bluuebunny/crossref_metadata_2025_split huggingface dataset:
Outcomes, Challenges, and Pitfalls after Targeted Muscle Reinnervation in High-Level Amputees: Is It Worth the Effort?
Authors: Salminger Stefan , Sturma Agnes , Roche Aidan D. , Mayer Johannes A. , Gstoettner Clemens , Aszmann Oskar C. 
Published: August 2019

Background:
Although the distal targets have been lost in proximal upper limb amputees, the neural signals for intuitive hand and arm function are still available and thus can be incorporated into more useful prosthetic function using targeted muscle reinnervation technique. In this article, the authors present their outcomes and range of indications in addition to experiences and pitfalls after 30 targeted muscle reinnervation cases at above-elbow and shoulder disarticulation level of amputation.

Methods:
Thirty patients with above-elbow or shoulder disarticulation amputations were enrolled between 2012 and 2017. Indications for targeted muscle reinnervation surgery differed between improvement of prosthetic function (n = 19) and/or pain (n = 11). Functional outcome was evaluated with the Action Research Arm Test, the Southampton Hand Assessment Procedure, and the Clothespin-Relocation Test. Functional evaluation was performed at least at 6 months after final prosthetic fitting.

Results:
All nerve transfers were successful and provided independent myoelectric signals. The 10 patients available for final functional evaluation showed Action Research Arm Test scores of 20.4 ± 1.9 and Southampton Hand Assessment Procedure scores of 40.5 ± 8.1. The Clothespin-Relocation Test showed a mean time of 34.3 ± 14.4 seconds.

Conclusions:
Targeted muscle reinnervation has improved prosthetic control and revolutionized neuroma treatment in upper limb amputees. Still, the rate of abandonment even after targeted muscle reinnervation surgery has been shown high, and several advances within the biotechnological interface will be needed to improve prosthetic function and acceptance in these patients.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Magnetic Resonance Imaging for the Follow-up of Treated Thymic Epithelial Malignancies
Authors: Kerpel Ariel , Beytelman Arkadi , Ofek Efrat , Marom Edith M. 
Published: August 2019

Purpose:
The purpose of this article was to compare magnetic resonance imaging (MRI) depiction of thymic malignancy progression/recurrence with that of computed tomography (CT).

Methods:
We retrospectively reviewed all surgically treated thymic epithelial malignancy (TEM) patients between 2011 and 2018 who were followed-up with chest CT and MRI. We compared the detection of recurrence and metastatic disease between the CT and MRI scans in each of these patients.

Results:
Of 187 patients treated in our institution for TEM, 22 were followed-up with both CT and MRI. TNM stage at diagnosis was as follows: I (n=14), II (n=1), IIIa (n=4), IIIb (n=2), IVa (n=1), and IVb (n=0). Patients were followed-up for a mean of 6.2 years, range 0.7 to 17.7 years. The mean interval between CT and MRI was 5.4 (range, 1 to 15) months. Most patients had no recurrence (n=16), 4 had recurrence after R0 or R1 resection, 1 had stable disease, and 1 had progression of disease after R2 resection. CT and MRI performed equally in the identification of pleural spread (n=5), lymphadenopathy (n=4), and pulmonary metastases (n=1). Retrosternal recurrence (n=1) was identified by MRI despite sternotomy wire artifacts. MRI identified bone involvement and extension of disease into the thecal sac earlier and more readily. Three patients had an indeterminate mediastinal finding on CT that was correctly identified as a benign cyst or pericardial fluid collection by MRI.

