bluuebunny/crossref_metadata_2025_split huggingface dataset:
Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors
Authors: Singh Manjulata , Warita Katsuhiko , Warita Tomoko , Faeder James R. , Lee Robin E. C. , Sant Shilpa , Oltvai Zoltán N. 
Published: June 2018

AbstractCell-to-cell differences in protein expression in normal tissues and tumors are a common phenomenon, but the underlying principles that govern this heterogeneity are largely unknown. Here, we show that in monolayer cancer cell-line cultures, the expression of the five metabolic enzymes of serine-glycine synthesis (SGS), including its rate-limiting enzyme, phosphoglycerate dehydrogenase (PHGDH), displays stochastic cell-to-cell variation. By contrast, in cancer cell line-derived three-dimensional (3D) microtumors PHGDH expression is restricted to the outermost part of the microtumors’ outer proliferative cell layer, while the four other SGS enzymes display near uniform expression throughout the microtumor. A mathematical model suggests that metabolic stress in the microtumor core activates factors that restrict PHGDH expression. Thus, intracellular enzyme expression in growing cell ecosystems can shift to spatially ordered patterns in 3D structured environments due to emergent cell-cell communication, with potential implications for the design of effective anti-metabolic cancer therapies.
Guideline-based stepped and collaborative care for patients with depression in a cluster-randomised trial
Authors: Härter Martin , Watzke Birgit , Daubmann Anne , Wegscheider Karl , König Hans-Helmut , Brettschneider Christian , Liebherz Sarah , Heddaeus Daniela , Steinmann Maya 
Published: June 2018

AbstractGuidelines recommend stepped and collaborative care models (SCM) for depression. We aimed to evaluate the effectiveness of a complex guideline-based SCM for depressed patients. German primary care units were cluster-randomised into intervention (IG) or control group (CG) (3:1 ratio). Adult routine care patients with PHQ-9 ≥ 5 points could participate and received SCM in IG and treatment as usual (TAU) in CG. Primary outcome was change in PHQ-9 from baseline to 12 months (hypothesis: greater reduction in IG). A linear mixed model was calculated with group as fixed effect and practice as random effect, controlling for baseline PHQ-9 (intention-to-treat). 36 primary care units were randomised to IG and 13 to CG. 36 psychotherapists, 6 psychiatrists and 7 clinics participated in SCM. 737 patients were included (IG: n = 569 vs. CG: n = 168); data were available for 60% (IG) and 64% (CG) after 12 months. IG showed 2.4 points greater reduction [95% confidence interval (CI): −3.4 to −1.5, p < 0.001; Cohen’s d = 0.45] (adjusted PHQ-9 mean change). Odds of response [odds ratio: 2.8; 95% CI: 1.6 to 4.7] and remission [odds ratio: 3.2; 95% CI: 1.58 to 6.26] were higher in IG. Guideline-based SCM can improve depression care.
Genome-Wide Survey and Comparative Analysis of Long Terminal Repeat (LTR) Retrotransposon Families in Four Gossypium Species
Authors: Liu Zhen , Liu Yuling , Liu Fang , Zhang Shulin , Wang Xingxing , Lu Quanwei , Wang Kunbo , Zhang Baohong , Peng Renhai 
Published: June 2018

AbstractLong terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome. Some LTR retrotransposon families that insert after polyploid formation may still distribute the majority of its copies in one of the subgenomes. The data also shows that families of 10~200 copies are abundant and they have a great influence on the Gossypium genome size; on the contrary, a small number of high copy LTR retrotransposon families have less contribution to the genome size. Kimura distance distribution indicates that high copy number family is not a recent outbreak, and there is no obvious relationship between family copy number and the period of evolution. Further analysis reveals that each LTR retrotransposon family may have their own distribution characteristics in cotton.
Causal role of the inferolateral prefrontal cortex in balancing goal-directed and habitual control of behavior
Authors: Bogdanov Mario , Timmermann Jan E. , Gläscher Jan , Hummel Friedhelm C. , Schwabe Lars 
Published: June 2018

