bluuebunny/crossref_metadata_2025_split huggingface dataset:
Treatment of Abdominal Surgical Wound Dehiscence With Bowel Exposure and Infection
Authors: Morinaga Keigo , Rikimaru Yukiko , Kiyokawa Kensuke 
Published: January 2019

Abstract
Abdominal surgical wound dehiscence with bowel exposure and infection carries a risk of intestinal fistula, making it extremely difficult to treat. The objective at this time is to heal such wounds safely and absolutely with using intrawound continuous negative pressure and irrigation treatment and artificial dermis. The subjects were 18 patients with abdominal wall dehiscence wounds with bowel exposure. Complications had already developed in 4 of the 18 cases of intestinal fistula. Subsequently, these 4 cases were treated with conservative treatment alone, whereas the other 14 were treated by split-thickness skin grafts. Intrawound continuous negative-pressure therapy has enabled the concomitant use of an artificial dermis inside the infected wound by maintaining irrigation of the wound. This method not only eliminated the danger of perforation from direct contact of the sponge with the bowel but also promoted the early proliferation of dermis-like tissue on the bowel surface, enabling safe and absolute healing.
A Test for the Clinical Evaluation of the Flexor Digitorum Superficialis of the Fifth Finger
Authors: Valdés-Flores Everardo , García-Álvarez Edgar , García-Pérez Mauricio M. , Castro-Govea Yanko , Santos-Ibarra Alejandro , Chacón-Martínez Hernán , Betancourt-Espericueta Lizbeth , Mecott Gabriel A. 
Published: January 2019

Physical examination is essential in diagnosing tendinous lesions. This is particularly true of the flexor digitorum superficialis of the little finger (FDS5), which is functionally absent in approximately 30% of the population. The objective of our study was to determine the diagnostic value of 3 clinical tests commonly used to assess the function of this tendon.

Methods
Patients with wounds of the FDS5 were included in this study. Under local or regional anesthesia, 3 described clinical tests were performed to assess the function of the FDS5: (i) the classic test; (ii) Stein's modified test, and (iii) Mecott's modified test. We determined sensitivity, specificity, and predictive values of all such tests. The integrity of the tendon was assessed surgically. Correlation among blinded observers was also established.

Results
A total of 28 subjects with a mean age of 28 years (ranging from 5 to 56) participated in this study. The classic test obtained a sensitivity of 100% and a specificity of 72%; Stein's test resulted in a sensitivity of 83% and a specificity of 95%, whereas Mecott's test reached a sensitivity of 100% and a specificity of 95%.

Conclusions
Among the 3 tests described and used in our study, Mecott's modified test proved to be more sensitive and specific than the other two; therefore, we consider this to be the test that should be used in determining the integrity of the FDS5.
Detecting M/EEG modular brain states in rest and task
Authors: Kabbara A. , Khalil M. , O’Neill G. , Dujardin K. , El Traboulsi Y. , Wendling F. , Hassan M. 
Published: January 2019

AbstractThe human brain is a dynamic networked system that continually reconfigures its connectivity patterns over time. Thus, developing approaches able to adequately detect fast brain dynamics is critical. Of particular interest are the methods that analyze the modular structure of brain networks, i.e. the presence of clusters of regions that are densely inter-connected. In this paper, we propose a novel framework to identify fast modular states that dynamically fluctuate over time during rest and task. We validated our method using MEG data recorded during a finger movement task, identifying modular states linking somatosensory and primary motor regions. The algorithm was also validated on dense-EEG data recorded during picture naming task, revealing the sub-second transition between several modular states which relate to visual processing, semantic processing and language. Next, we validated our method on a dataset of resting state dense-EEG signals recorded from 124 patients with Parkinson’s disease and different cognitive phenotypes. Results disclosed brain modular states that differentiate cognitively intact patients, patients with moderate cognitive deficits and patients with severe cognitive deficits. Our new approach tracks the brain modular states, in healthy subjects and patients, on an adequate task-specific timescale.
Genomic approaches reveal an endemic sub-population of gray wolves in Southern China
Authors: Wang Guo-Dong , Zhang Ming , Wang Xuan , Yang Melinda A. , Cao Peng , Liu Feng , Lu Heng , Feng Xiaotian , Skoglund Pontus , Wang Lu , Fu Qiaomei , Zhang Ya-Ping 
Published: January 2019