Conclusion:
MRI is an alternative option to follow-up patients after treatment for TEM. However, for those with metallic sternotomy wires, we recommend alternating the follow-up with CT as well.
An Analysis of Aesthetic Refinements in 120 Secondary Cleft Rhinoplasties
Authors: Kehrer Andreas , Nijhuis Tim H. J. , Lonic Daniel , Heidekrueger Paul I. , Kehrer Michael , Taeger Christian D. , Willemsen Sten , Prantl Lukas , van der Meulen Jacques J. J. N. M. 
Published: August 2019

Background
Secondary cleft nose rhinoplasty remains a challenging procedure. Cartilage memory and scar contraction are problematic factors. The need for more detailed procedures for secondary reconstruction in this patient population has arisen. Contemporary refinements demonstrate a highly structured approach. We conducted a retrospective study evaluating the aesthetic results of cleft patients who underwent secondary rhinoplasty.

Methods
In a retrospective study, a photometric analysis of cleft patients operated in the period 2003–2011 was conducted. Reconstructive methods were documented. Pre- and postoperative photographs of cleft rhinoplasty patients were evaluated using a standardized protocol. Nostril width ratio, columellar angle, tip projection ratio, and nasolabial angle served as objective instruments. The Unilateral Cleft Lip Surgical Outcomes Evaluation score was chosen for external photometric rating and rated blindly by 2 external individual plastic surgeons as independent nonbiased reviewers. The interrater and intrarater reliabilities were calculated using the Cohen kappa coefficient (κ).

Results
A total of 120 secondary rhinoplasties in 85 uni- and bilateral cleft patients could be included. Mean follow-up was 20 months. A total of 60 (71%) patients needed additional bone grafting (chin/pelvis), and 23 (27%) patients a LeFort I osteotomy. In one third of the secondary rhinoplasties, a medial and/or lateral osteotomy was performed (34%). In one fourth (24%), an external septoplasty was considered necessary. In 55% (47 patients) of the cases, a columellar strut was used. Excluding bone grafts, a total of 173 other grafts (mean of 2 grafts/patient) were applied. Postoperative measurements for nostril width ratio and columellar angle were statistically significant. A structured approach with contemporary refinements is described in detail. Intra- and interrater reliabilities for photometric assessment according to the Unilateral Cleft Lip Surgical Outcomes Evaluation score are shown.

Conclusions
A structured approach for secondary cleft rhinoplasty yields satisfying, reproducible, and stable results.
Magnetic Resonance Imaging Features of Collet-Sicard Syndrome Associated With Glomus Jugulare Paraganglioma
Authors: Mutlu Vahit , Ogul Hayri 
Published: August 2019

Abstract
Collet-Sicard syndrome is an unusual disorder. The authors here demonstrated the Magnetic resonance (MR) imaging findings of the Collet-Sicard syndrome associated with glomus jugulare tumor. Neoplastic or non-neoplastic lesion of skull base can cause Collet-Sicard syndrome. MR imaging can be used successfully to demonstrate the etiology of this syndrome.
Endothelial cell dysfunction during anoxia-reoxygenation is associated with a decrease in adenosine triphosphate levels, rearrangement in lipid bilayer phosphatidylserine asymmetry, and an increase in endothelial cell permeability
Authors: Sadjadi Javid , Strumwasser Aaron M. , Victorino Gregory P. 
Published: August 2019