AbstractSuccessful adaptation to complex environments depends on the balance of at least two systems: a flexible but slow goal-directed system encoding action-outcome associations and an efficient but rigid habitual system linking responses to preceding stimuli. Recent evidence suggests that the inferolateral prefrontal cortex (ilPFC), a region well known to contribute to cognitive control processes, may play a crucial role in the balance of goal-directed and habitual responding. This evidence, however, comes mainly from correlational data and whether the ilPFC is indeed causally involved in the goal-directed vs. habitual control of behavior is unclear. Here, we used neuro-navigated theta-burst stimulation (TBS) to either inhibit or enhance right ilPFC functionality before participants completed an instrumental learning task designed to probe goal-directed vs. habitual behavioral control. TBS did not affect overall learning performance. However, participants that had received inhibitory TBS were less able to adapt their behavior to altered task demands, indicating a shift from goal-directed towards more habitual control of behavior. Sham or excitatory TMS groups showed no such effect and were comparable in their performance to an unstimulated control group. Our findings indicate a causal role of the ilPFC in the balance of goal-directed vs. habitual control of behavior.
Knieprothesendesign und Kinematik: Unterschiede in Radien, Konformität und Rotation/Pivot
Authors: Calliess Tilman , Savov Peter , Ettinger Max , Karkosch Roman 
Published: June 2018

ZusammenfassungMittlerweile findet sich ein schier unendliches Angebot an Knieprothesenmodellen auf dem Markt, aus denen der Chirurg für seine Versorgung wählen kann. Obwohl sich die Designs auf den ersten Blick immer weiter annähern und ähneln, betreibt die Industrie einen hohen Aufwand, unterschiedliche Designmerkmale als Alleinstellung herauszuarbeiten. Für den Anwender ist es zunehmend schwierig, den Überblick zu behalten und die tatsächliche Relevanz der Features zu bewerten. Unabhängige vergleichende wissenschaftliche Arbeiten sind Mangelware und die Evidenz entsprechend gering. Dennoch erfordern unterschiedliche Designphilosophien ein tiefgründiges konzeptionelles Verständnis und besondere Operationsalgorithmen, sodass sich der Chirurg mit der von ihm benutzten Prothese entsprechend gut auskennen muss. Interessant ist auch eine sich aus diesem Wissen ergebende indikationsbezogene Prothesenauswahl. Im Folgenden wird ein kurzer Überblick über die wesentlichen Konzepte der ungekoppelten Primärprothesen gegeben und deren klinisch relevante Unterschiede in Bezug auf die Biomechanik und den klinischen Einsatz angesprochen.
Characterization of the Tissue and Stromal Cell Components of Micro-Superficial Enhanced Fluid Fat Injection (Micro-SEFFI) for Facial Aging Treatment
Authors: Rossi Martina , Roda Barbara , Zia Silvia , Vigliotta Ilaria , Zannini Chiara , Alviano Francesco , Bonsi Laura , Zattoni Andrea , Reschiglian Pierluigi , Gennai Alessandro 
Published: June 2018

Abstract

Background
New microfat preparations provide material suitable for use as a regenerative filler for different facial areas. To support the development of new robust techniques for regenerative purposes, the cellular content of the sample should be considered.

Objectives
To evaluate the stromal vascular fraction (SVF) cell components of micro-superficial enhanced fluid fat injection (SEFFI) samples via a technique to harvest re-injectable tissue with minimum manipulation. The results were compared to those obtained from SEFFI samples.

Methods
Microscopy analysis was performed to visualize the tissue structure. Micro-SEFFI samples were also fractionated using Celector,® an innovative non-invasive separation technique, to provide an initial evaluation of sample fluidity and composition. SVFs obtained from SEFFI and micro-SEFFI were studied. Adipose stromal cells (ASCs) were isolated and characterized by proliferation and differentiation capacity assays.

Results
Microscopic and quality analyses of micro-SEFFI samples by Celector® confirmed the high fluidity and sample cellular composition in terms of red blood cell contamination, the presence of cell aggregates, and extracellular matrix fragments. ASCs were isolated from adipose tissue harvested using SEFFI and micro-SEFFI systems. These cells were demonstrated to have a good proliferation rate and differentiation potential towards mesenchymal lineages.

