bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaporation and CO
2
fluxes in a coastal reef: an eddy covariance approach
Authors: Rey-Sánchez A. Camilo , Bohrer Gil , Morin Timothy H. , Shlomo Dekel , Mirfenderesgi Golnazalsadat , Gildor Hezi , Genin Amatzia 
Published: November 2017

ABSTRACT

Introduction:
We conducted season-long observations of evaporation and carbon flux at the Gulf of Aqaba coast, northern Red Sea. We used the eddy-covariance method with a two-tower setup to measure evaporation rates over land and sea and the advection between them. Using a three-dimensional mass balance approach, we calculated total evaporation as the sum of two main components in our site: horizontal advection and turbulent vertical flux, with half-hourly change of water vapor storage and horizontal flux divergence found to be negligible.

Outcomes:
Average evaporation rates were 11.4 [mm/day] from April through May (early summer) and 10.5 [mm/day] from June through August (summer). The coastal reef was a CO
2
sink over the period of measurements, significantly higher in June through August than in April through May. The main environmental drivers of CO
2
flux were humidity, water temperature, sensible heat flux, and wind speed.

Discussion:
The rates of evaporation near the shore were considerably higher than values reported in other studies typically used to represent the mean for the whole Gulf area. We found that evaporation rates computed by common bulk models approximate the mean values of evaporation but have poor representativeness of the intra-daily temporal variation of evaporation. There was a significant correlation between CO
2
flux and evaporation attributed to common environmental drivers of gas diffusion, turbulent fluxes, and horizontal transport.

Conclusion:
We conclude that observations of fluxes in coastal waters need to use at least a two-tower system to account for the effect of horizontal advection on the total flux.
MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action
Authors: Nelson Justin , Simpkins Scott W , Safizadeh Hamid , Li Sheena C , Piotrowski Jeff S , Hirano Hiroyuki , Yashiroda Yoko , Osada Hiroyuki , Yoshida Minoru , Boone Charles , Myers Chad L 
Published: November 2017

Abstract

Summary
Chemical-genomic approaches that map interactions between small molecules and genetic perturbations offer a promising strategy for functional annotation of uncharacterized bioactive compounds. We recently developed a new high-throughput platform for mapping chemical-genetic (CG) interactions in yeast that can be scaled to screen large compound collections, and we applied this system to generate CG interaction profiles for more than 13 000 compounds. When integrated with the existing global yeast genetic interaction network, CG interaction profiles can enable mode-of-action prediction for previously uncharacterized compounds as well as discover unexpected secondary effects for known drugs. To facilitate future analysis of these valuable data, we developed a public database and web interface named MOSAIC. The website provides a convenient interface for querying compounds, bioprocesses (Gene Ontology terms) and genes for CG information including direct CG interactions, bioprocesses and gene-level target predictions. MOSAIC also provides access to chemical structure information of screened molecules, chemical-genomic profiles and the ability to search for compounds sharing structural and functional similarity. This resource will be of interest to chemical biologists for discovering new small molecule probes with specific modes-of-action as well as computational biologists interested in analysing CG interaction networks.

Availability and implementation
MOSAIC is available at http://mosaic.cs.umn.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Chondrosarcoma of the cervical spine
Authors: Gietzen Lindsay , Pokorski Philip 
Published: November 2017

ABSTRACT
This case report describes the diagnosis, surgical treatment, and management of a patient with low-grade chondrosarcoma of the cervical spine that initially presented as myositis ossificans. Chondrosarcoma is rare in the cervical spine and in this patient, may have been the result of an injury from a motor vehicle crash. The management of this patient has been unusual in that a complete excision was not performed because the patient refused standard treatment.
Temperature management for out-of-hospital cardiac arrest
Authors: Coppler Patrick J. , Dezfulian Cameron , Elmer Jonathan , Rittenberger Jon C. 
Published: November 2017