BACKGROUNDPhosphatidylserine (PS) is normally confined in an energy-dependent manner to the inner leaflet of the lipid cell membrane. During cellular stress, PS is exteriorized to the outer layer, initiating a cascade of events. Because cellular stress is often accompanied by decreased energy levels and because maintaining PS asymmetry is an energy-dependent process, it would make sense that cellular stress associated with decreased energy levels is also associated with PS exteriorization that ultimately leads to endothelial cell dysfunction. Our hypothesis was that anoxia-reoxygenation (A-R) is associated with decreased adenosine triphosphate (ATP) levels, increased PS exteriorization on endothelial cell membranes, and increased endothelial cell membrane permeability.METHODSThe effect on ATP levels during A-R was measured via colorimetric assay in cultured cells. To measure the effect of A-R on PS levels, cultured cells underwent A-R and exteriorized PS levels and also total cell PS were measured via biofluorescence assay. Finally, we measured endothelial cell monolayer permeability to albumin after A-R.RESULTSThe ATP levels in cell culture decreased 27% from baseline after A-R (p< 0.02). There was over a twofold increase in exteriorized PS as compared with controls (p< 0.01). Interestingly, we found that during A-R, the total amount of cellular PS increased (p< 0.01). The finding that total PS changed twofold over normal cells suggested that not only is there a change in the distribution of PS across the cell membrane, but there may also be an increase in the amount of PS inside the cell. Finally, A-R increased endothelial cell monolayer permeability (p< 0.01).CONCLUSIONWe found that endothelial cell dysfunction during A-R is associated with decreased ATP levels, increased PS exteriorization, and increased in monolayer permeability. This supports the idea that PS exteriorization may a key event during clinical scenarios involving oxygen lack and may 1 day lead to novel therapies in these situations.
Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories
Authors: Doorenweerd Camiel , Jose Michael San , Barr Norman , Leblanc Luc , Rubinoff Daniel 
Published: August 2019

AbstractDistance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens ofBactrocera correcta, 214B. zonataand 372Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, whereB. zonatahas the highest diversity but most haplotypes were represented by singletons;B. correctahas ∼7 dominant haplotypes more evenly distributed;Z. cucurbitaehas a single dominant haplotype with closely related singletons in a ‘star-shape’ surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructuring.
Kin and group selection are both flawed but useful data analysis tools
Authors: smith jeff , Inglis R. Fredrik 
Published: August 2019

AbstractFor understanding the evolution of social behavior in microbes, mathematical theory can aid empirical research but is often only used as a qualitative heuristic. How to properly formulate social evolution theory has also been contentious. Here we evaluate kin and multilevel selection theory as tools for analyzing microbial data. We reanalyze published datasets that share a common experimental design and evaluate these theories in terms of data visualization, statistical performance, biological interpretation, and quantitative comparison across systems. We find that the canonical formulations of both kin and multilevel selection are almost always poor analytical tools because they use statistical regressions that are poorly specified for the strong selection and nonadditive fitness effects common in microbial systems. Analyzing both individual and group fitness outcomes helps clarify the biology of selection. We also identify analytical practices in empirical research that suggest how theory might better handle the challenges of microbial data. A quantitative, data-driven approach thus shows how kin and multilevel selection theory both have substantial room for improvement as tools for understanding social evolution in all branches of life.
Predicting changes in bee assemblages following state transitions at North American dryland ecotones
Authors: Kazenel Melanie R. , Wright Karen W. , Bettinelli Julieta , Griswold Terry L. , Whitney Kenneth D. , Rudgers Jennifer A. 
Published: August 2019

AbstractDrylands worldwide are experiencing ecosystem state transitions: the expansion of some ecosystem types at the expense of others. Bees in drylands are particularly abundant and diverse, with potential for large compositional differences and seasonal turnover across ecotones. To better understand how future ecosystem state transitions may influence bees, we compared bee assemblages and their seasonality among sites at the Sevilleta National Wildlife Refuge (NM, USA) that represent three dryland ecosystem types (and two ecotones) of the southwestern U.S. (Plains grassland, Chihuahuan Desert grassland, and Chihuahuan Desert shrubland). Using passive traps, we caught bees during two-week intervals from March – October, 2002 – 2014. The resulting dataset included 302 bee species and 56 genera. Bee abundance, composition, and diversity differed among ecosystems, indicating that future state transitions could alter bee assemblage composition in our system. We found strong seasonal bee species turnover, suggesting that bee phenological shifts may accompany state transitions. Common species drove the observed trends, and both specialist and generalist bee species were indicators of ecosystem types or months; these species could be sentinels of community-wide responses to future shifts. Our work suggests that predicting the consequences of global change for bee assemblages requires accounting for both within-year and among-ecosystem variation.
Plasma membrane damage causes NLRP3 activation and pyroptosis during Mycobacterium tuberculosis infection
Authors: Beckwith Kai S. , Beckwith Marianne S. , Ullmann Sindre , Sætra Ragnhild , Kim Haelin , Marstad Anne , Åsberg Signe E. , Strand Trine A. , Stenmark Harald A. , Flo Trude H. 
Published: August 2019

