bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bilateral Congenital Cholesteatoma
Authors: Lee Chang Ho , Kim Mi Kyung , Kim Hyoung-Mi , Won Cheongse , Shin Tae Hyun , Kim So Young 
Published: April 2018

Objective:
To report the first large case series of extremely rare bilateral congenital cholesteatoma (CC).

Study Design:
A retrospective cohort study.

Setting:
University hospital otology referral clinic.

Patients:
Six hundred four children with surgically confirmed CC.

Main Outcome Measures:
The bilateral CCs were compared with the unilateral CCs.

Results:
The incidence of bilateral CC was 3.6% (22/615) per case or 1.8% (11/604) per child. Bilateral CC did not differ from unilateral CC regarding its demographics, and invasiveness by the proportion of advanced CC as 31.8% (7/22) versus 28.2% (167/594). But the invasiveness or location randomly differed between the ears, that advanced CC per child was higher as 45.4% (5/11). Bilateral exploration was attempted with a concern for hearing loss, which featured a combination of laser myringotomy to treat early CC and endaural laser-assisted single-stage inside-out cholesteatoma surgery to treat advanced CC. Bilateral exploration was difficult in three children with initially negative otoendoscopy. Among the seven advanced CC, proportion of anterior type was 71.4% (5/7), who all exhibited more than 20 dB HL, but two posterior type retained normal hearing. Therefore, bilateral advanced CCs of anterior origin showed poorest hearing outcome as bilateral more than 20 dB HL, which were in two children. Six second-look operations and one third-look operation were required to treat six residual CCs (30%) in four children (40%), including bilateral residual CC in two (20%); such reoperations were significantly more frequent than in unilateral CC.

Conclusion:
The diagnosis of bilateral CC required high index of suspicion from TBCT, and early bilateral exploration.
Perfluorocarbon Emulsions, Platelet Counts, and Inflammation
Authors: Spiess Bruce D. 
Published: April 2018

ABSTRACT
Perfluorocarbon emulsions (PFC) are a class of lipid-coated micelle slurries wherein the active center of the micelle is a completely halogen/fluorine-substituted hydrocarbon capable of dissolving very large quantities of nonpolar gases. Due to their unique enhanced solubility for oxygen (O2) and nitrogen (N2), PFCs have been used in research as enhanced gas transport media for situations wherein the microcirculation is dysfunctional. In the early 1990s a PFC emulsion was approved for human use during coronary artery angioplasty and one is presently in use in Russia as well as other countries. The pharmaceutical class has had reported in the past associated with variable amounts of time-limited thrombocytopenia. Anxiety about cerebral embolism surfaced after a pivotal phase III trial leading to the cessation of all human research in the United States. At that time papers both published and submitted to the FDA opined (without proof) that the platelet count decrease might be caused by platelet white cell conjugates and/or platelet aggregates, thereby signaling a general inflammatory response to PFCs and a potential thrombosis risk. Although thrombocytopenia has been reported in response to PFC emulsion formulations, it is not ubiquitous and seems to be less associated with some formulations. As well, in some recent animal studies there is no evidence of platelet white cell adverse interactions. The mechanism for the reported thrombocytopenia is as yet not fully understood, and risk–benefit profiles will have to be carefully studied as contemporary human trials move forward.
Topographic somatosensory imagery for real-time fMRI Brain-Computer Interfacing
Authors: Kaas Amanda , Goebel Rainer , Valente Giancarlo , Sorger Bettina 
Published: April 2018

AbstractReal-time functional magnetic resonance imaging (fMRI) is a promising non-invasive method for brain computer interfaces (BCIs). BCIs translate brain activity into signals that allow communication with the outside world. Visual and motor imagery are often used as information-encoding strategies, but can be challenging if not grounded in recent experience in these modalities, e.g. in patients with locked-in-syndrome (LIS). In contrast, somatosensory imagery might constitute a more suitable information-encoding strategy as somatosensory function is often very robust. Somatosensory imagery has been shown to activate somatotopic cortex, but it has been unclear so far whether it can be reliably detected on a single-trial level and successfully classified according to specific somatosensory imagery content.Using ultra-high field 7-T fMRI, we show reliable and high-accuracy single-trial decoding of left-foot vs. right-hand somatosensory imagery. Correspondingly, higher decoding accuracies were associated with greater spatial separation of hand and foot decoding-weight patterns in primary somatosensory cortex (S1). Exploiting these novel neuroscientific insights, we developed – and provide a proof of concept for – basic BCI communication by showing that binary (yes/no) answers encoded by somatosensory imagery can be decoded with high accuracy not only offline but also in real-time.This study demonstrates that body part-specific somatosensory imagery differentially activates somatosensory cortex in a topographically specific manner; evidence which was surprisingly still lacking in the literature. It is also offers a promising novel somatosensory imagery based fMRI-BCI control strategy, with particularly high potential for visually and motor-impaired patients. The strategy could also be transferred to lower MRI field strengths and to mobile functional near-infrared spectroscopy. Finally, given that communication BCIs provide the BCI user with a form of feedback based on their brain signals and can thus be considered as a specific form of neurofeedback, and that repeated use of a BCI has been shown to enhance underlying representations, we expect that the current BCI could also offer an interesting new approach for somatosensory rehabilitation training in the context of stroke and phantom limb pain.
Two biological constants for accurate classification and evolution pattern analysis of Subgen.strobus and subgen. Pinus
Authors: zou Huabin 
Published: April 2018