Conclusions
Despite the small sizes and low cellularity observed in micro-SEFFI-derived tissue, we were able to isolate stem cells. This result partially explains the regenerative potential of autologous micro-SEFFI tissue grafts. In addition, using this novel Celector® technology, tissues used for aging treatment were characterized analytically, and the adipose tissue composition was evaluated with no need for extra sample processing.

Level of Evidence: 5
Shaping sustainability of seafood from capture fisheries integrating the perspectives of supply chain stakeholders through combining systems analysis tools
Authors: Hornborg Sara , Hobday Alistair J , Ziegler Friederike , Smith Anthony D M , Green Bridget S 
Published: June 2018

Abstract
Seafood from capture fisheries can be assessed in many ways and for different purposes, with sometimes divergent views on what characterizes “sustainable use”. Here we use two systems analysis tools—Ecological Risk Assessment for Effects of Fishing (ERAEF) and Life Cycle Assessment (LCA)—over the historical development of the Australian Patagonian toothfish fishery at Heard and McDonald Islands since the start in 1997. We find that ecological risks have been systematically identified in the management process using ERAEF, and with time have been mitigated, resulting in a lower risk fishery from an ecological impact perspective. LCA inventory data from the industry shows that fuel use per kilo has increased over the history of the fishery. Our results suggest that LCA and ERAEF may provide contrasting and complementary perspectives on sustainability and reveal trade-offs when used in combination. Incorporation of LCA perspectives in assessing impacts of fishing may facilitate refinement of ecosystem-based fisheries management, such as improved integration of the different perspectives of supply chain stakeholders.
Phenotypes of Thyroid Eye Disease
Authors: Uddin Jimmy M. , Rubinstein Tal , Hamed-Azzam Shirin 
Published: June 2018

Purpose:
To describe a new classification system of thyroid eye disease (TED) based on the phenotypic features (clinical and radiologic) of the disease.

Methods:
Clinical features, photographic, and orbital imaging of TED patients were considered in relation to their natural history and treatment response in the experience of the author. Phenotypically distinct categories of patients were identified and described.

Results:
Six phenotypes of TED are observed: 1) congestive (active inflammatory), 2) “white eye” expansion, 3) “hydraulic” apex, 4) “white eye” apex, 5) cicatricial active, and 6) cicatricial passive.

Conclusions:
The observable characteristics of TED are determined by the underlying pathophysiology of the disease. TED is heterogeneous in its underlying pathogenesis, clinical manifestations, and response to medical and surgical treatment modalities. Several previous categorizations of the clinical appearance of TED exist, but they are dichotomous and underrepresent the heterogeneity of the disease. The authors present clinical and radiologic features of 6 different classes or phenotypes of TED and their response to different treatments.
Screening for depression: Review of the Patient Health Questionnaire-9 for nurse practitioners
Authors: O'Byrne Patrick , Jacob Jean Daniel 
Published: June 2018

ABSTRACT

Background and purpose:
Depression is a major health concern encountered by nurse practitioners working in an array of health care settings. Many current guidelines and articles on this topic recommend using the Patient Health Questionnaire-9 (PHQ-9) as a screening tool. Nurse practitioners should have a sophisticated knowledge of this tool.

Methods:
Review of the criteria for diagnosing depression as well as depression screening tools. Database search of EMBASE, CINAHL, and MEDLINE for articles about the PHQ-9. Discussion of how the instrument is used in the clinical setting.

Conclusions:
The PHQ-9 is a free tool that nurse practitioners can use to screen patients in the primary care environment. Screening will detect more instances of depression, which is often missed in this population of patients.

