julilili42/papers huggingface dataset:
The role of echolocation strategies for niche differentiation in bats
2017-10-04

Guilds subdivide bat assemblages into basic structural units of species with similar patterns of habitat use and foraging modes, but do not explain mechanisms of niche differentiation. Bats have evolved four different echolocation strategies allowing the access to four different trophic niche spaces differing in niche dimensions. Bats foraging in open and edge spaces use the “aerial hawking or trawling strategy” and detect and localize prey by evaluating pulse–echo trains in which the prey echo is unmasked. The pulse–echo pairs deliver mainly positional information on the prey and only little information on its nature. Signals are highly variable and are adapted for detection and localization in open space and (or) edge space. In narrow space, bats identify prey by solving a pattern recognition task. Bats using the “flutter detecting strategy” evaluate glint pattern in prey echoes; bats using the “active gleaning strategy” evaluate the spectral–temporal pattern of the prey–clutter echo complex; and bats using the “passive gleaning strategy” evaluate the pattern of prey-generated cues to find food and use echolocation only for spatial orientation. The less variable signals of narrow space bats are adapted for pattern recognition. The diverse and species-rich tropical bat assemblage at Barro Colorado Island, Panama, is here used as an exemplar for assigning bats to guilds, and we discuss the role of echolocation and other adaptations for niche differentiation within guilds.
Actigraphy-Derived Daily Rest–Activity Patterns and Body Mass Index in Community-Dwelling Adults
2017-10-04

Lower RA, reflecting both higher night activity and lower daytime activity, was associated with higher BMI. Independent of the duration of rest or activity during the day or night, 24-hour rest, and activity patterns from actigraphy provide aggregated measures of activity that associate with BMI in community-dwelling adults.
A jack of all trades: the RNA‐binding protein vigilin
2017-10-04

The vigilin family of proteins is evolutionarily conserved from yeast to humans and characterized by the proteins’ 14 or 15 hnRNP K homology ( KH ) domains, typically associated with RNA ‐binding. Vigilin is the largest RNA ‐binding protein ( RBP ) in the KH domain‐containing family and one of the largest RBP known to date. Since its identification 30 years ago, vigilin has been shown to bind over 700 mRNAs and has been associated with cancer progression and cardiovascular disease. We provide a brief historic overview of vigilin research and outline the proteins’ different functions, focusing on maintenance of genome ploidy, heterochromatin formation, RNA export, as well as regulation of translation, mRNA transport, and mRNA stability. The multitude of associated functions is reflected by the large number of identified interaction partners, ranging from tRNAs , mRNAs , ribosomes and ribosome‐associated proteins, to histone methyltransferases and DNA ‐dependent protein kinases. Most of these partners bind to vigilin's carboxyterminus, and the two most C‐terminal KH domains of the protein, KH13 and KH14 , represent the main mRNA ‐binding interface. Since the nuclear functions of vigilins in particular are not conserved, we outline a model for the basal functions of vigilins, as well as those which were acquired during the transition from unicellular organisms to metazoa. WIREs RNA 2017, 8:e1448. doi: 10.1002/wrna.1448 This article is categorized under: RNA Interactions with Proteins and Other Molecules &gt; Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules &gt; Protein–RNA Interactions: Functional Implications Translation &gt; Translation Regulation
WIPI β-propellers function as scaffolds for STK11/LKB1-AMPK and AMPK-related kinase signaling in autophagy
2017-10-04

The article discusses new findings on the role of the 4 human WIPI proteins at the onset of macroautophagy/autophagy. New insights revealing a circuit scaffold function of WIPI β-propellers that interconnect autophagy signaling control with appropriate autophagosome formation are summarized.
Boudin trafficking reveals the dynamic internalisation of specific septate junction components in Drosophila
2017-10-04