AbstractMycobacterium tuberculosis (Mtb) is a major global health problem and causes extensive cytotoxicity in patient cells and tissues. Here we define an NLRP3, caspase-1 and gasdermin D-mediated pathway to pyroptosis in human monocytes following exposure to Mtb. We demonstrate an ESX-1 mediated, contact-induced plasma membrane (PM) damage response that occurs during phagocytosis or from the cytosolic side of the PM after phagosomal rupture in Mtb infected cells. This PM injury in turn causes K+ efflux and activation of NLRP3 dependent IL-1β release and pyroptosis, facilitating the spread of Mtb to neighbouring cells. Further we reveal a dynamic interplay of pyroptosis with ESCRT-mediated PM repair. Collectively, these findings reveal a novel mechanism for pyroptosis and spread of infection acting through dual PM disturbances both during and after phagocytosis. We also highlight dual PM damage as a common mechanism utilized by other NLRP3 activators that have previously been shown to act through lysosomal damage.Graphical abstract
Independent evolution towards large body size in the distinctive Faroe Island mice
Authors: Wilches Ricardo , Beluch William H. , McConnell Ellen , Tautz Diethard , Chan Yingguang Frank 
Published: August 2019

AbstractMost traits in nature involve the collective action of many genes. Traits that evolve repeatedly are particularly revealing about how selection may act on traits. In mice, large body size has evolved repeatedly on islands and under artificial selection in the laboratory. Identifying the loci and genes involved in this process may shed light on the evolution of complex, polygenic traits. Here, we have mapped the genetic basis of body size variation by making a genetic cross between mice from the Faroe Islands, which are among the largest and most distinctive populations of mice in the world, and a laboratory mouse strain selected for small body size, SM/J. Using this F2 intercross of 841 animals, we have identified 102 loci controlling various aspects of body size, weight and growth hormone levels. By comparing against other studies, including the use of a joint meta-analysis, we found that the loci involved in the evolution of large size in the Faroese mice were largely independent from those of a different island population or other laboratory strains. We conclude that colonization bottleneck, historical hybridization, or the redundancy between multiple loci have resulted in the Faroese mice achieving an outwardly similar phenotype through a distinct evolutionary path.
Comparative pathway enrichment analysis in gastrointestinal cell lines Caco-2, HT-29, HEPG2, and colon fibroblasts using a custom expression panel for tight-junction and cytoskeletal regulatory genes
Authors: Robinson JM 
Published: August 2019

AbstractThis brief report details results from a comparative analysis of Nanostring expression data between cell lines HEPG2, Caco-2, HT-29, and colon fibroblasts. Raw and normalized data are available publicly in the NCBI GEO/Bioproject databases. Results identify cell-line specific variations in gene expression relevant to intestinal epithelial function.
Genome sequencing and neurotoxin diversity of a wandering spider Pardosa pseudoannulata (pond wolf spider)
Authors: Yu Na , Li Jingjing , Liu Meng , Huang Lixin , Bao Haibo , Yang Zhiming , Zhang Yixi , Gao Haoli , Wang Zhaoying , Yang Yuanxue , Van Leeuwen Thomas , Millar Neil S. , Liu Zewen 
Published: August 2019