Implications for practice:
Nurse practitioners can and should use the PHQ-9 when screening for depression. However, they should do so with full knowledge and awareness of its strengths and limitations.
LncRNA Spehd regulates hematopoietic stem cells and progenitors and is required for multilineage differentiation
Authors: Joaquina Delás M , Jackson Benjamin T , Kovacevic Tatjana , Vangelisti Silvia , Maravilla Ester Munera , Wild Sophia A , Stork Eva Maria , Erard Nicolas , Knott Simon RV , Hannon Gregory J 
Published: June 2018

SummaryLong non-coding RNAs (lncRNAs) show patterns of tissue- and cell-type-specific expression that are very similar to those of protein coding genes and consequently have the potential to control stem and progenitor cell fate decisions along a differentiation trajectory. To understand the roles that lncRNAs might play in hematopoiesis, we selected a subset of mouse lncRNAs with potentially relevant expression patterns and refined our candidate list using evidence of conserved expression in human blood lineages. For each candidate, we assessed its possible role in hematopoietic differentiation in vivo using competitive transplantation. Our studies identified two lncRNAs that were required for hematopoiesis. One of these, Spehd, showed defective multi-lineage differentiation, and its silencing yielded common myeloid progenitors deficient in their oxidative phosphorylation pathway. This effort not only suggests that lncRNAs can contribute to differentiation decisions during hematopoiesis but also provides a path toward the identification of functional lncRNAs in other differentiation hierarchies.
Inductance in Neural Systems
Authors: Wang Hao , Wang Jiahui , Yuan Thow Xin , Lee Sanghoon , Xian Peh Wendy Yen , Ann Ng Kian , He Tianyiyi , Thakor Nitish V. , Chen Chia-Hung , Lee Chengkuo 
Published: June 2018

Abstract:A neural circuit model involving inductance is established to explain the neural networks’ behavior. A parallel resistor-inductor-capacitor (RLC) circuit was used to fit the stimulus artifacts in the electromyography (EMG) recording of cortical and pelvic electrical nerve stimulations. This parallel RLC circuit model also predicts the resonance effect in both stimulus artifacts and EMG signals. Moreover, the well-known strength-duration relationship was directly derived to be a precise format with this parallel RLC circuit model. A theoretical explanation is provided to show the inductance is generated by the coil structure of the myelin sheath and the piezoelectric effect of the plasma membrane.One Sentence Summary:The inductance in the neural systems is generated by the coil structure of the myelin sheath and the piezoelectric effect of the plasma membrane.
Robust and conserved stochastic self-assembly mechanism for dynamic ParB-parSpartition complexes on bacterial chromosomes and plasmids
Authors: Diaz Roxanne , Sanchez Aurore , Rech Jérôme , Labourdette Delphine , Dorignac Jérôme , Geniet Frédéric , Palmeri John , Parmeggiani Andrea , Boudsocq François , Leberre Véronique Anton , Walter Jean-Charles , Bouet Jean-Yves 
Published: June 2018

SummaryChromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a fewparS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parametersin vivousing the plasmid F partition system. We found that ‘Nucleation & caging’ is the only coherent model recapitulatingin vivodata. We also showed that the stochastic self-assembly of partition complexes (i) does not directly involve ParA, (ii) results in a dynamic structure of discrete size independent of ParB concentration, and (iii) is not perturbed by active transcription but is by protein complexes. We refined the ‘Nucleation & Caging’ model and successfully applied it to the chromosomally-encoded Par system ofVibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes.
Optimally designed vs intuition-driven inputs: the study case of promoter activity modelling
Authors: Bandiera L. , Kothamachu V. , Balsa-Canto E. , Swain P. S. , Menolascina F. 
Published: June 2018

AbstractSynthetic biology is an emerging engineering discipline that aims at synthesising logical circuits into cells to accomplish new functions. Despite a thriving community and some notable successes, the basic task of assembling predictable gene circuits is still a key challenge. Mathematical models are uniquely suited to help solve this issue. Yet in biology they are perceived as expensive and laborious to obtain because low-information experiments have often been used to infer model parameters. How much additional information can be gained using optimally designed experiments? To tackle this question we consider a building block in Synthetic Biology, an inducible promoter in yeast S. cerevisiae. Using in vivo data we re-fit a mathematical model for such a system; we then compare in silico the quality of the parameter estimates when model calibration is done using typical (e.g. step inputs) and optimally designed experiments. We find that Optimal Experimental Design leads to ~70% improvement in the predictive ability of the inferred models. We conclude providing suggestions on how optimally designed experiments can be implemented in vivo.
Structural evolutionary analysis predicts functional sites in the artemisinin resistance malaria protein K13
Authors: Coppée Romain , Jeffares Daniel C. , Sabbagh Audrey , Clain Jérôme 
Published: June 2018