The maintenance of paracellular barriers in invertebrate epithelia depends on the integrity of specific cell adhesion structures known as septate junctions (SJ). Multiple studies in Drosophila have revealed that these junctions have a stereotyped architecture resulting from the association in the lateral membrane of a large number of components. However, little is known about the dynamic organisation adopted by these multi-protein complexes in living tissues. We have used live imaging techniques to show that the Ly6 protein Boudin is a component of these adhesion junctions and can diffuse systemically to associate with the SJ of distant cells. We also observe that this protein and the claudin Kune-kune are endocytosed in epidermal cells during embryogenesis. Our data reveal that the SJ contain a set of components exhibiting a high membrane turnover, a feature that could contribute in a tissue-specific manner to the morphogenetic plasticity of these adhesion structures.
Mechanistic Aspects of Redox‐Induced Assembly and Disassembly of S‐Bridged [2M‐2S] Structures
2017-10-04

Abstract Sulfur‐bridged binuclear structures [2M‐2S] play a pivotal role in a variety of chemical processes such as bond breaking and formation and electron transfer. In general, structural persistence is deemed essential to the respective function but owing to the lack of a suitable molecular model system, the current understanding of the factors that control the thermodynamic and kinetic stability of [2M‐2S] cores clearly is limited. This work reports a series of binuclear complexes of nickel derived from a 1,4‐terphenyldithiophenol ligand platform that is ideally suited for mechanistic work to overcome this limitation. Redox‐induced assembly and disassembly of S‐bridged [2M‐2S] fragments have been investigated at the molecular level. As part of an extended square scheme, metastable binuclear structures that are significant mechanistically have been identified, characterized, and their reactivity studied quantitatively. Electronic properties that are inherent to [2M‐2S] structures and determine thermodynamic and kinetic stability are differentiated from steric effects imposed by co‐ligands.
Heterogeneities of Carbonate Ramp Reservoirs - Characterization and Modelling of a Shoal Outcrop Analogue (Mid-Triassic)
2017-10-04

Summary In order to improve the understanding of sedimentological heterogeneities on varies scales, from micro-scale thin section to macro-scale correlations, a joint project was initiated between the University of Tübingen (Germany) and ENI S.p.A. This outcrop study focused on the characterization and modelling of the largest and thickest wedge (wedge 3) of the Quaderkalk Formation. The Middle Triassic Quaderkalk Formation in SW Germany composed of four lithostratigraphic separated bioclast-rich wedges and represents an outcrop analogue for sub-seismic scale carbonate ramp reservoirs. Facies range from mud-rich, low-energy offshoal (non-reservoir facies) to bioclast-rich, high-energy shoal (potential reservoir facies), deposited on an epeiric carbonate ramp. Instead of a continuous facies belt, tens of kilometres-scale correlations indicate several separated high-energy shoal areas forming a shoal complex “mosaic”, which is controlled by a cycle architecture. Integrating all data of an intensive field study, two 3D facies models were produced: (1) a 30 × 30 km model to simulate the large-scale facies pattern and (2) a more detailed 10 × 10 km small-scale model to simulate internal shoal reservoir heterogeneities. The results highlight the importance of realistic geological, especially sequence-stratigraphic input in order to optimize the simulations of carbonate shoals.
Cognitive changes in prodromal Parkinson's disease: A review
2017-10-05

Abstract Although other nonmotor phenomena representing possible prodromal symptoms of Parkinson's disease have been described in some detail, the occurrence and characteristics of cognitive decline in this early phase of the disease are less well understood. The aim of this review is to summarize the current state of research on cognitive changes in prodromal PD. Only a small number of longitudinal studies have been conducted that examined cognitive function in individuals with a subsequent PD diagnosis. However, when we consider data from at‐risk groups, the evidence suggests that cognitive decline may occur in a substantial number of individuals who have the potential for developing PD. In terms of specific cognitive domains, executive function in particular and, less frequently, memory scores are reduced. Prospective longitudinal studies are thus needed to clarify whether cognitive, and specifically executive, decline might be added to the prodromal nonmotor symptom complex that may precede motor manifestations of PD by years and may help to update the risk scores used for early identification of PD. © 2017 International Parkinson and Movement Disorder Society
A parametric texture model based on deep convolutional features closely matches texture appearance for humans
2017-10-05