ABSTRACT
More than 300,000 Americans suffer a cardiac arrest outside of the hospital each year and even among those who are successfully resuscitated and survive to hospital admission, outcomes remain poor. Temperature management (previously known as therapeutic hypothermia) is the only intervention that has been reproducibly demonstrated to ameliorate the neurologic injury that follows cardiac arrest. The results of a recent large randomized controlled trial have highlighted the uncertainty about temperature management strategies following cardiac arrest. This article reviews the issues and recommendations.
Musculoskeletal development in patients with Down syndrome
Authors: Dupre Corey , Weidman-Evans Emily 
Published: November 2017

ABSTRACT
Down syndrome is a chromosomal aneuploidy that results in disruptions in multiple body systems, including musculoskeletal function. Early intervention to focus on bone mineral density, gait correction, agility, balance, and muscle strength is imperative in order for patients to achieve maximum potential.
Cochlear Implant Insertion Axis Into the Basal Turn: A Critical Factor in Electrode Array Translocation
Authors: Torres Renato , Drouillard Mylène , De Seta Daniele , Bensimon Jean-Loup , Ferrary Evelyne , Sterkers Olivier , Bernardeschi Daniele , Nguyen Yann 
Published: November 2017

Hypothesis:
An inappropriate insertion axis leads to intracochlear trauma during cochlear implantation (CI).

Background:
Few studies assessed the relationship between the insertion axis and the electrode scalar location.

Methods:
Preimplantation cone-beam CT (CBCT) was performed on 12 human temporal bones. In five temporal bones, an optimal insertion axis was planned, due to the impossibility to attain the ST centerline from the posterior tympanotomy, because of facial canal position. In the seven other temporal bones, an inaccurate insertion axis was intentionally planned (optimal axis+15 degrees). Automated CI array insertion according to the planned axis was performed with a motorized insertion tool driven by a navigated robot-based arm. The cochlea and basilar membrane were segmented from the preimplantation CBCT and the array segmented from the postimplantation CBCT to construct a merged final three-dimensional (3D) model. Microscopical and 3D analysis were performed to determine the intracochlear trauma at the level of each electrode.

Results:
A good agreement was observed in determining electrode position between microscopic analysis and the 3D model (Cohen's kappa k = 0.67). The angle of approach to the ST centerline was associated with the number of electrodes inserted into the ST (r = −0.65, p = 0.02, [95% CI −0.90 to −0.11] Spearman's rank correlation).

Conclusion:
A 3D reconstruction model was effective in determining the array position in the cochlea scalae. Our data indicate that the angle of approach to the ST centerline is a critical factor in intracochlear trauma. Additional studies should be conducted to assess the importance of the insertion axis with other array designs.
Anterior Skull Base Tumors: The Role of Transfacial Approaches in the Endoscopic Era
Authors: Dini Leandro Infantini , Isolan Gustavo Rassier , Flores Evelise , Lombardo Eduardo Madruga , Heitz Cláiton 
Published: November 2017

Abstract
The basis of craniofacial tumor surgery is complete surgical extirpation, preferably en bloc or with free borders. Craniofacial techniques are the gold standard and primary strategies in the treatment of anterior skull base tumors. In the last decade, the reports favoring results of endoscopic techniques have increased. One could conclude that the classical transfacial approaches might become useless, but, in fact, there is little research comparing these techniques.
In this article, the authors present their experience with combined craniofacial resection of anterior craniofacial skull base tumors in 9 consecutive patients between January 2013 and July 2015. This article aims to review some of the traditional transfacial approaches, illustrating them with this series of surgical patients. Benefits and drawbacks of these approaches are discussed.
Recurrence of de novo mutations in families
Authors: Jónsson Hákon , Sulem Patrick , Arnadottir Gudny A. , Pálsson Gunnar , Eggertsson Hannes P. , Kristmundsdottir Snaedis , Zink Florian , Kehr Birte , Hjorleifsson Kristjan E. , Jensson Brynjar Ö , Jonsdottir Ingileif , Marelsson Sigurdur Einar , Gudjonsson Sigurjon Axel , Gylfason Arnaldur , Jonasdottir Adalbjorg , Jonasdottir Aslaug , Stacey Simon N. , Magnusson Olafur Th. , Thorsteinsdottir Unnur , Masson Gisli , Kong Augustine , Halldorsson Bjarni V. , Helgason Agnar , Gudbjartsson Daniel F. , Stefansson Kari 
Published: November 2017