SUMMARYDespite being one of the most widely distributed terrestrial mammals, the history of gray wolves (Canis lupus) in China is not well understood as their habitats have been destroyed with growing economic development. Using six specimens from wolf skins in Chinese Natural History museums, we sequenced their genome using a modified ancient DNA procedure. Using whole genome sequence analysis, we showed that gray wolves from Southern China (SC) derive from a single lineage, distinct from gray wolves from the Tibetan Plateau (Canis lupus chanco) and Northern China, suggesting that SC gray wolves may form a distinct sub-population. Of SC gray wolves, one wolf from Zhejiang carries a genetic component from a canid that must have diverged earlier from other wolves than jackals did, perhaps through gene flow from a population related to or further diverged from wolves than the dhole, a species distributed in Southern China and Southeast Asia. This may indicate that interspecific gene flow likely played an important role in shaping the speciation patterns and population structure in the genus Canis. Our study is the first to survey museum genomes of gray wolves from Southern China, revealing the presence of an endemic population with ancient interspecific gene flow from a population related to the dhole, and highlighting how sequencing the paleogenome from museum specimens can help us to study extinct species.
The effect of pre-analytical conditions on blood metabolomics in epidemiological studies
Authors: Santos Ferreira Diana L , Maple Hannah J , Goodwin Matt , Brand Judith S , Yip Vikki , Min Josine L , Groom Alix , Lawlor Debbie A , Ring Susan 
Published: January 2019

AbstractBackgroundSerum and plasma are commonly used biofluids for large-scale metabolomic-epidemiology studies. Their metabolomic profile is susceptible to changes due to variability in pre-analytical conditions and the impact of this is unclear.MethodsParticipant-matched EDTA-plasma and serum samples were collected from 37 non-fasting volunteers and profiled using a targeted nuclear magnetic resonance (NMR) metabolomics platform (N=151 traits). Metabolic concentrations were compared between reference (pre-storage: 4°C, 1.5h; post-storage: no sample preparation or NMR-analysis delays) and four, pre-storage, blood processing conditions, where samples were incubated at (i) 4°C, 24h; (ii) 4°C, 48h; (iii) 21°C, 24h; (iv) 21°C, 48h, before centrifugation; and two, post-storage, sample processing conditions in which samples (i) thawed overnight, then left for 24h before addition of sodium buffer followed by immediate NMR analysis; (ii) thawed overnight, addition of sodium buffer, then left for 24h before profiling. Linear regression models with random-intercepts were used to assess the impact of these six pre-analytical conditions on EDTA-plasma/serum metabolome.ResultsFatty acids, beta-hydroxybutyrate, glycoprotein-acetyls and most lipid-related traits, in serum and plasma, were robust to the tested pre and post-storage conditions. Pre-storage conditions impacted concentrations of glycolysis metabolites, acetate, albumin and amino-acids by levels that could potentially bias research results (up to 1.4SD difference compared with reference). Post-storage conditions affected histidine, phenylalanine and LDL-particle-size, with differences up to 1.4SD.ConclusionsMost metabolic traits are robust to the pre- and post-storage conditions tested here and that may commonly occur in large-scale cohorts. However, concentrations of glycolysis metabolites, and amino-acids may be compromised.Key messagesIn large scale epidemiological studies, blood processing delays, incubation at high temperature prior to long term storage, and NMR profiling delays after long term storage, may occur.Concentrations of fatty acids, beta-hydroxybutyrate, glycoprotein acetyls and most lipid-related traits are robust to variations in pre-storage temperature and duration of incubation (4°C or 21°C for up to 48h prior to centrifugation) and post-storage sample handling (24h delay in sample preparation or NMR profiling).Glycolytic metabolite concentrations are altered by pre-storage conditions and amino-acids, particularly histidine and phenylalanine, by both, pre and post-storage conditions.
Neofunctionalisation of basic helix loop helix proteins occurred when plants colonised the land
Authors: Bonnot Clémence , Hetherington Alexander J. , Champion Clément , Breuninger Holger , Kelly Steven , Dolan Liam 
Published: January 2019