AbstractSpiders constitute an extensive and diverse branch of the phylum Arthropoda. Whereas the genomes of four web-weaver spider species and a single cave-living spider have been determined, similar studies have not been reported previously for a wandering spider. The pond wolf spider, Pardosa pseudoannulata, is a wandering hunter that immobilizes prey using venom rather than a web. It is also an important predator against a range of agriculturally important insect pests. The increasing interest in its wandering lifestyle and in the potential of spider venom as a tool for pest control have prompted a detailed study on this wandering spider species. We have generated a high-quality genome sequence of P. pseudoannulata and analysed genes associated with the production of silk and venom toxins. Sequencing reveals that P. pseudoannulata has a large genome of 4.26 Gb. The presence of only 16 spidroin genes and four types of silk glands is consistent with the moderate use of silk and the lack of a prey-catching web. A large number of genes encode neurotoxins and there is evidence that the majority are highly selective for invertebrates. Comparison between spider species reveals a correlation between spider neurotoxin selectivity for target organisms and spider prosoma size, suggesting a possible coevolution of these two features. The genome data provides valuable insights into the biology of P. pseudoannulata and its potential role as a natural enemy in pest control.
Spooky interaction at a distance in cave and surface dwelling electric fishes
Authors: Fortune Eric S. , Andanar Nicole , Madhav Manu , Jayakumar Ravi , Cowan Noah J. , Bichuette Maria Elina , Soares Daphne 
Published: August 2019

ABSTRACTGlass knifefish (Eigenmannia) are a group of weakly electric fishes found throughout the Amazon basin. We made recordings of the electric fields of two populations of freely behavingEigenmanniain their natural habitats: a troglobitic population of blind cavefish (Eigenmannia vicentespelaea) and a nearby epigean (surface) population (Eigenmannia trilineata). These recordings were made using a grid of electrodes to determine the movements of individual fish in relation to their electrosensory behaviors. The strengths of electric discharges in cavefish were larger than in surface fish, which may be a correlate of increased reliance on electrosensory perception and larger size. Both movement and social signals were found to affect the electrosensory signaling of individualEigenmannia. Surface fish were recorded while feeding at night and did not show evidence of territoriality. In contrast, cavefish appeared to maintain territories. Surprisingly, we routinely found both surface and cavefish with sustained differences in electric field frequencies that were below 10 Hz despite being within close proximity of less than one meter. A half century of analysis of electrosocial interactions in laboratory tanks suggest that these small differences in electric field frequencies should have triggered the jamming avoidance response. Fish also showed significant interactions between their electric field frequencies and relative movements at large distances, over 1.5 meters, and at high differences in frequencies, often greater than 50 Hz. These interactions are likely envelope responses in which fish alter their EOD frequency in relation to changes in the depth of modulation of electrosocial signals.
Single cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination
Authors: Mayère Chloé , Neirijnck Yasmine , Sararols Pauline , Rands Chris M , Stévant Isabelle , Kühne Françoise , Chassot Anne-Amandine , Chaboissier Marie-Christine , Dermitzakis Emmanouil T. , Nef Serge 
Published: August 2019

SummaryDespite the importance of germ cell (GC) differentiation for sexual reproduction, the gene networks underlying their fate remain unclear. Here, we comprehensively characterize the gene expression dynamics during sex determination based on single-cell RNA sequencing of 14,914 XX and XY mouse GCs between embryonic days (E) 9.0 and 16.5. We found that XX and XY GCs diverge transcriptionally as early as E11.5 with upregulation of genes downstream of the Bone morphogenic protein (BMP) and Nodal/Activin pathways in XY and XX GCs, respectively. We also identified a sex-specific upregulation of genes associated with negative regulation of mRNA processing and an increase in intron retention consistent with a reduction in mRNA splicing in XY testicular GCs by E13.5. Using computational gene regulation network inference analysis, we identified sex-specific, sequential waves of putative key regulator genes during GC differentiation and revealed that the meiotic genes are regulated by positive and negative master modules acting in an antagonistic fashion. Finally, we found that rare adrenal GCs enter meiosis similarly to ovarian GCs but display altered expression of master genes controlling the female and male genetic programs, indicating that the somatic environment is important for GC function. Our data is available on a web platform and provides a molecular roadmap of GC sex determination at single-cell resolution, which will serve as a valuable resource for future studies of gonad development, function and disease.