ABSTRACTDe novo mutations (DNMs) cause a large fraction of severe rare diseases of childhood. DNMs that occur in early embryos may result in mosaicism of both somatic and germ cells. Such early mutations may be transmitted to more than one offspring and cause recurrence of serious disease. We scanned 1,007 sibling pairs from 251 families and identified 885 DNMs shared by siblings (ssDNMs) at 451 genomic sites. We estimated the probability of DNM recurrence based on presence in the blood of the parent, sharing by other siblings, parent-of-origin, mutation type, and genomic position. We detected 52.1% of ssDNMs in the parental blood. The probability of a DNM being shared goes down by 2.28% per year for paternal DNMs and 1.82% for maternal DNMs. Shared paternal DNMs are more likely to be T>C mutations than maternal ones, but less likely to be C>T mutations. Depending on DNM properties, the probability of recurrence in a younger sibling ranges from 0.013% to 29.6%. We have launched an online DNM recurrence probability calculator, to use in genetic counselling in cases of rare genetic diseases.
Targeting regulatory T cells with Interleukin-2 treatment in type 1 diabetes: a response-adaptive, non-randomised, open-label trial of repeat doses of Aldesleukin (DILfrequency)
Authors: Seelig Eleonora , Howlett James , Porter Linsey , Truman Lucy , Heywood James , Kennet Jane , Arbon Emma L , Anselmiova Katerina , Walker Neil M. , Atkar Ravinder , Pekaiski Marcin L , Rytina Ed , Evans Mark , Wicker Linda S. , Todd John A. , Mander Adrian P. , Bond Simon , Waldron-Lynch Frank 
Published: November 2017

SummaryBackgroundType 1 diabetes (T1D) results from loss of immune regulation leading to the development of autoimmunity to pancreatic beta-cells, involving autoreactive T effector cells (Teffs). Regulatory T cells (Tregs), that prevent autoimmunity, require Interleukin-2 (IL-2) for maintenance of immunosuppressive functions and, alterations in the IL-2 pathway predispose to T1D. Using an adaptive trial design we aimed to determine the optimal regimen of aldesleukin (recombinant human IL-2) to physiologically enhance Tregs while limiting expansion of autoreactive Teffs.MethodsDILfrequency is a single-center, non-randomised, open-label, response-adaptive study of participants aged 18 to 70 years with T1D. The initial learning phase allocated 12 participants to six different predefined dose-frequency regimens. Then, three cohorts of 8 participants were sequentially allocated dose-frequencies, based on repeated interim analyses of all accumulated trial data. The co-primary endpoints were percentage change in Tregs, Teffs and, CD25 (α subunit of the IL-2 receptor) expression by Tregs, from baseline to steady state. Trial registration ISRCTN40319192 and ClinicalTrials.gov (NCT02265809).Findings115 participants were assessed between November 17th 2014 and May 22nd 2016, 38 participants were enrolled with 36 completing treatment. The optimal regimen to maintain a steady state increase in Tregs of 30% and CD25 expression of 25% without Teff expansion is 0.26 × 106 IU/m2 (95% CI (−0.007 to 0.485)) every 3 days (1.3 to 4.4). Tregs and CD25 were dose-frequency responsive, while Teffs were not. The commonest adverse event was injection site reaction (464/694 events), with a single participant developing transient eosinophilia at the highest dose (0.47 × 106 IU/m2).InterpretationThis response-adaptive trial defined a well-tolerated aldesleukin regimen that specifically induces Treg expansion that can now be trialled to treat T1D.FundingSir Jules Thorn Trust, Wellcome, JDRF, SNSF, NIHR
Causal inference in cancer epidemiology: what is the role of Mendelian randomization?
Authors: Yarmolinsky James , Wade Kaitlin H , Richmond Rebecca C , Langdon Ryan J , Bull Caroline J , Tilling Kate M , Relton Caroline L , Smith George Davey , Martin Richard M 
Published: November 2017

