bluuebunny/crossref_metadata_2025 huggingface dataset:
VS01.03: ROBOTIC-ASSISTED D2-LYMPHADENECTOMY IN SURGERY FOR CANCER OF THE ESOPHAGEAL CARDIA
Authors: Dubecz Attila , Giulini Luca , Stein Hubert
Published: September 2018

Description

BACKGROUND

Widespread acceptance of minimally-invasive surgery for adenocarcinoma for the distal esophagus limited by the feasibility of an oncologically correct complete D2-lymphadenectomy which can be facilitated by using robotic-assisted surgery. The aim of this presentation is to describe our technique and short-term results of a series of robotic-assisted esophagectomies with D2-lymphadenectomy for esophageal cancer, using the da Vinci Surgical System.

MATERIALS AND METHODS

Between November 2016 and January 2018, we performed 48 consecutive robotic-assisted esophagectomies with an extended D2-lymphadenectomy for histologically-proven adeno- or squamous-cell-carcinoma of the cardia and distal esophagus. Data were collected in a database and retrospectively analyzed.

RESULTS

Median operative time was 333 min (200–536). Conversion to open technique occured in 10.4% (abdominal 2.1%, thoracic 8.3%). Median intraoperative blood loss was 50 mL. Median number of harvested lymph nodes was 28 (13–68). Resection margins were negative in all cases (91.7% R0, 2.1% Rx, 6.2% R1). Surgery-related morbidity attributed to the extended D2-Lymphadenectomy was 2.1%. The over-all 30 days-mortality for this series was 2.1%.

CONCLUSIONS

Robotic-assisted surgery with modern tissue sealing techiques allows optimal hemostasis and a fast, safe and effective D2-lymphadenectomy with an adequate lymph node harvest with low postoperative morbidity. Technique of the robotic assisted D2-Lymphadenectomy will be presented in the accompanying video.

Disclosure

All authors have declared no conflicts of interest.
VS02.01: FLEXIBLE ENDOSCOPIC CRICOPHARYNGEAL MYOTOMY WITH THULIUM LASER
Authors: Siboni Stefano , Aiolfi Alberto , Sozzi Marco , Ceriani Chiara , Bonavina Luigi
Published: September 2018

Description

Flexible endoscopic treatment of Zenker's diverticulum is feasible, but electrocautery and CO2 laser technology carry the risk of collateral thermal injury. Thulium laser septum incision may overcome this limitation. We describe for the first time the use of thulium laser through flexible endoscopy in a small cohort of patients with Zenker diverticulum.

Methods

Thulium laser septum division was performed via flexible endoscopy under general anesthesia in 11 consecutive symptomatic patients with primary or recurrent Zenker diverticulum. Primary study aims were feasibility and safety of the procedure. To improve exposure and stabilize the septum during the procedure, either a transparent cap or a bivalve soft overtube were used. The laser system used was Opera® (Quanta System SpA, Varese, Italy), emitting a 1.9 μm Thulium wavelength radiation. A continuous laser configuration and an emission power of 5 to 16 W were chosen to allow incision of the mucosa and cricopharyngeal myotomy. Using 272 and 365 μm optical fibres in a non-contact mode, laser incision was performed in the midline of the septum until cricopharyngeal muscle fibers were encountered and a V-shaped myotomy was completed under visual control.

Results

Between May and January 2018, 11 consecutive patients were treated. Four patients presented with recurrent symptomatic diverticulum after previous transoral septum stapling or endoscopic myotomy. Median dysphagia and regurgitation scores were 4.1 ± 0.7 and 3.3 ± 0.8 respectively. Complete division of the septum was achieved in all patients. There was no bleeding nor need of adjunctive electrocautery devices to complete the procedure. The post-operative course was uneventful in all patients; the chest film and gastrographin swallow study on post-operative day one were negative for pneumomediastinum or leaks. All patients were discharged within 48 hours on a soft diet. At the 2-month follow-up visit, all patients were satisfied with the procedure with a post-operative dysphagia score of 2.0 ± 0.6 and a regurgitation score of 1.5 ± 0.4.

Conclusions

Division of Zenker's septum with Thulium laser is feasible and safe through flexible endoscopy. Longer term follow-up is required to establish effectiveness and reproducibility of this novel procedure.

Disclosure

All authors have declared no conflicts of interest.
VS02.03: LAPAROSCOPIC EXCISION OF ESOPHAGEAL FISTULA TRACT (LEEFT) IN A SPONTANEOUS ESOPHAGOCUTANEOUS FISTULA WITH KIKUCHI DISEASE
Authors: Voon Kelvin , Hamidi Osman Mohd , Mohammed Taher Mustafa , Rajan Reynu , Ritza Kosai Nik
Published: September 2018

Description

Spontaneous esophagocutaneous fistula is rare and necrotizing mediastinal lymphadenopathy is one of the causes. We report a case of spontaneous esophagocutaneous fistula in a 38-year-old lady with Kikuchi disease that was treated with laparoscopic excision of esophageal fistula tract (LEEFT). On endoscopy, the fistula opening was located at right posterolateral wall of distal esophagus, 3cm above esophagogastric junction. Esophageal stenting and endoscopic clipping of fistula were attempted but the fistula tract persisted. She then underwent laparoscopic excision of esophageal fistula tract. Laparoscopic excision of esophageal fistula tract (LEEFT) is a novel transhiatal technique as compared to the usual transthoracic aproach. Patient is placed in french position and it is done via 4-laparoscopic port technique with liver retraction. LEEFT is feasible in distally located esophageal fistula. In comparison to transthoracic aproach, the dissection and control of esophagus is easier with this technique as dissection through the chronic inflammatory tissue in the posterior mediastinum is avoided. Moreover, it spares the morbidity associated with single lung ventilation and transthoracic approach.

