Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of endosomal membrane traffic by a Gadkin/AP-1/kinesin KIF5 complex

Endosomes and endosomal vesicles (EVs) rapidly move along cytoskeletal filaments allowing them to exchange proteins and lipids between different endosomal compartments, lysosomes, the trans-Golgi network (TGN), and the plasma membrane. The precise mechanisms that connect membrane traffic between the TGN and perinuclear endosomal compartments with motor-protein driven transport have largely remained elusive. Here we show that Gadkin (also termed γ-BAR), a peripheral membrane protein localized to the TGN and to TGN-derived EVs, directly associates with the clathrin adaptor AP-1 and with the motor protein kinesin KIF5, thereby potentially regulating EV dynamics. Gadkin overexpression induced the dispersion of transferrin (Tf)- and Rab4-positive EVs to the cell periphery, whereas KIF5B-depleted cells displayed a perinuclear concentration. Functional experiments suggest that the role of Gadkin as a regulator of endosomal membrane traffic critically depends on complex formation with both AP-1 and KIF5. Our data thus provide a direct molecular link between TGN-derived EVs and the microtubule-based cytoskeleton.
Spatiotemporally separable Shh domains in the midbrain define distinct dopaminergic progenitor pools

Midbrain dopamine neurons (mDA) are important regulators of diverse physiological functions, including movement, attention, and reward behaviors. Accordingly, aberrant function of dopamine neurons underlies a wide spectrum of disorders, such as Parkinson's disease (PD), dystonia, and schizophrenia. The distinct functions of the dopamine system are carried out by neuroanatomically discrete subgroups of dopamine neurons, which differ in gene expression, axonal projections, and susceptibility in PD. The developmental underpinnings of this heterogeneity are undefined. We have recently shown that in the embryonic CNS, mDA originate from the midbrain floor plate, a ventral midline structure that is operationally defined by the expression of the molecule Shh. Here, we develop these findings to reveal that in the embryonic midbrain, the spatiotemporally dynamic Shh domain defines multiple progenitor pools. We deduce 3 distinct progenitor pools, medial, intermediate, and lateral, which contribute to different mDA clusters. The earliest progenitors to express Shh, here referred to as the medial pool, contributes neurons to the rostral linear nucleus and mDA of the ventral tegmental area/interfascicular regions, but remarkably, little to the substantia nigra pars compacta. The intermediate Shh+ progenitors give rise to neurons of all dopaminergic nuclei, including the SNpc. The last and lateral pool of Shh+ progenitors generates a cohort that populates the red nucleus, Edinger Westphal nucleus, and supraoculomotor nucleus and cap. Subsequently, these lateral Shh+ progenitors produce mDA. This refined ontogenetic definition will expand understanding of dopamine neuron biology and selective susceptibility, and will impact stem cell-derived therapies and models for PD.
A theory for the evolution of other-regard integrating proximate and ultimate perspectives

Although much previous work describes evolutionary mechanisms that promote or stabilize different social behaviors, we still have little understanding of the factors that drive animal behavior proximately. Here we present a modeling approach to answer this question. Our model rests on motivations to achieve objectives as the proximate determinants of behavior. We develop a two-tiered framework by first modeling the dynamics of a social interaction at the behavioral time scale and then find the evolutionarily stable objectives that result from the outcomes these dynamics produce. We use this framework to ask whether “other-regarding” motivations, which result from a kind of nonselfish objective, can evolve when individuals are engaged in a social interaction that entails a conflict between their material payoffs. We find that, at the evolutionarily stable state, individuals can be other-regarding in that they are motivated to increase their partners' payoff as well as their own. In contrast to previous theories, we find that such motivations can evolve because of their direct effect on fitness and do not require kin selection or a special group structure. We also derive general conditions for the evolutionary stability of other-regarding motivations. Our conditions indicate that other-regarding motivations are more likely to evolve when social interactions and behavioral objectives are both synergistic.
Interactive microbial distribution analysis using BioAtlas