AbstractObservational epidemiological studies are prone to confounding, measurement error, and reverse causation, undermining their ability to generate reliable causal estimates of the effect of risk factors to inform cancer prevention and treatment strategies. Mendelian randomization (MR) is an analytical approach that uses genetic variants to proxy potentially modifiable exposures (e.g. environmental factors, biological traits, and druggable pathways) to permit robust causal inference of the effects of these exposures on diseases and their outcomes. MR has seen widespread adoption within population health research in cardio-metabolic disease, but also holds much promise for identifying possible interventions (e.g., dietary, behavioural, or pharmacological) for cancer prevention and treatment. However, some methodological and conceptual challenges in the implementation of MR are particularly pertinent when applying this method to cancer aetiology and prognosis, including reverse causation arising from disease latency and selection bias in studies of cancer progression. These issues must be carefully considered to ensure appropriate design, analysis, and interpretation of such studies.In this review, we provide an overview of the key principles and assumptions of MR focusing on applications of this method to the study of cancer aetiology and prognosis. We summarize recent studies in the cancer literature that have adopted a MR framework to highlight strengths of this approach compared to conventional epidemiological studies. Lastly, limitations of MR and recent methodological developments to address them are discussed, along with the translational opportunities they present to inform public health and clinical interventions in cancer.
Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex
Authors: Florio Marta , Heide Michael , Brandl Holger , Pinson Anneline , Winkler Sylke , Wimberger Pauline , Huttner Wieland B. , Hiller Michael 
Published: November 2017

AbstractTo understand the molecular basis underlying the expansion of the neocortex during primate, and notably human, evolution, it is essential to identify the genes that are particularly active in the neural stem and progenitor cells of developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. In addition to the previously studied gene ARHGAP11B, we show that ten known and two newly identified human-specific genes exhibit such expression, however with distinct neural progenitor cell-type specificity compared to their ancestral paralogs. Furthermore, we identify 41 additional human genes with progenitor-enriched expression which have orthologs only in primates. Our study not only provides a resource of genes that are candidates to exert specific, and novel, roles in neocortical development, but also reveals that distinct mechanisms gave rise to these genes during primate, and notably human, evolution.
Tracking and optimizing human performance using deep reinforcement learning in closed-loop behavioral- and neuro- feedback: a proof of concept
Authors: Dinov Martin , Leech Robert 
Published: November 2017

AbstractReinforcement learning (RL) is a general-purpose powerful machine learning framework within which we can model various deterministic, non-deterministic and complex environments. We applied RL to the problem of tracking and improving human sustained attention during a simple sustained attention to response task (SART) in a proof of concept study with two subjects, using state-of-the-art deep neural network-based RL in the form of Deep Q Networks (DQNs). While others have used RL in EEG settings previously, none have applied it in a neurofeedback (NFB) setting, which seems a natural problem within Brain Computer Interfaces (BCIs) to tackle using end-to-end RL in the form of DQNs, due to both the problem’s non-stationarity and the ability of RL to learn in a continuous setting. Furthermore, while many have explored phasic alerting previously, learning optimal alerting in a personalized way in real time is a less explored field, which we believe RL to be an most suitable solution for. First, we used empirically-derived simulated data of EEG and reaction times and subsequent parameter/algorithmic exploration within this simulated model to pick parameters for the DQN that are more likely to be optimal for the experimental setup and to explore the behavior of DQNs in this task setting. We then applied the method on two subjects and show that we get different but plausible results for both subjects, suggesting something about the behavior of DQNs in this setting. For this experimental part, we used parameters suggested to us by the simulation results. This RL-based behavioral- and neuro-feedback BCI method we have developed here is input feature agnostic and allows for complex continuous actions to be learned in other more complex closed-loop behavioral or neuro-feedback approaches.
PWO1 interacts with PcG proteins and histones to regulate Arabidopsis flowering and development
Authors: Hohenstatt Mareike L. , Mikulski Pawel , Komarynets Olga , Klose Constanze , Kycia Ina , Jeltsch Albert , Farrona Sara , Schubert Daniel 
Published: November 2017