Disclosure

All authors have declared no conflicts of interest.
VS02.06: ROBOTIC RE-DO GIANT HIATAL HERNIA WITH MESH
Authors: Sallum Rubens , Takeda Flavio , Santo Marco , Cecconello Ivan
Published: September 2018

Description

The authors present a video of reoperation of relapsed giant hiatal hérnia (twice). Tactics of static presentation of 2 robotic arms allowing safe dissection with 2 concomitant energy modalities: ultrasonic scalpel and bipolar. The endowrist movments allow intrathoracic safe dissection. The hiatal repair with barbed suture at different angles was followed by a biological U-shape mesh. Total fundoplication with 3 lines of suture and hiatal fixation are highlighted.

Disclosure

All authors have declared no conflicts of interest.
VS02.07: ROBOTIC RESSECTION OF A GIANT THORACIC ESOPHAGEAL LEIOMYOMA
Authors: Sallum Rubens , Takeda Flavio , Santo Marco , Cecconello Ivan
Published: September 2018

Description

The authors present the video of robotic resection of extensive leiomyoma of the thoracic esophagus. We highlight the use of 4 robotic arms that allow the rotation of the leiomyoma of great proportions, as well as presentation of the contralateral face of the muscular breach to perform the repair of the esophageal wall. The removal of the tumor (in bag peacemeal) is still observed.

Disclosure

All authors have declared no conflicts of interest.
VS03.06: RADICAL OPERATION OF ESOPHAGEAL CANCER UNDER 3D THORACOSCOPE (ABDOMINAL PART)
Authors: Jiang Jie , Yu Xiuyi , Geng Guojun , Liu Hongming
Published: September 2018

Description

To show the main operation procedure of the abdominal part of the radical operation of esophageal carcinoma.

Disclosure

All authors have declared no conflicts of interest.
The Central Nervious System Acts as a Transducer of Stress-Induced Masculinization through Corticotropin-Releasing Hormone B
Authors: Castañeda Cortés DC , Arias Padilla LF , Langlois VS , Somoza GM , Fernandino JI
Published: September 2018

Exposure to environmental stressors during early development has important implications for rescheduling many cellular and molecular mechanisms. In some fish species, environmental stressors, like high temperatures (HT), cause an increase in cortisol levels. In turn, this mechanism induces sex reversal of genotypic females, overriding genetic factors related to development of the gonad. However, the involvement of the brain in this process is not well clarified. In the present work, we investigated the mRNA levels of corticotropin-releasing hormone b (crhb) and its receptors (crhr1 and crhr2), and found out that they were up-regulated at HT during the critical period of gonadal sex determination in medaka (Oryzias latipes), i.e., when the gonadal primordium is sexually labile. In order to clarify their roles in sex reversal, biallelic mutants for crhr1 and crhr2 were produced by CRISPR/Cas9 technology. Remarkably, biallelic mutant of both loci (crhr1 and crhr2) did not undergo female-to-male sex reversal upon HT exposition, whereas mutants for either crhr1 or crhr2 showed partial, or intersex phenotypes, suggesting that both crh receptors are required for HT-induced masculinization. Inhibition of this process in double crhrs mutants could be successfully rescued through the administration of the downstream effector of the hypothalamic-pituitary interrenal axis, the cortisol. Taken together, these results revealed for the first time the participation of the central nervous system acting as a transducer of masculinization induced by thermal stress.
Sentence processing is modulated by the current linguistic environment and a priori information: An fMRI study
Authors: Weber K. , Micheli C. , Ruigendijk E. , Rieger J.W.
Published: September 2018

Words are not processed in isolation but in rich contexts that are used to modulate and facilitate language comprehension. Here, we investigate distinct neural networks underlying two types of contexts. Firstly, the current linguistic environment, presented as the relative frequencies of two syntactic structures (prepositional object (PO) and double-object (DO)), which would either follow everyday linguistic experience or not. Secondly, preference towards one or the other structure depending on the verb; learned in everyday language use and stored in memory. German participants were reading PO and DO sentences in German while brain activity was measured with functional magnetic resonance imaging. Firstly, the anterior cingulate cortex (ACC) showed a pattern of activation that integrated the current linguistic environment with everyday linguistic experience. When the input did not match everyday experience, the unexpectedly frequent structure showed higher activation in the ACC than the other conditions and more connectivity from the ACC to posterior parts of the language network. Secondly, verb-based surprisal of seeing a structure given a verb (PO verb preference but DO structure presentation) resulted, within the language network (left inferior frontal and left middle/superior temporal gyrus) and the precuneus, in increased activation compared to a predictable situation. In conclusion, 1) beyond the canonical language network, brain areas engaged in cognitive control, such as the ACC, might use the statistics of syntactic structures to facilitate language comprehension, 2) the language network is directly engaged in processing verb preferences. These two networks show distinct influences on sentence processing.
Fungal community assembly in soils and roots under plant invasion and nitrogen deposition
Authors: Phillips Michala L. , Weber S□ren E. , Andrews Lela V. , Aronson Emma L. , Allen Michael F. , Allen Edith B.
Published: September 2018