AbstractCurrently, biological classification and determination of different categories are all based on empirical knowledge,which is obtained relying on morphological and molecular characters. For these methods they lacks of absolutely quantitative criteria ground on intrinsically scientific principles. In fact, accurate science classification must depend on the correct description of biology evolution rules.In this article a new theoretical approach was proposed, in which two characteristic constants were gained from biological common heredity and variation information theory equation, when it is at the maximum information states, corresponding to symmetric and asymmetric variation states. They are common composition ratios, Pg =0.61, and Pg=0.70. By analyzing the common composition ratios of compounds among oleoresins, two pine subgenus:Subgen.Strobus (Sweet) Held and Subgen. Pinus could be integrated into one class, Genus pinus, excellently, when Pg = 0.61.These two pine subgenus could be classified into two groups clearly,when Pg = 0.70.The results is somewhat different from that achieved by means of classical classification relying on morphological characters. On the other hand, the evolution relationship of two subgenus was analyzed based on characteristic sequences of samples, it indicated that white pine origin from pinus tabuliformis. The two constants should be used as the classification constants of some biological categories of plants.
Careful deployment of oilseed rape crops with Rlm6 resistance gene against L. maculans is recommended to prevent the loss of efficacy of this resistance gene in French condiment mustard
Authors: Bousset L. , Ermel M. , Delourme R. 
Published: April 2018

AbstractBreeding varieties for increased disease resistance is a major means to control epidemics. However, the deployment of resistance genes through space and time drives the genetic composition of the pathogen population, with predictable changes in pathotype frequencies. In France, Leptosphaeria maculans causes disease on Brassica napus oilseed rape crops but not on B. juncea condiment mustard. Prior to the deployment of winter B. napus varieties with Rlm6 resistance gene introduced from B. juncea, the aim of our study was to investigate if this deployment could impact disease control in condiment mustard. We assessed the presence of resistance genes against phoma stem canker in a set of current French B. juncea varieties and breeding lines. Rlm6 was detected in all the 12 condiment mustard varieties. Rlm5 was also detected in 8 varieties. No additional resistance genes were detected with the set of isolates used. Because frequency of isolates virulent on Rlm6 is very low, these results indicate that Rlm6 gene is a major component of disease control in the French B. juncea mustards tested. Using Rlm6 in oilseed rape varieties will very likely induce an increase in frequency of Rlm6 virulent isolates. This raises the acute concern of a wise deployment of oilseed rape around the condiment mustard growing area. Scientific knowledge on adaptation dynamics, spatial segregation of crops and cooperation between actors is currently available in order to mitigate the risk and advert negative consequences of the introduction of Rlm6 resistance gene in oilseed rape varieties.
Model testing for distinctive functional connectivity gradients with resting-state fMRI data
Authors: O’Rawe Jonathan F. , Ide Jaime S. , Leung Hoi-Chung 
Published: April 2018

AbstractIn accordance with the concept of topographic organization of neuroanatomical structures, there is an increased interest in estimating and delineating continuous changes in the functional connectivity patterns across neighboring voxels within a region of interest using resting-state fMRI data. Fundamental to this functional connectivity gradient analysis is the assumption that the functional organization is stable and uniform across the region of interest. To evaluate this assumption, we developed a model testing procedure to arbitrate between overlapping, shifted, or different topographic connectivity gradients across subdivisions of a structure. We tested the procedure using the striatum, a subcortical structure consisting of the caudate nucleus and putamen, in which an extensive literature, primarily from rodents and non-human primates, suggest to have a shared topographic organization of a single diagonal gradient. We found, across multiple resting state fMRI data samples of different spatial resolutions in humans, and one macaque resting state fMRI data sample, that the models with different functional connectivity gradients across the caudate and putamen was the preferred model. The model selection procedure was validated in control conditions of checkerboard subdivisions, demonstrating the expected overlapping gradient. More specifically, while we replicated the diagonal organization of the functional connectivity gradients in both the caudate and putamen, our analysis also revealed a medial-lateral organization within the caudate. Not surprisingly, performing the same analysis assuming a unitary gradient obfuscates the medial-lateral organization of the caudate, producing only a diagonal gradient. These findings demonstrate the importance of testing basic assumptions and evaluating interpretations across species. The significance of differential topographic gradients across the putamen and caudate and the medial-lateral gradient of the caudate in humans should be tested in future studies.
Balancing selection drives maintenance of genetic variation inDrosophilaantimicrobial peptides
Authors: Chapman Joanne R. , Hill Tom , Unckless Robert L. 
Published: April 2018