AbstractPolycomb-group (PcG) proteins mediate epigenetic gene regulation by setting H3K27me3 via Polycomb Repressive Complex 2 (PRC2). In plants, it is largely unclear how PcG proteins are recruited to their target genes.Here, we identified the PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) protein which interacts with all threeArabidopsisPRC2 histone methyltransferases and is required for keeping full H3 occupancy at several Arabidopsis genes. PWO1 localizes and recruits CLF to nuclear speckles in tobacco nuclei, suggesting a role in spatial organization of PcG regulation.PWO1belongs to a gene family with three members acting redundantly:pwo1 pwo2 pwo3triple mutants are seedling lethal and show shoot and root meristem arrest, whilepwo1single mutants are early flowering. Interestingly, PWO1’s PWWP domain confers binding to histones, which is reduced by a point mutation in a highly conserved residue of this domain and blocked by phosphorylation of H3S28. PWO1 carrying this mutation is not able to fully complement thepwo1 pwo2 pwo3triple mutant, indicating the requirement of this domain for PWO1in vivoactivity. Thus, the PWO family may present a novel class of histone readers which are involved in recruiting PcG proteins to subnuclear domains and in promoting Arabidopsis development.
RodZ promotes MreB polymer formation and curvature localization to determine the cylindrical uniformity of E. coli shape
Authors: Morgenstein Randy M. , Bratton Benjamin P. , Shaevitz Joshua W. , Gitai Zemer 
Published: November 2017

AbstractCell shape in bacteria is determined by the cell wall, which is synthesized by a variety of proteins whose actions are coordinated by the actin-like MreB protein. MreB uses local geometric cues of envelope curvature to avoid the cell poles and localize to specific regions of the cell body. However, it remains unclear whether MreB’s curvature preference is regulated by additional factors, and which features of MreB are essential for specific aspects of rod shape growth, such as cylindrical uniformity. Here we show that in addition to its previously-described role in mediating MreB motion, RodZ also modulates MreB polymer number and curvature preference. MreB polymer number and curvature localization can be regulated independently. Quantitative 3D measurements and a series of mutant strains show that among various properties of MreB, polymer number, total length of MreB polymers, and MreB curvature preference are the key determinants of cylindrical uniformity, a measure of the variability in radius within a single cell. Changes in the values of these parameters are highly predictive of the resulting changes in cell shape (r2=0.93). Our data suggest a model for rod shape in which RodZ promotes the assembly of multiple long MreB polymers that ensure the growth of a uniform cylinder.
Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes
Authors: Tangirala Sivateja , Patel Chirag J 
Published: November 2017

AbstractWhile both genes and environment contribute to phenotype, deciphering environmental contributions to phenotype is a challenge. Furthermore, elucidating how different phenotypes may share similar environmental etiologies also is challenging. One way to identify environmental influences is through a discordant monozygotic (MZ) twin study design. Here, we assessed differential gene expression in MZ discordant twin pairs (affected vs. non-affected) for seven phenotypes, including chronic fatigue syndrome, obesity, ulcerative colitis, major depressive disorder, intermittent allergic rhinitis, physical activity, and intelligence quotient, comparing the spectrum of genes differentially expressed across seven phenotypes individually. Second, we performed meta-analysis for each gene to identify commonalities and differences in gene expression signatures between the seven phenotypes. In our integrative analyses, we found that there may be a common gene expression signature (with small effect sizes) across the phenotypes; however, differences between phenotypes with respect to differentially expressed genes were more prominently featured. Therefore, defining common environmentally induced pathways in phenotypes remains elusive. We make our work accessible by providing a new database (DiscTwinExprDB:http://apps.chiragjpgroup.org/disctwinexprdb/) for investigators to study non-genotypic influence on gene expression.