Our visual environment is full of texture-"stuff" like cloth, bark, or gravel as distinct from "things" like dresses, trees, or paths-and humans are adept at perceiving subtle variations in material properties. To investigate image features important for texture perception, we psychophysically compare a recent parametric model of texture appearance (convolutional neural network [CNN] model) that uses the features encoded by a deep CNN (VGG-19) with two other models: the venerable Portilla and Simoncelli model and an extension of the CNN model in which the power spectrum is additionally matched. Observers discriminated model-generated textures from original natural textures in a spatial three-alternative oddity paradigm under two viewing conditions: when test patches were briefly presented to the near-periphery ("parafoveal") and when observers were able to make eye movements to all three patches ("inspection"). Under parafoveal viewing, observers were unable to discriminate 10 of 12 original images from CNN model images, and remarkably, the simpler Portilla and Simoncelli model performed slightly better than the CNN model (11 textures). Under foveal inspection, matching CNN features captured appearance substantially better than the Portilla and Simoncelli model (nine compared to four textures), and including the power spectrum improved appearance matching for two of the three remaining textures. None of the models we test here could produce indiscriminable images for one of the 12 textures under the inspection condition. While deep CNN (VGG-19) features can often be used to synthesize textures that humans cannot discriminate from natural textures, there is currently no uniformly best model for all textures and viewing conditions.
Longitudinal development of subtraction performance in elementary school
2017-10-05

A major goal of education in elementary mathematics is the mastery of arithmetic operations. However, research on subtraction is rather scarce, probably because subtraction is often implicitly assumed to be cognitively similar to addition, its mathematical inverse. To evaluate this assumption, we examined the relation between the borrow effect in subtraction and the carry effect in addition, and the developmental trajectory of the borrow effect in children using a choice reaction paradigm in a longitudinal study. In contrast to the carry effect in adults, carry and borrow effects in children were found to be categorical rather than continuous. From grades 3 to 4, children became more proficient in two‐digit subtraction in general, but not in performing the borrow operation in particular. Thus, we observed no specific developmental progress in place‐value computation, but a general improvement in subtraction procedures. Statement of contribution What is already known on this subject? The borrow operation increases difficulty in two‐digit subtraction in adults. The carry effect in addition, as the inverse operation of borrowing, comprises categorical and continuous processing characteristics. What does this study add? In contrast to the carry effect in adults, the borrow and carry effects are categorical in elementary school children. Children generally improve in subtraction performance from grades 3 to 4 but do not progress in place‐value computation in particular.
Membrane lipid order of sub‐synaptic T cell vesicles correlates with their dynamics and function
2017-10-05

During an immune response, T cells survey antigen presenting cells for antigenic peptides via the formation of an interface known as an immunological synapse. Among the complex and dynamic biophysical phenomena occurring at this interface is the trafficking of sub‐synaptic vesicles carrying a variety of proximal signalling molecules. Here, we show that rather than being a homogeneous population, these vesicles display a diversity of membrane lipid order profiles, as measured using the environmentally sensitive dye di‐4‐ANEPPDHQ and multi‐spectral TIRF microscopy. Using live‐cell imaging, vesicle tracking and a variety of small molecule drugs to manipulate components of the actin and tubulin cytoskeleton, we show that the membrane lipid order of these vesicles correlate with their dynamics. Furthermore, we show that the key proximal signalling molecule Linker for Activation of T cells (LAT) is enriched in specific vesicle populations as defined by their higher membrane order. These results imply that vesicle lipid order may represent a novel regulatory mechanism for the sorting and trafficking of signalling molecules at the immunological synapse, and, potentially, other cellular structures.
Positivity for Operator Matrices
2017-10-05

We consider two Banach spaces, (E, |·|) and (D, ||·||) with D continuously imbedded in E and denote by D ̄ https://s3-euw1-ap-pe-df-pch-content-public-p.s3.eu-west-1.amazonaws.com/9781315141244/3614d45d-5842-4d20-a390-261e22b5beeb/content/in6_1.tif"/> the closure of D in E.
An Application of Polynomial Operator Matrices to a Second Order Cauchy Problem
2017-10-05

In this note we are concerned with the asymptotic behavior of a system of ordinary differential equations which describe a class of chemical reactions. We consider a model chemical system consisting of m species A 1,..., Am and m – 1 independent reactions. The reaction mechanism for this system is assumed to be
Nonclassical nucleation pathways in protein crystallization
2017-10-06