Abstract Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps. It further allows for (iv) uploading of own sample data, which can be placed on existing maps to (v) browse the distribution of the associated taxonomies. Finally, BioAtlas enables users to (vi) contribute custom maps (e.g. for plants or animals) and to map taxonomies to pre-defined map locations. In summary, BioAtlas facilitates map-supported browsing of public 16S rRNA sequence data and analyses of user-provided sequences without requiring manual mapping to taxonomies and existing databases. Availability: http://bioatlas.compbio. sdu.dk/
The Design of a Heterocellular 3D Architecture and its Application to Monitoring the Behavior of Cancer Cells in Response to the Spatial Distribution of Endothelial Cells

The spatial cell distribution is one of the critical features for governing cellular interactions and their consequent behaviors. Here we suggest a novel method of building a hierarchical cellular structure by stacking cell-attached microplate structures with specific configurations within hydrogel layers. This method is applied to the reconstruction of the 3D architecture of a liver lobule and the development of an experimental model of the various phases of cancer angiogenesis.
Capillary morphogenesis protein-2 is the major receptor mediating lethality of anthrax toxin in vivo

Anthrax toxin, a major virulence factor of Bacillus anthracis, gains entry into target cells by binding to either of 2 von Willebrand factor A domain-containing proteins, tumor endothelium marker-8 (TEM8) and capillary morphogenesis protein-2 (CMG2). The wide tissue expression of TEM8 and CMG2 suggest that both receptors could play a role in anthrax pathogenesis. To explore the roles of TEM8 and CMG2 in normal physiology, as well as in anthrax pathogenesis, we generated TEM8- and CMG2-null mice and TEM8/CMG2 double-null mice by deleting TEM8 and CMG2 transmembrane domains. TEM8 and CMG2 were found to be dispensable for mouse development and life, but both are essential in female reproduction in mice. We found that the lethality of anthrax toxin for mice is mostly mediated by CMG2 and that TEM8 plays only a minor role. This is likely because anthrax toxin has approximately 11-fold higher affinity for CMG2 than for TEM8. Finally, the CMG2-null mice are also shown to be highly resistant to B. anthracis spore infection, attesting to the importance of both anthrax toxin and CMG2 in anthrax infections.
Plasma and Microwave Flash Sintering of a Tailored Silver Nanoparticle Ink, Yielding 60% Bulk Conductivity on Cost‐Effective Polymer Foils

A combination of plasma and microwave flash sintering is used to sinter an inkjet-printed and tailored silver nanoparticle formulation. By using two sintering techniques sequentially, the obtained conductivity is 60%, while keeping the processing temperature well below the glass transition temperature (T(g)) of the used polymer substrate. This approach leads to highly conductive features on cost-effective polymer substrates in relatively short times, which are compatible with roll-to-roll (R2R) production. An electroluminescence device is prepared as an example.
Effects of lower extremity posture on hip strength and their influence on lower extremity motion during a single leg squat

"This research investigated the effects of static lower extremity posture on hip strength, and then examined their collective influence on knee and hip joint kinematics during a single leg squat in males and females. Thirty one healthy males and 31 healthy females, predominantly college students, between the ages of 18 and 35 participated in a single data collection session during which six lower extremity posture characteristics were measured, followed by measurement of hip abduction and extension strength and concluded with neuromuscular and kinematic analysis of the hip and knee during a single leg squat. Hip torque was normalized to body mass and electromyographic data were normalized to maximum voluntary isometric contractions. Five single leg squats were performed on the dominant stance limb to a depth of 60° of knee flexion. Path analysis, implemented by structural equation modeling, was used to examine whether greater lower extremity posture characteristics predicted decreased hip torque and whether greater lower extremity posture characteristics and decreased hip torque collectively predicted greater dynamic valgus knee motion (increased hip adduction and internal rotation, and knee external rotation and valgus). Separate multivariate analyses of variance determined whether females and males differed on measures of lower extremity posture, hip strength, and total hip and knee motion during the single leg squat. The findings were that greater hip anteversion predicted decreased hip abduction torque, and greater tibiofemoral angle predicted decreased hip extension torques. Direct relationships were noted between greater hip anteversion and genu recurvatum with greater knee external rotation, and between greater navicular drop and hip anteversion with greater hip internal rotation during the single leg squat. Furthermore, decreased hip abduction torque predicted greater knee external rotation while decreased hip extension torque predicted greater knee valgus during a single leg squat. Hence, it was concluded that greater lower extremity posture characteristics predicted decreased posterio-lateral hip strength, and collectively, greater lower extremity posture characteristics and decrease posterio-lateral hip strength predicted greater functional valgus collapse during the single leg squat. "--Abstract from author supplied metadata.
“Cut and Stick” Rubbery Ion Gels as High Capacitance Gate Dielectrics