AbstractGenes involved in immune defense against pathogens provide some of the most well-known examples of both directional and balancing selection. Antimicrobial peptides (AMPs) are innate immune effector genes, playing a key role in pathogen clearance in many species, includingDrosophila. Conflicting lines of evidence have suggested AMPs may be under directional, balancing or purifying selection. Here, we use a case-control gene approach to show that balancing selection is an important force shaping AMP diversity in two species ofDrosophila. InD. melanogaster, this is most clearly observed in ancestral African populations. Furthermore, the signature of balancing selection is even clearer once background selection has been accounted for. Balancing selection also acts on AMPs inD. mauritiana, an isolated island endemic separated fromD. melanogasterby about 4 million years of evolution. This suggests that balancing selection may be acting to maintain adaptive diversity in AMPs in insects as it does in other taxa.
word2brain
Authors: Nunes Abraham 
Published: April 2018

AbstractMapping brain functions to their underlying neural substrates is a central goal of cognitive neuroscience. Functional magnetic resonance imaging (fMRI) has proven indispensable in this endeavour. Recently, there has been growing interest in tackling this problem by mapping semantic concepts onto brain regions using repositories of images and text from the neuroimaging literature. However, no study has thus far approached this problem using (dense) vector representations of words. Using data from the Neurosynth database, we sought to develop a model that could (A) capture local correlations between words in text, as well as topics, (B) capture representation of distributed brain networks in relation to word embeddings, and (C) generate synthetic images given word inputs. We show that jointly embedding words and brain imaging data on a vector space can yield semantic representations that sensibly relate concepts across biological, psychological, and observational levels of analysis. Moreover, our proposed model makes no assumption about spatial orientation of fMRI voxels, which allows for embedding of distributed brain networks onto the semantic space. We demonstrate this capability by generating synthetic brain activation vectors from word inputs. Our model has the potential to advance neuroimaging meta-analysis as well as contextual word-embedding methods more broadly.
Robust Perfect Adaptation in Biomolecular Reaction Networks
Authors: Xiao Fangzhou , Doyle John C. 
Published: April 2018

AbstractFor control in biomolecular systems, the most basic objective of maintaining a small error in a target variable, say the expression level of some protein, is often difficult due to the presence of both large uncertainty of every type and intrinsic limitations on the controller’s implementation. This paper explores the limits of biochemically plausible controller design for the problem of robust perfect adaptation (RPA), biologists’ term for robust steady state tracking. It is well-known that for a large class of nonlinear systems, a system has RPA iff it has integral feedback control (IFC), which has been used extensively in real control systems to achieve RPA. However, we show that due to intrinsic physical limitations on the dynamics of chemical reaction networks (CRNs), cells cannot implement IFC directly in the concentration of a chemical species. This contrasts with electronic implementations, particularly digital, where it is trivial to implement IFC directly in a single state. Therefore, biomolecular systems have to achieve RPA by encoding the integral control variable into the network architecture of a CRN. We describe a general framework to implement RPA in CRNs and show that well-known network motifs that achieve RPA, such as (negative) integral feedback (IFB) and incoherent feedforward (IFF), are examples of such implementations. We also develop methods to solve the problem of designing integral feedback variables for unknown plants. This standard control notion is surprisingly nontrivial and relatively unstudied in biomolecular control. The methods developed here connect different existing fields and approaches on the problem of biomolecular control, and hold promise for systematic chemical reaction controller synthesis as well as analysis.
Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore
Authors: Kohl Kevin D. , Oakeson Kelly F. , Orr Teri J. , Miller Aaron W. , Forbey Jennifer Sorensen , Phillips Caleb D. , Dale Colin , Weiss Robert B. , Dearing M. Denise 
Published: April 2018