Abstract Fungal community composition in the Anthropocene is driven by rapid changes in environmental conditions caused by human activities. This study examines the relative importance of two global change drivers – atmospheric nitrogen (N) deposition and annual grass invasion – on structuring fungal communities in a California chaparral ecosystem, with emphasis on arbuscular mycorrhizal fungi. We used molecular markers, functional groupings, generalized linear statistics and joint distribution modeling, to examine how environmental variables structure taxonomic and functional composition of fungal communities. Invasion of a chaparral ecosystem decreased richness and relative abundance of non-AMF symbionts and rhizophilic AMF (e.g. Glomeraceae) as well as the proportion of edaphophilic AMF (e.g. Gigasporaceae). We found increased richness and the proportion of rhizophilic and edaphophilic AMF with increasing soil NO3. Our findings suggest that invasive persistence may decrease the presence of multiple soil symbionts that native species depend on for pathogen protection and increased access to soil resources.
Marine Fe-oxidizingZetaproteobacteria: Historical, ecological, and genomic perspectives
Authors: McAllister Sean M. , Moore Ryan M. , Gartman Amy , Luther George W. , Emerson David , Chan Clara S.
Published: September 2018

TheZetaproteobacteriaare a class of bacteria typically associated with marine Fe oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount, Hawaii, they have become model organisms for marine microbial Fe oxidation. In addition to deep sea and shallow hydrothermal vents,Zetaproteobacteriaare found in coastal sediments, other marine subsurface environments, steel corrosion biofilms, as well as saline terrestrial aquifers and springs. Isolates from a range of environments all grow by Fe oxidation. Their success lies partly in their microaerophily, which enables them to compete with abiotic Fe oxidation at the low O2concentrations common to Fe(II)-rich oxic/anoxic transition zones. Also,Zetaproteobacteriamake a variety of biomineral morphologies as a repository for Fe(III) waste, and as attachment structures. To determine the known diversity of theZetaproteobacteria, we have used 16S rRNA gene sequences to define 59 operational taxonomic units (OTUs), at 97% similarity. While someZetaproteobacteriataxa appear to be cosmopolitan, various habitats enrich for different sets ofZetaproteobacteria. OTU networks show that certainZetaproteobacteriaco-exist, sharing compatible niches. These niches may correspond with adaptations to O2, H2, and nitrate availability, based on genomic analyses. Also, a putative Fe oxidation gene has been found in diverseZetaproteobacteriataxa, suggesting that theZetaproteobacteriaevolved as specialists in Fe oxidation. In all, culture, genomic, and environmental studies suggest thatZetaproteobacteriaare widespread, and therefore have a broad influence on marine and saline terrestrial Fe cycling.
Polygenic Prediction via Bayesian Regression and Continuous Shrinkage Priors
Authors: Ge Tian , Chen Chia-Yen , Ni Yang , Anne Feng Yen-Chen , Smoller Jordan W.
Published: September 2018

Polygenic prediction has shown promise in identifying individuals at high risk for complex diseases, and may become clinically useful as the predictive performance of polygenic risk scores (PRS) improves. Here, we present PRS-CS, a novel polygenic prediction method that infers posterior SNP effect sizes using GWAS summary statistics and an external linkage disequilibrium (LD) reference panel. PRS-CS utilizes a high-dimensional Bayesian regression framework, and is distinct from previous work by placing a continuous shrinkage (CS) prior on SNP effect sizes, which is robust to varying genetic architectures, provides substantial computational advantages, and enables multivariate modeling of local LD patterns. Simulation studies using data from the UK Biobank show that PRS-CS outperforms existing methods across a wide range of effect size distributions, especially when the training sample size is large. We apply PRS-CS to predict six complex diseases and six quantitative traits in the Partners HealthCare Biobank, and further demonstrate the improvement of PRS-CS in prediction accuracy over alternative methods.
Human cortical dynamics during full-body heading changes
Authors: Gramann Klaus , Hohlefeld Friederike U. , Gehrke Lukas , Klug Marius
Published: September 2018