A free-standing polymer electrolyte called an ion gel is employed in both organic and inorganic thin-film transistors as a high capacitance gate dielectric. To prepare a transistor, the free-standing ion gel is simply laid over a semiconductor channel and a side-gate electrode, which is possible because of the gel's high mechanical strength.
Mobility as a Differential Factor of HIV Among Female Sex Workers in Belgaum District, Karnataka, India

Mobility among female sex workers (FSWs) contributes to increased sexual risk behaviors. Previous studies about the correlation between HIV status and mobility in India are rare. The present authors explore the association between mobility and HIV status among FSWs. Data were obtained from a cross-sectional study conducted in 2008 among FSWs (N = 405) in Belgaum who participated in an integrated biological and behavioral assessment. Analysis was conducted with HIV prevalence as an outcome variable and mobility status as a predictor after controlling for sociodemographic characteristics. A logistic regression model indicates that FSWs who were mobile were more likely to have HIV infection than a local group (odds ratio 1.93, 95% confidence interval 1.17 to 3.22, p < .01). FSWs who have ever practiced sex work in Mumbai were more likely to have HIV (odds ratio 2.10, 95% confidence interval 0.89 to 4.91, p = .03). Thus, there is a need to design HIV interventions for mobile FSWs in India.
Supramolecular design of self-assembling nanofibers for cartilage regeneration

Molecular and supramolecular design of bioactive biomaterials could have a significant impact on regenerative medicine. Ideal regenerative therapies should be minimally invasive, and thus the notion of self-assembling biomaterials programmed to transform from injectable liquids to solid bioactive structures in tissue is highly attractive for clinical translation. We report here on a coassembly system of peptide amphiphile (PA) molecules designed to form nanofibers for cartilage regeneration by displaying a high density of binding epitopes to transforming growth factor β-1 (TGFβ-1). Growth factor release studies showed that passive release of TGFβ-1 was slower from PA gels containing the growth factor binding sites. In vitro experiments indicate these materials support the survival and promote the chondrogenic differentiation of human mesenchymal stem cells. We also show that these materials can promote regeneration of articular cartilage in a full thickness chondral defect treated with microfracture in a rabbit model with or even without the addition of exogenous growth factor. These results demonstrate the potential of a completely synthetic bioactive biomaterial as a therapy to promote cartilage regeneration.
Self-assembled artificial cilia

Due to their small dimensions, microfluidic devices operate in the low Reynolds number regime. In this case, the hydrodynamics is governed by the viscosity rather than inertia and special elements have to be introduced into the system for mixing and pumping of fluids. Here we report on the realization of an effective pumping device that mimics a ciliated surface and imitates its motion to generate fluid flow. The artificial biomimetic cilia are constructed as long chains of spherical superparamagnetic particles, which self-assemble in an external magnetic field. Magnetic field is also used to actuate the cilia in a simple nonreciprocal manner, resulting in a fluid flow. We prove the concept by measuring the velocity of a cilia-pumped fluid as a function of height above the ciliated surface and investigate the influence of the beating asymmetry on the pumping performance. A numerical simulation was carried out that successfully reproduced the experimentally obtained data.
Effects of Capnometry-Assisted Breathing Therapy on Symptoms and Respiration in Panic Disorder