Classical nucleation theory (CNT), which was established about 90 years ago, has been very successful in many research fields, and continues to be the most commonly used theory in describing the nucleation process. For a fluid-to-solid phase transition, CNT states that the solute molecules in a supersaturated solution reversibly form small clusters. Once the cluster size reaches a critical value, it becomes thermodynamically stable and favored for further growth. One of the most important assumptions of CNT is that the nucleation process is described by one reaction coordinate and all order parameters proceed simultaneously. Recent studies in experiments, computer simulations and theory have revealed nonclassical features in the early stage of nucleation. In particular, the decoupling of order parameters involved during a fluid-to-solid transition leads to the so-called two-step nucleation mechanism, in which a metastable intermediate phase (MIP) exists between the initial supersaturated solution and the final crystals. Depending on the exact free energy landscapes, the MIPs can be a high density liquid phase, mesoscopic clusters, or a pre-ordered state. In this review, we focus on the studies of nonclassical pathways in protein crystallization and discuss the applications of the various scenarios of two-step nucleation theory. In particular, we focus on protein solutions in the presence of multivalent salts, which serve as a model protein system to study the nucleation pathways. We wish to point out the unique features of proteins as model systems for further studies.
Somatic USP8 mutations are frequent events in corticotroph tumor progression causing Nelson’s tumor
2017-10-06

Objective Somatic mutations in the ubiquitin-specific protease 8 ( USP8 ) gene are frequent in corticotroph tumors causing Cushing’s disease (CD). Corticotroph tumor progression, the so-called Nelson’s syndrome (NS), is a potentially life-threatening complication of bilateral adrenalectomy in patients with refractory CD that is caused by the development of an ACTH-secreting tumor of the pituitary gland. Whether USP8 alterations are also present in progressive Nelson’s tumors has not been studied in detail so far. Design and Methods Retrospective, multicenter study involving tumors from 33 patients with progressive corticotroph tumors (29 females) and screening for somatic mutations on the mutational hotspot of the USP8 gene in the exon 14 with Sanger sequencing. Results Fifteen out of 33 tumors (45%) presented with a mutation in the exon 14 of USP8 , with c.2159C&gt;A (p.Pro720Gln) being the most frequent (9/33), followed by c.2155_2157delTCC (p.Ser718del, 4/33) and c.2152T&gt;C (p.Ser718Pro, 2/33). This prevalence is similar to that previously reported for CD. Mutations were found exclusively in females. Other variables, such as age at diagnosis with NS, body mass index, hyperpigmentation, visual field defects, adenoma size or mortality, did not significantly differ between patients with wild-type and mutant tumors. Patients with USP8 mutant tumors exhibited higher levels of plasma ACTH after surgery (median: 640 vs 112 pg/mL, P = 0.03). No differences were observed in ACTH normalization (&lt;50 pg/mL) and tumor control after surgery for Nelson’s tumor. Conclusion Somatic mutations in USP8 are common in Nelson’s tumors, indicating that they do not drive the corticotroph tumor progression that leads to NS, and may be associated with a less favorable biochemical outcome after surgery for Nelson’s tumor.
Highly identified power‐holders feel responsible: The interplay between social identification and social power within groups
2017-10-06

Power relations affect dynamics within groups. Power‐holders’ decisions not only determine their personal outcomes, but also the outcomes of others in the group that they control. Yet, power‐holders often tend to overlook this responsibility to take care of collective interests. The present research investigated how social identification – with the group to which both the powerful and the powerless belong – alters perceived responsibility among power‐holders (and the powerless). Combining research on social power and social identity, we argue that power‐holders perceive more responsibility than the powerless when strongly (rather than when weakly) identifying with the group. A study among leaders and an experiment supported this, highlighting that although power‐holders are often primarily concerned about personal outcomes, they do feel responsible for considering others’ interests when these others are included in the (social) self.
GFR estimation based on standardized creatinine and cystatin C: a European multicenter analysis in older adults
2017-10-06