The retrosplenial complex (RSC) plays a crucial role in spatial orientation by computing heading direction and translating between distinct spatial reference frames based on multi-sensory information. While invasive studies allow investigating heading computation in moving animals, established non-invasive analyses of human brain dynamics are restricted to stationary setups. To investigate the role of the RSC in heading computation of actively moving humans, we used a Mobile Brain/Body Imaging approach synchronizing electroencephalography with motion capture and virtual reality. Data from physically rotating participants were contrasted with rotations based only on visual flow. During physical rotation, varying rotation velocities were accompanied by pronounced wide frequency band synchronization in RSC, the parietal and occipital cortices. In contrast, the visual flow rotation condition was associated with pronounced alpha band desynchronization, replicating previous findings in desktop navigation studies, and notably absent during physical rotation. These results suggest an involvement of the human RSC in heading computation based on visual, vestibular, and proprioceptive input and implicate revisiting traditional findings of alpha desynchronization in areas of the navigation network during spatial orientation in movement-restricted participants.
Hyperconnectivity of the default mode network in multiorgan dysfunction syndrome
Authors: Jimenez-Marin Antonio , Rivera Diego , Boado Victoria , Diez Ibai , Labayen Fermin , Garrido Irati , Ramos-Usuga Daniela , Rasero Javier , Cabrera Alberto , Stramaglia Sebastiano , Arango-Lasprilla Juan Carlos , Cortes Jesus M.
Published: September 2018

Multiple Organ Dysfunction Syndrome (MODS) is a systemic physiological disorder affecting two or more body organs triggered after an insult complication. Beyond the systemic failure, patients who survive MODS present cognitive and neurological impairments that remain stable even several years after Intensive Care Unit (ICU) discharge. Here, we focus on the specific situation of MODS patients with no apparent brain damage (NABD), where the mechanisms driving cognitive impairment at long term are not well-understood. We recruit N1 = 13 MODS patients with NABD at 6 months after ICU discharge, together with N2 = 13 healthy controls (matched by age, sex and years of education), and acquire functional magnetic resonance imaging at rest to find that, as compared to control, MODS patients with NABD present an overall increase of the functional connectivity (FC) at rest. In particular, we find that the default mode network (DMN) hyperconnects (increasing the node strength of the FC matrix) to three classes of networks: primary sensory (such as auditory, sensory-motor and visual), multimodal integration (such as dorsal attention and salience) and higher order cognition networks (such as fronto-parietal, language and executive control). Therefore, although these patients do not have an apparent structural damage after MODS, at the functional level, we found brain network alterations coexisting with hyperconnectivity of the DMN, that similar to what happens at the onset of other pathologies, might indicate a possible mechanism for brain compensation occurring after MODS.
Uncured PDMS Inhibits Myosin In Vitro Motility in a Microfluidic Flow Cell
Authors: Wang Yihua , Burghardt Thomas P.
Published: September 2018

The myosin motor powers cardiac contraction and is frequently implicated in hereditary heart disease by its mutation. Principal motor function characteristics include myosin unitary step size, duty cycle, and force-velocity relationship for translating actin under load. These characteristics are sometimes measured in vitro with a motility assay detecting fluorescent labeled actin filament gliding velocity over a planar array of surface immobilized myosin. Assay miniaturization in a polydimethylsiloxane/glass (PDMS/glass) hybrid microfluidic flow channel is an essential component to a small sample volume assay applicable to costly protein samples however the PDMS substrate dramatically inhibits myosin motility. Myosin in vitro motility in a PDMS/glass hybrid microfluidic flow cell was tested under a variety of conditions to identify and mitigate the effect of PDMS on myosin. Substantial contamination by the monomeric species in polymerized PDMS flow cells is shown to be the cause of myosin motility inhibition. Normal myosin motility recovers by either extended cell aging (∼20 days) to allow more complete polymerization or by direct chemical extraction of the free monomers from the polymer substrate. PDMS flow cell aging is the low cost alternative compatible with the other PDMS and glass modifications needed for in vitro myosin motility assaying.
Mitotic replisome disassembly in vertebrates
Authors: Moreno Sara Priego , Jones Rebecca M. , Poovathumkadavil Divyasree , Gambus Agnieszka
Published: September 2018

Recent years have brought a breakthrough in our understanding of the process of eukaryotic DNA replication termination. We have shown that the process of replication machinery (replisome) disassembly at the termination of DNA replication forks in S-phase of the cell cycle is driven through polyubiquitylation of one of the replicative helicase subunits Mcm7. Our previous work in C.elegans embryos suggested also an existence of a back-up pathway of replisome disassembly in mitosis. Here we show, that in Xenopus laevis egg extract, any replisome retained on chromatin after S-phase is indeed removed from chromatin in mitosis. This mitotic disassembly pathway depends on formation of K6 and K63 ubiquitin chains on Mcm7 by TRAIP ubiquitin ligase and activity of p97/VCP protein segregase. The mitotic replisome pathway is therefore conserved through evolution in higher eukaryotes. However, unlike in lower eukaryotes it does not require SUMO modifications. This process can also remove any helicases from chromatin, including “active” stalled ones, indicating a much wider application of this pathway than just a “back-up” for terminated helicases.
Chromatin changes in Anopheles gambiae induced by a Plasmodium falciparum infection
Authors: Ruiz José L. , Yerbanga Rakiswendé S. , Lefèvre Thierry , Ouedraogo Jean B. , Corces Victor G. , Gómez-Díaz Elena
Published: September 2018

Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso. We report 15,916 regions containing differential histone modification enrichment, of which 8,339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection responsive genes showing differential enrichment in various histone modifications, such as CLIP pro-teases, anti-microbial peptides encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways. The analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to a P. falciparum infection but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.
Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks
Authors: Koo Peter K. , Anand Praveen , Paul Steffan B. , Eddy Sean R.
Published: September 2018

To infer the sequence and RNA structure specificities of RNA-binding proteins (RBPs) from experiments that enrich for bound sequences, we introduce a convolutional residual network which we call ResidualBind. ResidualBind significantly outperforms previous methods on experimental data from many RBP families. We interrogate ResidualBind to identify what features it has learned from high-affinity sequences with saliency analysis along with 1st-order and 2nd-orderin silicomutagenesis. We show that in addition to sequence motifs, ResidualBind learns a model that includes the number of motifs, their spacing, and both positive and negative effects of RNA structure context. Strikingly, ResidualBind learns RNA structure context, including detailed base-pairing relationships, directly from sequence data, which we confirm on synthetic data. ResidualBind is a powerful, flexible, and interpretable model that can uncovercis-recognition preferences across a broad spectrum of RBPs.
A Genome-Wide Association Study Identifies SNP Markers for Virulence in Magnaporthe oryzae Isolates from Sub-Saharan Africa
Authors: Ganeshan Veena Devi , Opiyo Stephen O. , Mutiga Samuel K. , Rotich Felix , Thuranira David M. , Were Vincent M. , OuéDraogo Ibrahima , Zhou BO , Soanes Darren M. , Correll James C. , Wang Guo-Liang , Talbot Nicholas J. , Mitchell Thomas K.
Published: September 2018

The fungal phytopathogen Magnaporthe oryzae causes blast disease in cereals such as rice and finger millet worldwide. In this study, we assessed genetic diversity of 160 isolates from nine sub-Saharan Africa (SSA) and other principal rice producing countries and conducted a genome-wide association study (GWAS) to identify the genomic regions associated with virulence of M. oryzae. GBS of isolates provided a large and high-quality 617K single nucleotide polymorphism (SNP) dataset. Disease ratings for each isolate was obtained by inoculating them onto differential lines and locally-adapted rice cultivars. Genome-wide association studies were conducted using the GBS dataset and sixteen disease rating datasets. Principal Component Analysis (PCA) was used an alternative to population structure analysis for studying population stratification from genotypic data. A significant association between disease phenotype and 528 SNPs was observed in six GWA analyses. Homology of sequences encompassing the significant SNPs was determined to predict gene identities and functions. Seventeen genes recurred in six GWA analyses, suggesting a strong association with virulence. Here, the putative genes/genomic regions associated with the significant SNPs are presented.
Visualizing Deep Mutational Scan Data
Authors: Sruthi C. K. , Balaram Hemalatha , Prakash Meher K.
Published: September 2018

Site-directed and random mutagenesis are biochemical tools to obtain insights into the structure and function of proteins. Recent advances such as deep mutational scan have allowed a complete scan of all the amino acid positions in a protein with each of the 19 possible alternatives. Mapping out the phenotypic consequences of thousands of single point mutations in the same protein is now possible. Visualizing and analysing the rich data offers an opportunity to learn more about the effects of mutations, for a better understanding and engineering of proteins. This work focuses on such visualization analyses applied to the mutational data of TEM-1 β-lactamase. The data is examined in the light of the expected biochemical effects of single point mutations, with the goal of reinforcing or retraining the intuitions. Individual attributes of the amino acid mutations such as the solvent accessible area, charge type change, and distance from the catalytic center capture most of the relevant functional effects. Visualizing the data suggests how combinations of these attributes can be used for a better classification of the effects of mutations, when independently they do not offer a high predictability.
Olfactory object recognition based on fine-scale stimulus timing inDrosophila
Authors: Sehdev Aarti , Mohammed Yunusa G. , Triphan Tilman , Szyszka Paul
Published: September 2018

Odorants of behaviorally relevant objects (e.g., food sources) intermingle with those from other sources. Therefore, to sniff out whether an odor source is good or bad – without actually visiting it – animals first need to segregate the odorants from different sources. To do so, animals could use temporal cues, since odorants from one source exhibit correlated fluctuations, while odorants from different sources are less correlated. However, it remains unclear whether animals can rely solely on temporal cues for odor source segregation. Here we show that 1) flies can use a few milliseconds differences in odorant arrival to segregate a target odorant from a binary mixture, 2) segregation does not improve when the target odorant arrives first, and 3) segregation works for odorants with innate, as well as learned valences. These properties of odor segregation parallel those of concurrent sound segregation and figure-ground segregation by onset asynchrony in humans.
IL-10 and ICOS differentially regulate T cell responses in the brain during chronicToxoplasma gondiiinfection
Authors: O’Brien Carleigh A. , Batista Samantha J. , Still Katherine M. , Harris Tajie H.
Published: September 2018