ABSTRACTROOT HAIR DEFECTIVE SIX-LIKE (RSL)genes control the development of structures – rhizoids, root hairs, gemmae, mucilage papillae – that develop from single cells at the surface of diverse groups of land plants. RSL proteins constitute a subclass (VIIIc) of the basic helix loop helix (bHLH) class VIII transcription factor family. We set out to determine if the function of RSL genes in the control of cell differentiation in land plants was inherited from streptophyte algal ancestor. The Charophyceae are a monophyletic class of streptophyte algae with tissue-like structures and rhizoids. We identified the single class VIII bHLH gene from the charophyceaen algaChara braunii(CbbHLHVIII). Phylogenetic analysis suggests that this protein is sister to the RSL (bHLH subclass VIIIc) proteins and together they constitute a monophyletic group. Expression of CbbHLHVIIIdoes not compensate for loss of the RSL function in either Marchantia polymorpha or Arabidopsis thaliana. Furthermore, CbbHLHVIII is expressed at sites of morphogenesis inC. braunii– the apices, nodes and gametangia – but not in rhizoids. This indicates thatC. brauniiclass VIII protein is functionally different from land plant RSL proteins; they control rhizoid development in land plants but not in the charophycean algae. These data are consistent with the hypothesis that RSL proteins and their function in the differentiation of cells at the plant surface evolved in the lineage leading to land plants after the divergence of the land plants andC. brauniifrom their last common ancestor. This may have occurred by neofunctionalisation at or before the colonisation of the land by streptophytes.
Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.)
Authors: Herniter Ira A. , Lo Ryan , Muñoz-Amatriaín María , Lo Sassoum , Guo Yi-Ning , Huynh Bao-Lam , Lucas Mitchell , Jia Zhenyu , Roberts Philip A. , Lonardi Stefano , Close Timothy J. 
Published: January 2019

AbstractThe appearance of the seed is an important aspect of consumer preference for cowpea (Vigna unguiculata [L.] Walp.). Seed coat pattern in cowpea has been a subject of study for over a century. This study makes use of newly available resources, including mapping populations, a reference genome and additional genome assemblies, and a high-density single nucleotide polymorphism genotyping platform, to map various seed coat pattern traits to three loci, concurrent with the Color Factor (C), Watson (W), and Holstein (H) factors identified previously. Several gene models encoding proteins involved in regulating the later stages of the flavonoid biosynthesis pathway have been identified as candidate genes, including a basic helix-loop-helix gene (Vigun07g110700) for the C locus, a WD-repeat gene (Vigun09g139900) for the W locus and an E3 ubiquitin ligase gene (Vigun10g163900) for the H locus. A model of seed coat development, consisting of six distinct stages, is described to explain some of the observed pattern phenotypes.
False-positive neuroimaging: Undisclosed flexibility in testing spatial hypotheses allows presenting anything as a replicated finding
Authors: Hong YongWook , Yoo Yejong , Han Jihoon , Wager Tor D. , Woo Choong-Wan 
Published: January 2019

AbstractHypothesis testing in neuroimaging studies relies heavily on treating named anatomical regions (e.g., “the amygdala”) as unitary entities. Though data collection and analyses are conducted at the voxel level, inferences are often based on anatomical regions. The discrepancy between the unit of analysis and the unit of inference leads to ambiguity and flexibility in analyses that can create a false sense of reproducibility. For example, hypothesizing effects on “amygdala activity” does not provide a falsifiable and reproducible definition of precisely which voxels or which patterns of activation should be observed. Rather, it comprises a large number of unspecified sub-hypotheses, leaving room for flexible interpretation of findings, which we refer to as “model degrees of freedom.” From a survey of 135 functional Magnetic Resonance Imaging studies in which researchers claimed replications of previous findings, we found that 42.2% of the studies did not report any quantitative evidence for replication such as activation peaks. Only 14.1% of the papers used exact coordinate-based ora prioripattern-based models. Of the studies that reported peak information, 42.9% of the ‘replicated’ findings had peak coordinates more than 15 mm away from the ‘original’ findings, suggesting that different brain locations were activated, even when studies claimed to replicate prior results. To reduce the flexible and qualitative region-level tests in neuroimaging studies, we recommend adopting quantitative spatial models and tests to assess the spatial reproducibility of findings. Techniques reviewed here include permutation tests on peak distance, Bayesian MANOVA, anda priorimultivariate pattern-based models. These practices will help researchers to establish precise and falsifiable spatial hypotheses, promoting a cumulative science of neuroimaging.
A neuroprosthetic system to restore neuronal communication in modular networks
Authors: Buccelli S. , Bornat Y. , Colombi I. , Ambroise M. , Martines L. , Pasquale V. , Bisio M. , Tessadori J. , Nowak P. , Grassia F. , Averna A. , Tedesco M. , Bonifazi P. , Difato F. , Massobrio P. , Levi T. , Chiappalone M. 
Published: January 2019

