained pleiotropic and failed to recapitulate responses to ER load with unfolded proteins. These required unfolded protein association with BiP and induced a much smaller subset of genes participating in a chaperone complex that binds unfolded peptide chains. In conclusion, UPR resulting from ER load with unfolded proteins proceed via a well-defined and fine-tuned pathway, whereas even mild chemical stresses caused by compounds often used to stimulate UPR induce cellular responses largely unrelated to the UPR or ER-mediated protein secretion.

With hundreds of thousands of chemicals in the environment, effective monitoring requires high-throughput analytical techniques. This paper presents a quantitative screening method for 1550 chemicals based on statistical modeling of responses with identification and integration performed using deconvolution reporting software. The method was evaluated with representative environmental samples. We tested biological extracts, low-density polyethylene, and silicone passive sampling devices spiked with known concentrations of 196 representative chemicals. A multiple linear regression (R2 = 0.80) was developed with molecular weight, logP, polar surface area, and fractional ion abundance to predict chemical responses within a factor of 2.5. Linearity beyond the calibration had R2 > 0.97 for three orders of magnitude. Median limits of quantitation were estimated to be 201 pg/μL (1.9× standard deviation). The number of detected chemicals and the accuracy of quantitation were similar for environmental samples and standard solutions. To our knowledge, this is the most precise method for the largest number of semi-volatile organic chemicals lacking authentic standards. Accessible instrumentation and software make this method cost effective in quantifying a large, customizable list of chemicals. When paired with silicone wristband passive samplers, this quantitative screen will be very useful for epidemiology where binning of concentrations is common. Graphical abstractA multiple linear regression of chemical responses measured with GC-MS allowed quantitation of 1550 chemicals in samples such as silicone wristbands. Electronic supplementary material The online version of this article (10.1007/s00216-018-0997-7) contains supplementary material, which is available to authorized users.