Control of chronic CNS infection with the parasiteToxoplasma gondiirequires an ongoing T cell response in the brain. Immunosuppressive cytokines are also important for preventing lethal immunopathology during chronic infection. To explore the loss of suppressive cytokine exclusively during the chronic phase of infection we blocked IL-10 receptor (IL-10R). Blockade was associated with widespread changes in the inflammatory response, including increased antigen presenting cell (APC) activation, expansion of CD4+ T cells, and increased neutrophil recruitment to the brain, consistent with previous reports. We then sought to identify regulatory mechanisms contributing to IL-10 production, focusing on ICOS (inducible T cell costimulator), a molecule that promotes IL-10 production in many systems. Unexpectedly, ICOS-ligand (ICOSL) blockade led to a local expansion of effector T cells in the inflamed brain without affecting IL-10 production or APC activation. Instead, we found that ICOSL blockade led to changes in T cells associated with their proliferation and survival. Specifically, we observed increased expression of IL-2 associated signaling molecules, including CD25, STAT5 phosphorylation, Ki67, and Bcl-2 in T cells in the brain. Interestingly, increases in CD25 and Bcl-2 were not observed following IL-10R blockade. Also unlike IL-10R blockade, ICOSL blockade led to an expansion of both CD8+ and CD4+ T cells in the brain, with no expansion of peripheral T cell populations or neutrophil recruitment to the brain Overall, these results suggest that IL-10 and ICOS differentially regulate T cell responses in the brain during chronicT. gondiiinfection.
Active and repressed chromatin domains exhibit distinct nucleosome segregation during DNA replication
Authors: Escobar Thelma M. , Oksuz Ozgur , Descostes Nicolas , Bonasio Roberto , Reinberg Danny
Published: September 2018

Chromatin domains and their associated structures must be faithfully inherited through cellular division to maintain cellular identity. Yet, accessing the localized strategies preserving chromatin domain inheritance, specifically the transfer of parental, pre-existing nucleosomes with their associated post-translational modifications (PTMs) during DNA replication is challenging in living cells. We devised an inducible, proximity-dependent labeling system to irreversibly mark replication-dependent H3.1 and H3.2 histone-containing nucleosomes at single desired loci in mouse embryonic stem cells such that their fate after DNA replication could be followed. Strikingly, repressed chromatin domains are preserved through the local re-deposition of parental nucleosomes. In contrast, nucleosomes decorating active chromatin domains do not exhibit such preservation. Notably, altering cell fate leads to an adjustment in the positional inheritance of parental nucleosomes that reflects the corresponding changes in chromatin structure. These findings point to important mechanisms that contribute to parental nucleosome segregation to preserve cellular identity.
A fully automated spike sorting algorithm using t-distributed neighbor embedding and density based clustering
Authors: Nadian Mohammad Hossein , Karimimehr Saeed , Doostmohammadi Jafar , Ghazizadeh Ali , Lashgari Reza
Published: September 2018

In this study, a new spike sorting method was developed based on a combination of two methods, t-Distributed Stochastic Neighbor Embedding (t-SNE) and Density-Based Spatial Clustering of Applications with Noise (DBSCAN). Parameters of both methods were simultaneously optimized using a Genetic Algorithm (GA) using a simulated dataset containing 2 to 20 simultaneously recorded neurons. The performance of this method was evaluated using both the simulated dataset as well as real multichannel electrophysiological data. The results indicated that our fully automated algorithm using t-SNE-DBSCAN outperforms other state-of-the-art algorithms and human experts in spike sorting especially when there are a large number of simultaneously recorded units. Our algorithm also determines the noise waveforms and has an overall high sensitivity, precision and accuracy for correctly classifying waveforms belonging to each neuron (all >90%) without the need for manual corrections afterwards. Our method can be a crucial part of the analysis pipeline in particular when manual sorting of units is becoming prohibitive due to the sheer number of recorded neurons per session.
Theory on the looping mediated directional-dependent propulsion of transcription factors along DNA
Authors: Murugan R.
Published: September 2018

We show that the looping mediated transcription activation by the combinatorial transcription factors (TFs) can be achieved via directional-dependent propulsion, tethered sliding and tethered binding-sliding-unbinding modes. In the propulsion mode, the first arrived TF at the cis-regulatory motifs (CRMs) further recruits other TFs via protein-protein interactions. Such TFs complex has two different types of DNA binding domains (DBDs) viz. DBD1 which forms tight site-specific complex with CRMs via hydrogen bonding network and the promoter specific DBD2s which form nonspecific interactions around CRMs. When the sum of these specific and cumulative nonspecific interactions is sufficient, then the flanking DNA of CRMs will be bent into a circle over the TFs complex. The number of TFs involved in the combinatorial regulation plays critical role here. When the site-specific interactions and the cumulative nonspecific interactions are strong enough to resist the dissociation, then the sliding of DBD2s well within the Onsager radius associated with the DBD2s-DNA interface towards the promoter is the only possible way to release the elastic stress of the bent DNA. The DBD2s form tight synaptosome complex upon finding the promoter via sliding. When the number of TFs is not enough to bend the DNA in to a circle, then tethered sliding or tethered binding-sliding-unbinding modes are the possibilities. In tethered sliding, the CRMs-TFs complex forms nonspecific contacts with DNA via dynamic loops and then slide along DNA towards promoter without dissociation. In tethered binding-sliding-unbinding, the CRMs-TFs performs several cycles of nonspecific binding-sliding-unbinding before finding the promoter. Elastic and entropic energy barriers associated with the looping of DNA shape up the distribution of distances between CRMs and promoters. The combinatorial regulation of TFs in eukaryotes has evolved to overcome the looping energy barrier.
Dengue fever is an emerging public health concern in the city of Multan, Pakistan: its seroprevalence and associated risk factors
Authors: Mukhtar Muhammad Uzair , Mukhtar Maria , Iqbal Naveed
Published: September 2018