Voluntary hyperventilation tests have been used to induce behavioral reactions similar to those of naturally occurring panic attacks. Such tests have been applied experimentally to advance the understanding of psychophysiological mechanisms in the production and maintenance of anxiety. In behavioral therapy, voluntary hyperventilation is a way of expos ing patients with anxiety disorders to sensations associated with panic. It is commonly practiced as part of breathing training to help eliminate habitual breathing patterns that can lead to hypocapnia. In this article we review studies that have applied voluntary hyperventilation in breathing training, and differentiate its roles in diagnosis, education about symptoms, training of breathing strategies, and outcome measurement. We discuss methodological issues specific to these roles and procedures. Insufficient evidence for the reliability and validity of voluntary hyperventilation tests currently limit their usefulness. We give recommendations for standardization of test procedures for research and therapy.
Nanocomposite Microcontainers

Versatile all-nanocomposite capped microcontainers are made using layer-by-layer (LBL) assembly. The microcontainers can act as inert packaging with slow/controlled release for virtually any type of encapsulating material based on clay nanocomposites 3D molded by PDMS templates and capped with another LBL film.
Planarian Hedgehog/Patched establishes anterior–posterior polarity by regulating Wnt signaling

Despite long-standing interest, the molecular mechanisms underlying the establishment of anterior–posterior (AP) polarity remain among the unsolved mysteries in metazoans. In the planarians (a family of flatworms), canonical Wnt/β-catenin signaling is required for posterior specification, as it is in many animals. However, the molecular mechanisms regulating the posterior-specific induction of Wnt genes according to the AP polarity have remained unclear. Here, we demonstrate that Hedgehog (Hh) signaling is responsible for the establishment of AP polarity via its regulation of the transcription of Wnt family genes during planarian regeneration. We found that RNAi gene knockdown of Dugesia japonica patched (Djptc) caused ectopic tail formation in the anterior blastema of body fragments, resulting in bipolar-tails regeneration. In contrast, RNAi of hedgehog (Djhh) and gli (Djgli) caused bipolar-heads regeneration. We show that Patched-mediated Hh signaling was crucial for posterior specification, which is established by regulating the transcription of Wnt genes via downstream Gli activity. Moreover, differentiated cells were responsible for the posterior specification of undifferentiated stem cells through Wnt/β-catenin signaling. Surprisingly, Djhh was expressed in neural cells all along the ventral nerve cords (along the AP axis), but not in the posterior blastema of body fragments, where the expression of Wnt genes was induced for posteriorization. We therefore propose that Hh signals direct head or tail regeneration according to the AP polarity, which is established by Hh signaling activity along the body's preexisting nervous system.
Plasmodium falciparum var gene expression is modified by host immunity

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a potentially important family of immune targets, which play a central role in the host–parasite interaction by binding to various host molecules. They are encoded by a diverse family of genes called var, of which there are ≈60 copies in each parasite genome. In sub-Saharan Africa, although P. falciparum infection occurs throughout life, severe malarial disease tends to occur only in childhood. This could potentially be explained if (i) PfEMP1 variants differ in their capacity to support pathogenesis of severe malaria and (ii) this capacity is linked to the likelihood of each molecule being recognized and cleared by naturally acquired antibodies. Here, in a study of 217 Kenyan children with malaria, we show that expression of a group of var genes “cys2,” containing a distinct pattern of cysteine residues, is associated with low host immunity. Expression of cys2 genes was associated with parasites from young children, those with severe malaria, and those with a poorly developed antibody response to parasite-infected erythrocyte surface antigens. Cys-2 var genes form a minor component of all genomic var repertoires analyzed to date. Therefore, the results are compatible with the hypothesis that the genomic var gene repertoire is organized such that PfEMP1 molecules that confer the most virulence to the parasite tend also to be those that are most susceptible to the development of host immunity. This may help the parasite to adapt effectively to the development of host antibodies through modification of the host–parasite relationship.
How the brain integrates costs and bene fi ts during decision making