AbstractK13 is an essential Plasmodium falciparum protein that plays a key role in malaria resistance to artemisinins. Although K13 resembles BTB- and Kelch/propeller-containing proteins involved in ubiquitin ligase complexes, its functional sites remain uncharacterized. Using evolutionary and structural information, we searched for the most conserved K13 sites across Apicomplexa species evolution to identify sub-regions of K13 that are likely functional. An amino acid electropositive ‘patch’ in the K13 propeller domain has a dense concentration of extraordinarily conserved positions located at a shallow pocket, suggesting a role as binding surface. When applied to experimentally-characterized BTB-Kelch proteins, our strategy successfully identifies the validated substrate-binding residues within their own propeller shallow pocket. Another patch of slowly evolving sites is identified in the K13 BTB domain which partially overlaps the surface that binds to Cullin proteins in BTB-Cullin complexes. We provide candidate binding sites in K13 propeller and BTB domains for functional follow-up studies.
Carriage of Supernumerary Sex Chromosomes Decreases the Volume and Alters the Shape of Limbic Structures
Authors: Nadig Ajay , Reardon Paul K. , Seidlitz Jakob , McDermott Cassidy L. , Blumenthal Jonathan D. , Clasen Liv S. , Lalonde Francois , Lerch Jason P. , Chakravarty Mallar M. , Raznahan Armin 
Published: June 2018

AbstractSex chromosome aneuploidy (SCA) enhances risk for several psychiatric disorders associated with the limbic system, including mood and autism spectrum disorders. These patients provide a powerful genetics-first model for understanding the biological basis of psychopathology. Additionally, these disorders are frequently sex-biased in prevalence, further suggesting an etiological role for sex chromosomes. To clarify how limbic anatomy varies across sex and sex chromosome complement, we characterized amygdala and hippocampus structure in a uniquely large sample of patients carrying supernumerary sex chromosomes (n = 132) and typically developing controls (n=166). After correction for sex-differences in brain size, karyotypically normal males (XY) and females (XX) did not differ in volume or shape of either structure. In contrast, all SCAs were associated with lowered amygdala volume relative to gonadally-matched controls. This effect was robust to three different methods for total brain volume correction, including an allometric analysis that derived normative scaling rules for these structures in a separate, typically developing population (n = 79). Hippocampal volume was insensitive to SCA after correction for total brain volume. However, surface-based analysis revealed that SCA, regardless of specific karyotype, was consistently associated with a spatially specific pattern of shape change in both amygdala and hippocampus. In particular, SCA was accompanied by contraction around the basomedial nucleus of the amygdala and an area within the hippocampal surface that cuts across hippocampal subfields. These results demonstrate the power of SCA as a model to understand how copy number variation can precipitate changes in brain systems relevant to psychiatric disease.
A multilevel statistical toolkit to study animal social networks: Animal Network Toolkit (ANT) R package
Authors: Sebastian Sosa , Ivan Puga-Gonzalez , He Hu Feng , Peng Zhang , Xie Xiaohua , Cédric Sueur 
Published: June 2018

AbstractHow animals interact and develop social relationships regarding, individual attributes, sociodemographic and ecological pressures is of great interest. New methodologies, in particular Social Network Analysis, allow us to elucidate these types of questions. However, the different methodologies developed to that end and the speed at which they emerge make their use difficult. Moreover, the lack of communication between the different software developed to provide an answer to the same/different research questions is a source of confusion. The R package Animal Network Toolkit (ANT) was developed with the aim of implementing in one package the many different social network analysis techniques currently used in the study of animal social networks. Hence, ANT is a toolkit for animal research allowing among other things to: 1) measure global, dyadic and nodal networks metrics; 2) perform data randomization: pre-network and network (node and link) permutations; 3) perform statistical permutation tests. The package is partially coded in C++ for an optimal coding speed, and it gives researchers a workflow from raw data to the achievement of statistical analyses, allowing for a multilevel approach: from individual position and role within the network, to the identification of interaction patterns, and the analysis of the overall network properties.