The prevalence of dengue IgG and IgM antibodies was investigated in 689 patients with suspected dengue. Of the 689 suspected cases, 373 (54.1%) were found to be positive for dengue antibodies, IgM being dominant. There was a significant relationship between incidence of dengue fever and season: all cases were reported during the rainy season, especially the post‐monsoon season (89.5%), with none during the dry season. More male (79.3%) than female individuals were positive cases and the incidence was highest in the 21–49 year age group (63%). This is the first seroprevalence study reported from Multan, Pakistan.
Effects of urbanisation and management practices on pollinators in tropical Africa
Authors: Guenat Solène , Kunin William E. , Dougill Andrew J. , Dallimer Martin
Published: September 2018

Urban expansion is an increasing threat to biodiversity, especially in tropical Africa where biodiversity hot spots are being encroached upon by fast‐growing cities. Threatened species include bees and other pollinators, which deliver important ecosystem services but are sensitive to land use changes.

We investigated the impact of urbanisation and vegetation management practices on pollinator abundance, bee diversity, and bee functional traits. We sampled 126 locations in a stratified random design across an urbanisation gradient in two medium‐sized cities in the West African Forests biodiversity hot spot, encompassing three management practices (farmed sites; amenity lands, i.e. green spaces managed for aesthetics; informal green spaces), and tested their effect with generalised linear models.

Urbanisation did not affect bee abundances or diversity but had a negative impact on both wasp and beetle abundances. There was also a management‐mediated impact of urbanisation on bee abundances, which decreased with urbanisation on farmed sites but not amenity land or informal green spaces. Management practices alone influenced bee abundances with farms harbouring fewer bees, and amenity lands fewer beetles.

Bee genera occurrence and dominance patterns were influenced by both urbanisation and management, with some otherwise common genera rare in urban areas.

Most functional traits were influenced by management, with fewer polylectic bees, cavity‐nesting bees and long‐tongued bees in farmed sites. Amenity lands hosted smaller bees and fewer savanna specialists. Some traits were influenced by urbanisation, with more long‐tongued bees and cavity‐nesting bees found in urban areas.

Synthesis and applications. Pollinator responses to urbanisation are complex. In our research, we demonstrate how bee, lepidopteran, and non‐fruit fly abundances have been maintained across an urbanisation gradient in tropical Africa, but not wasp and beetle abundances. Moreover, bee community composition and the distribution of traits shifted markedly. How green spaces were managed was also critical. We found that farmed sites hosted the lowest bee abundances and amenity lands the fewest beetles. Retaining informal green spaces and amenity lands in African cities, including protecting nesting sites for stingless bees, and limiting pesticide application would be important for conserving bees and the pollination service they provide to both crops and native vegetation.
Testing rangeland health theory in the Northern Great Plains
Authors: Reinhart Kurt O. , Rinella Matthew J. , Waterman Richard C. , Petersen Mark K. , Vermeire Lance T.
Published: September 2018

Correctly assessing whether rangeland ecosystem services are stable, improving, or degrading is of global importance. Soil aggregate stability (SAS) is widely used to infer rangeland health, partly because high SAS is thought to reduce run‐off by increasing infiltration. We studied the sensitivity of SAS to grazing and other disturbances, the effects of SAS on infiltration, and the utility of alternative indicators of infiltration in the Northern Great Plains.

To test grazing effects on SAS, we compared SAS between paired areas that were lightly to moderately grazed or excluded from grazing for 6 years. Additionally, we compared SAS between grazed and not‐grazed plots of a 2‐year controlled grazing experiment with moderate and severe grazing. We also applied herbicide, mowing, and fungicide treatments to test SAS responses to disturbances more generally, as well as effects of SAS and other factors on infiltration. To more generally test for a SAS–infiltration relationship, we performed a meta‐analysis of our data combined with other data from the region.

Grazing often reduced stability of small macroaggregates (0.25–1 mm) in the controlled grazing experiment but not the paired grazing area experiment. Grazing had no detectible effect on SAS of larger macroaggregates (1–2 mm). Herbicide tended to reduce SAS, and mowing sometimes increased SAS. Infiltration exhibited high plot‐to‐plot variation and was not significantly affected by treatments. Variation in infiltration was best explained by plant community composition variables and was not explained by either SAS or other soil properties. Our meta‐analysis revealed no general SAS–infiltration relationship.