Abstract Background: Although recommended by the Kidney Disease Improving Global Outcomes, the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI CR ) creatinine equation was not targeted to estimate glomerular filtration rate (eGFR) among older adults. The Berlin Initiative Study (BIS1 CR ) equation was specifically developed in older adults, and the Lund-Malmö revised (LMR CR ) and the Full Age Spectrum (FAS CR ) equations have shown promising results in older adults. Our aim was to validate these four creatinine equations, including addition of cystatin C in a large multicenter cohort of Europeans ≥70 years. Methods: A total of 3226 individuals (2638 with cystatin C) underwent GFR measurement (mGFR; median, 44 mL/min/1.73 m 2 ) using plasma iohexol clearance. Bias, precision (interquartile range [IQR]), accuracy (percent of estimates ±30% of mGFR, P 30 ), eGFR accuracy diagrams and probability diagrams to classify mGFR&lt;45 mL/min/1.73 m 2 were compared. Results: The overall results of BIS1 CR /CKD-EPI CR /FAS CR /LMR CR were as follows: median bias, 1.7/3.6/0.6/−0.7 mL/min/1.73 m 2 ; IQR, 11.6/12.3/11.1/10.5 mL/min/1.73 m 2 ; and P 30 , 77.5%/76.4%/80.9%/83.5% (significantly higher for LMR, p&lt;0.001). Substandard P 30 (&lt;75%) was noted for all equations at mGFR&lt;30 mL/min/1.73 m 2 , and at body mass index values &lt;20 and ≥35 kg/m 2 . LMR CR had the most stable performance across mGFR subgroups. Only LMR CR and FAS CR had a relatively constant small bias across eGFR levels. Probability diagrams exhibited wide eGFR intervals for all equations where mGFR&lt;45 could not be confidently ruled in or out. Adding cystatin C improved P 30 accuracy to 85.7/86.8/85.7/88.7 for BIS2 CR+CYS /CKD-EPI CR+CYS /FAS CR+CYS /MEAN LMR+CAPA . Conclusions: LMR CR and FAS CR seem to be attractive alternatives to CKD-EPI CR in estimating GFR by creatinine-based equations in older Europeans. Addition of cystatin C leads to important improvement in estimation performance.
Polycyclic Polyprenylated Acylphloroglucinols: An Emerging Class of Non‐Peptide‐Based MRSA‐ and VRE‐Active Antibiotics
2017-10-06

Abstract In the past 20 years, peptide‐based antibiotics, such as vancomycin, teicoplanin, and daptomycin, have often been considered as second‐line antibiotics. However, in recent years, an increasing number of reports on vancomycin resistance in pathogens appeared, which forces researchers to find novel lead structures for potent new antibiotics. Herein, we report the total synthesis of a defined endo‐type B PPAP library and their antibiotic activity against multiresistant S. aureus and various vancomycin‐resistant Enterococci . Four new compounds that combine high activities and low cytotoxicity were identified, indicating that the PPAP core might become a new non‐peptide‐based lead structure in antibiotic research.
Organ‐on‐a‐Chip Systems for Women's Health Applications
2017-10-06

Abstract Biomedical research, for a long time, has paid little attention to the influence of sex in many areas of study, ranging from molecular and cellular biology to animal models and clinical studies on human subjects. Many studies solely rely on male cells/tissues/animals/humans, although there are profound differences in male and female physiology, which can significantly impact disease mechanisms, toxicity of compounds, and efficacy of pharmaceuticals. In vitro systems have been traditionally very limited in their capacity to recapitulate female‐specific physiology and anatomy such as dynamic sex‐hormone levels and the complex interdependencies of female reproductive tract organs. However, the advent of microphysiological organ‐on‐a‐chip systems, which attempt to recreate the 3D structure and function of human organs, now gives researchers the opportunity to integrate cells and tissues from a variety of individuals. Moreover, adding a dynamic flow environment allows mimicking endocrine signaling during the menstrual cycle and pregnancy, as well as providing a controlled microfluidic environment for pharmacokinetic modeling. This review gives an introduction into preclinical and clinical research on women's health and discusses where organ‐on‐a‐chip systems are already utilized or have the potential to deliver new insights and enable entirely new types of studies.