AbstractRecent advances in neurotechnology allow neurological impairments to be treated or reduced by brain machine interfaces and neuroprostheses. To develop energy-efficient and real-time capable devices, neuromorphic computing systems are envisaged as the core of next-generation ‘neurobiohybrid’ systems for brain repair. We demonstrate here the first exploitation of a neuromorphic prosthesis to restore bidirectional interactions between two neuronal populations, even when one is damaged or completely missing. We used in vitro modular cell cultures to mimic the mutual interaction between neuronal assemblies and created a focal lesion to functionally disconnect the two populations. Then, we employed our neuromorphic prosthesis for two specific applications with future clinical implications: bidirectional bridging to artificially reconnect two disconnected neuronal modules and hybrid bidirectional bridging to replace the activity of one module with a neuromorphic spiking neural network. Our neuroprosthetic system opens up new avenues for the development of novel bioelectrical therapeutics for human applications.
Mice carrying a humanizedFoxp2knock-in allele show region-specific shifts of striatal Foxp2 expression levels
Authors: Schreiweis C , Irinopoulou T , Vieth B , Laddada L , Oury F , Burguière E , Enard W , Groszer M 
Published: January 2019

ABSTRACTGenetic and clinical studies of speech and language disorders are providing starting points to unravel underlying neurobiological mechanisms. The gene encoding the transcription factorFOXP2has been the first example of a gene involved in the development and evolution of this human-specific trait. A number of autosomal-dominantFOXP2mutations are associated with developmental speech and language deficits indicating that gene dosage plays an important role in the disorder. Comparative genomics studies suggest that two human-specific amino acid substitutions in FOXP2 might have been positively selected during human evolution. A knock-in mouse model carrying these two amino acid changes in the endogenous mouseFoxp2gene(Foxp2hum/hum)shows profound changes in striatum-dependent behaviour and neurophysiology, supporting a functional role for these changes. However, how this affects Foxp2 expression patterns in different striatal regions and compartments has not been assessed. Here, we characterized Foxp2 protein expression patterns in adult striatal tissue inFoxp2hum/hummice. Consistent with prior reports in wildtype mice, we find that striatal neurons inFoxp2hum/hummice and wildtype littermates express Foxp2 in a range from low to high levels. However, we observe a shift towards more cells with higher Foxp2 expression levels inFoxp2hum/hummice, significantly depending on the striatal region and the compartment. As potential behavioural readout of these shifts in Foxp2 levels across striatal neurons, we employed a morphine sensitization assay. While we did not detect differences in morphine-induced hyperlocomotion during acute treatment, there was an attenuated hyperlocomotion plateau during sensitization inFoxp2hum/hummice. Taken together, these results suggest that the humanizedFoxp2allele in a mouse background is associated with a shift in striatal Foxp2 protein expression pattern.
CellSIUS provides sensitive and specific detection of rare cell populations from complex single cell RNA-seq data
Authors: Wegmann Rebekka , Neri Marilisa , Schuierer Sven , Bilican Bilada , Hartkopf Huyen , Nigsch Florian , Mapa Felipa , Waldt Annick , Cuttat Rachel , Salick Max R. , Raymond Joe , Kaykas Ajamete , Roma Guglielmo , Keller Caroline Gubser 
Published: January 2019