Synthesis and applications. Our findings counter prevailing expectations that soil aggregate stability (SAS) is consistently sensitive to rangeland disturbance(s) and a leading indicator of soil water transport. Plant community composition properties were better predictors of infiltration. Our findings support the theory that excessive grazing increases the prevalence of a grazing tolerant species, which was associated with low levels of infiltration irrespective of SAS.
Individual‐based models of community assembly: Neighbourhood competition drives phylogenetic community structure
Authors: Tatsumi Shinichi , Cadotte Marc W. , Mori Akira S.
Published: September 2018

It is now commonplace for community ecologists to infer assembly processes from the evolutionary relatedness of co‐occurring species. Such inferences, however, have typically depended on assembly theories that assume competitive equilibrium and that are species based. In reality, all natural communities are dynamic, particularly during the course of succession, and the ecological interactions which drive phylogenetic community structure actually occur among neighbouring individuals rather than species.

To bridge this gap between theory and reality, we examine how colonisation, competition, and consequent replacement of individuals translate into phylogenetic community structure by using an individual‐based model. The model we use assumes a trade‐off between competition and colonisation abilities and that the points where species fall on the trade‐off curve are phylogenetically conserved.

We find that the phylogenetic alpha diversity of a given community will be equal to or greater than the null expectation generated by randomly drawing individuals from communities at the same time step (i.e. phylogenetic overdispersion). This pattern results from the combination of interspecific differences in colonisation ability and neighbourhood competition that lead to individuals being regularly distributed in two‐dimensional space.

We also show that phylogenetic beta diversity increases with increasing temporal differences between two communities. However, when this positive relationship is analysed only among the communities at close time steps, it becomes insignificant as they approach competitive equilibrium. We find similar patterns for functional alpha and beta diversity when phylogeny is replaced with functional traits.

Synthesis. Though questions concerning community assembly have often been spatially framed, our model shows that the span of the time frame can also affect, or even reverse, inferences about assembly processes. Our model also implies that a shift in the frame of reference from species to individuals brings a new perspective to community assembly. Careful consideration of non‐equilibrium and individual‐level aspects provides better insights into the consequences of the evolutionary and functional similarities of individuals on community assembly.
Tree crown overlap improves predictions of the functional neighbourhood effects on tree survival and growth
Authors: Zambrano Jenny , Fagan William F. , Worthy Samantha J. , Thompson Jill , Uriarte Maria , Zimmerman Jess K. , Umaña Maria N. , Swenson Nathan G.
Published: September 2018

Investigations of forest community structure and dynamics have been facilitated by the use of neighbourhood models that examine the interactions between a focal tree and its neighbours using a fixed radius. However, different studies have chosen different radii without clear reasons, hampering the understanding of mechanisms structuring tree communities.

Using functional trait and tree demography data from the Luquillo subtropical forest in Puerto Rico, we compared fixed‐neighbourhood models with a canopy overlap model, in which tree crown overlap is used as an indicator of neighbourhood crowding. Analyses that combine functional trait and demographic data provide a mechanistic understanding of observed patterns of community structure and dynamics as they provide insights into the linkages between phenotypes and the environment.

Overall, canopy overlap models had better support when compared to neighbourhood models using a fixed radius, suggesting that the fixed radius approach does not capture the full extent of competitive interactions among trees. Moreover, the effects of functional neighbourhood on tree survival and growth differ depending on the type of approach used and lead to different conclusions with respect to the drivers of tree community dynamics.

Synthesis. In summary, our findings highlight the utility of neighbourhood models based on tree crown overlap, and suggest that applying this same approach to different plots and forests will facilitate comparisons across systems and improve our understanding of the mechanisms that drive the structure and dynamics of tree communities.
Processes and challenges in clinical decision‐making for children with speech‐sound disorders
Authors: Furlong Lisa , Serry Tanya , Erickson Shane , Morris Meg E.
Published: September 2018

Background

Children with speech‐sound disorders (SSD) constitute a significant proportion of speech–language pathologists’ (SLPs) caseloads. Previous research has investigated the clinical practice of SLPs intervening with children with SSD; however, little is known about the clinical decision‐making underpinning their practice.

Aims

The clinical decision‐making of SLPs working with children with SSD was explored to understand how their clinical decisions were influenced by: (1) beliefs about what works in therapy; (2) prior clinical experience; and (3) client and service‐related variables.

Methods & Procedures

Semi‐structured, individual, in‐depth interviews were conducted with 11 SLPs. Inductive thematic analysis was used to identify and explore key ideas and themes.

Outcomes & Results

Four themes emerged: (1) clinical decision‐making procedures were highly individualized; (2) parental involvement was viewed as central to the success and progression of therapy; (3) therapy procedures were influenced by practice‐setting constraints; and (4) engaging in evidence‐based practice within clinical settings was perceived as challenging.

Conclusions & Implications

In clinical settings, a range of factors influence decision‐making and therapy provided by SLPs to children with SSD. These SLPs had a high regard for clients’ values and preferences. Prior clinical experiences also shaped clinical practice. Clinical decision‐making was influenced by practice‐setting constraints. SLPs are under pressure in their workplaces and are struggling to manage the competing demands on their time. Large clinical caseloads, heavy workloads, current service‐delivery models and changing family structures are all impacting on the provision of therapy to children with SSD and therapy outcomes. As a profession, there is a need to consider these barriers and identify ways to overcome them in order to assist SLPs to routinely adopt the highest standards of clinical practice for children with SSD.