Department of Psychology, Goethe University Frankfurt, D-60325 Frankfurt, Germany; Max Planck Institute for Human Development, D-14195 Berlin, Germany; Department of Education and Psychology, Cluster of Excellence “Languages of Emotion”, and Dahlem Institute for Neuroimaging of Emotion (D.I.N.E.), Freie Universität, Berlin, D-14195 Berlin, Germany; Center for the Study of Human Cognition, University of Oslo, N-0136 Oslo, Norway; Bernstein Center for Computational Neurosciences, Heidelberg/Mannheim, D-69120 Heidelberg, Germany; and Donders Institute for Brain, Cognition, and Behavior, Radboud University Nijmegen, 6525 HR, Nijmegen, The Netherlands
Functional Nanoporous Graphene Foams with Controlled Pore Sizes

A simple hydrophobic-affinity-derived assembly approach to pack graphene sheets into a nanoporous foam structure has been developed. Nanoporous graphene foams with the highest pore volume and large surface area are obtained. The pore diameter of the graphene foams can be finely adjusted from the mesopore to the macropore range by employing spherical templates with different sizes.
The Intrinsic Mechanical Properties of Rubrene Single Crystals

The study of the electrical properties of rubrene single crystals ( Figure 1 ) has provided a better understanding of the charge transport mechanisms in organic semiconductors while opening the doors to a new generation of high-performance electronic devices. [ 1–4 ] Despite the high charge carrier mobilities of rubrene crystals, their fragile nature and associated handling diffi culty have limited their use to fundamental charge transport studies, where throughput and bendability are not a requirement. Recent advances in the patterning techniques of organic single crystals over large-areas, [ 5 , 6 ] bring new promise for the utilization of these materials beyond charge transport studies, especially in the fi eld of fl exible electronics. [ 7 ] However, in order to effectively take advantage of the electrical properties of rubrene single-crystals in fl exible devices, their fundamental mechanical properties need to be understood and characterized. Here we present an experimental and computational investigation of the mechanical properties of rubrene single-crystals. The in-plane elastic constants are obtained by inducing the wrinkling instability in crystals laminated on elastomeric substrates. Our results demonstrate a dependence of wrinkling wavelength on crystallographic direction resembling the well-known anisotropic charge-transport properties of rubrene. The observed elastic anisotropy can be correlated to the crystal structure of rubrene (Figure 1 b) and suggests a non-linear coupling between mechanical and electrical properties. This fi nding expands the knowledge of structure-property correlations in organic semiconductors. Furthermore, insight into the mechanical properties of organic single crystals will be useful in defi ning limits on performance, processing, and manufacturing of devices, as well as elucidating their failure under mechanical and thermal loadings. [ 8 ]
Novel Solution Processing of High‐Efficiency Earth‐Abundant Cu2ZnSn(S,Se)4 Solar Cells

A novel solution-based approach is presented to process earth-abundant Cu(2)ZnSn(S,Se)(4) absorbers using fully dissolved CZTS precursors in which each of the elemental constituents intermix on a molecular scale. This method enables the low-temperature processing of chemically clean kesterite films with excellent homogeneity. The high performance of resulting optoelectronic devices represents a chance to extend the impact of CZTS into the next chapter of thin-film solar cells.
Stretchable Spin Valves on Elastomer Membranes by Predetermined Periodic Fracture and Random Wrinkling

The first highly stretchable and sensitive spin valve sensor on elastomeric membranes are demonstrated. The sensor elements exhibit stable GMR behavior up to tensile strains of 29% in in situ stretching experiments and show no fatigue over 500 loading cycles. This remarkable stretchability is achieved by a predetermined periodic fracture mechanism that creates a meander-like pattern upon stretching.