AbstractComprehensive benchmarking of computational methods for single-cell RNA sequencing (scRNA-seq) analysis is scarce. Using a modular workflow and a large dataset with known cell composition, we benchmarked feature selection and clustering methodologies for scRNA-seq data. Results highlighted a methodology gap for rare cell population identification for which we developed CellSIUS (Cell Subtype Identification from Upregulated gene Sets). CellSIUS outperformed existing approaches, enabled the identification of rare cell populations and, in contrast to other methods, simultaneously revealed transcriptomic signatures indicative of the rare cells’ function. We exemplified the use of our workflow and CellSIUS for the characterization of a human pluripotent cell 3D spheroid differentiation protocol recapitulating deep-layer corticogenesis in vitro. Results revealed lineage bifurcation between Cajal-Retzius cells and layer V/VI neurons as well as rare cell populations that differ by migratory, metabolic, or cell cycle status, including a choroid plexus neuroepithelial subgroup, revealing previously unrecognized complexity in human stem cell-derived cellular populations.
System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells
Authors: Wigger Leonore , Casals-Casas Cristina , Baruchet Michaël , Trang Khanh B. , Pradervand Sylvain , Naldi Aurélien , Desvergne Béatrice 
Published: January 2019

AbstractTranscriptional regulations exert a critical control of metabolic homeostasis. In particular, the nuclear receptors (NRs) are involved in regulating numerous pathways of the intermediate metabolism. The purpose of the present study was to explore in liver cells the interconnectedness between three of them, LXR, FXR, and PPARα, all three known to act on lipid and glucose metabolism, and also on inflammation. The human cell line HepaRG was selected for its best proximity to human primary hepatocytes. Global gene expression of differentiated HepaRG cells was assessed after 4 hours and 24 hours of exposure to GW3965 (LXR agonist), GW7647 (PPARα agonist), and GW4064 and CDCA (FXR synthetic and natural agonist, respectively). Our work revealed that, contrary to our expectations, NR specificity is largely present at the level of target genes, with a smaller than expected overlap of the set of genes targeted by the different NRs. It also highlighted the much broader activity of the synthetic FXR ligand compared to CDCA. More importantly, our results revealed that activation of FXR has a pro-proliferative effect and decreases polyploidy of hepatocytes, while LXR inhibits the cell cycle progression, inducing hepatocyte differentiation and a higher polyploidism. Conclusion: these results highlight the importance of analyzing the different NR activities in a context allowing a direct confrontation of each receptor outcome, and reveals the opposite role of FXR and LXR in hepatocyte cells division and maturation.
Community size affects the signals of ecological drift and niche selection on biodiversity
Authors: Siqueira Tadeu , Saito Victor S. , Bini Luis M. , Melo Adriano S. , Petsch Danielle K. , Landeiro Victor L. , Tolonen Kimmo T. , Jyrkänkallio-Mikkola Jenny , Soininen Janne , Heino Jani 
Published: January 2019

AbstractEcological drift can override the effects of deterministic niche selection on small populations and drive the assembly of small communities. We tested the hypothesis that smaller local communities are more dissimilar among each other because of ecological drift than larger communities, which are mainly structured by niche selection. We used a unique, comprehensive dataset on insect communities sampled identically in a total of 200 streams in climatically different regions (Brazil and Finland) that differ in community size by fivefold. Null models allowed us to estimate the magnitude to which beta diversity deviates from the expectation under a random assembly process while taking differences in species richness and relative abundance into account, i.e., beta deviation. Beta diversity of small tropical communities was consistently higher but closer to null expectations than β-diversity of large communities. However, although β-deviation and community size were strongly related in both regions, the direction of the relationship varied according to dissimilarity metrics. While incidence-based β-diversity was lower than expected (communities were less dissimilar than null expectations) and negatively related to community size in Brazil, abundance-based β-diversity was higher than expected (communities were more dissimilar than null expectations) and positively related to community size in both regions. We suggest that ecological drift drives variation in small communities by increasing the chances of species with low abundance and narrow distribution to occur within the metacommunity. Also, while weak niche selection and high dispersal rates likely reduced variation in community structure among large tropical streams, niche selection was likely sufficient to cause non-random variations in the relative abundances of genera among large communities in both regions. Habitat destruction, overexploitation, pollution, and reductions in connectivity have been reducing the size of biological communities. These environmental pressures will make smaller communities more vulnerable to novel conditions and render community dynamics more unpredictable, as random demographic processes should prevail under these conditions. Incorporation of community size into ecological models should provide conceptual, empirical and applied insights into a better understanding of the processes driving changes in biodiversity.