AbstractMicrobial detoxification of plant defense compounds influences the use of certain plants as food sources by herbivores. The location of microbial detoxification along the gut could have profound influences on the distribution, metabolism, and tolerance to toxic compounds. Stephen’s woodrats (Neotoma stephensi) specialize on juniper, which is heavily defended by numerous defensive compounds, such as oxalate, phenolics, and monoterpenes. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location of microbial detoxification in the woodrat gut. First, we measured levels of toxins across gut chambers. Compared to food material, oxalate concentrations were immediately lower in the foregut chamber, while concentrations of terpenes remain high in the foregut, and are lowest in the cecal chamber. We also conducted metagenomic sequencing of the foregut and cecal chambers to compare microbial functions. We found that the majority of genes associated with detoxification functions were more abundant in the cecal chamber. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut. Thus, it seems that microbial detoxification may take place in various chambers depending on the class of chemical compound. We hypothesize that the location of microbial detoxification could impact the tolerance of animals to these compounds, which may have ecological and evolutionary consequences.
Expression levels of glycoprotein O (gO) vary between strains of human cytomegalovirus, influencing the assembly of gH/gL complexes and virion infectivity
Authors: Zhang Le , Zhou Momei , Stanton Richard , Kamil Jeremy , Ryckman Brent J. 
Published: April 2018

ABSTRACTTropism of human cytomegalovirus (HCMV) is influenced by the envelope glycoprotein complexes gH/gL/gO and gH/gL/UL128-131. During virion assembly, gO and the UL128-131 proteins compete for binding to gH/gL in the ER. This assembly process clearly differs among strains since Merlin (ME) virions contain abundant gH/gL/UL128-131 and little gH/gL/gO, whereas TR contains much higher levels of total gH/gL, mostly in the form of gH/gL/gO, but much less gH/gL/UL128-131 than ME. Remaining questions include 1) what are the mechanisms behind these assembly differences, and 2) do differences reflectin vitroculture adaptations or natural genetic variations? Since the UL74(gO) ORF differs by 25% of amino acids between TR and ME, we analyzed recombinant viruses in which the UL74(gO) ORF was swapped. TR virions were >40-fold more infectious than ME. Transcriptional repression of UL128-131 enhanced infectivity of ME to the level of TR, despite still far lower levels of gH/gL/gO. Swapping the UL74(gO) ORF had no effect on either TR or ME. A quantitative immunoprecipitation approach revealed that gH/gL expression was within 4-fold between TR and ME, but gO expression was 20-fold less by ME, and suggested differences in mRNA transcription, translation or rapid ER-associated degradation of gO. Trans-complementation of gO expression during ME replication gave 6-fold enhancement of infectivity beyond the 40-fold effect of UL128-131 repression alone. Overall, strain variations in assembly of gH/gL complexes result from differences in expression of gO and UL128-131, and selective advantages for reduced UL128-131 expression during fibroblast propagation are much stronger than for higher gO expression.IMPORTANCESpecific genetic differences between independently isolated HCMV strains may result from purifying selection onde novomutations arising during propagation in culture, or random sampling among the diversity of genotypes present in clinical specimens. Results presented indicate that while reduced UL128-131 expression may confer a powerful selective advantage during cell-free propagation of HCMV in fibroblast cultures, selective pressures for increased gO expression are much weaker. Thus, variation in gO expression among independent strains may represent natural genotype variability presentin vivo. This may have important implications for virus-host interactions such as immune recognition, and underscores the value of studying molecular mechanisms of replication using multiple HCMV strains.
Detection of Leishmania DNA in saliva among patients with HIV/AIDS in Trang Province, southern Thailand
Authors: Pandey Netranapha , Siripattanapipong Suradej , Leelayoova Saovanee , Manomat Jipada , Mungthin Mathirut , Tan-ariya Peerapan , Bualert Lertwut , Naaglor Tawee , Siriyasatien Padet , Phumee Atchara , Piyaraj Phunlerd 
Published: April 2018

ABSTRACTLeishmaniasis is a neglected tropical disease causing opportunistic infection among patients with HIV/AIDS. The fatal form of this disease is visceral leishmaniasis (VL). DNA of Leishmania can be detected in saliva, for which the collection is noninvasive and requires little expertise. This study aimed to evaluate the sensitivity and specificity of a nested-PCR to amplify the Internal Transcribed Spacer 1 (ITS1) to detect Leishmania DNA in paired saliva and buffy coat samples of 305 Thai patients with HIV/AIDS in Trang Hospital, Trang Province, southern Thailand. For asymptomatic Leishmania infection among Thai patients with HIV/AIDS, the sensitivity and specificity of the nested-PCR-ITS1 in buffy coat were 73.9 and 100%, respectively. However, the sensitivity in saliva was 26.1% and specificity was 100%. Using the nested-PCR-ITS1, saliva and buffy coat samples showed positive agreement in only 52.0% of patients. Saliva tested results with the nested-PCR-ITS1 showed positive agreement with the Direct Agglutination Test (DAT) in 46.5% of patients. Only 12.1% of the samples showed positive agreement for Leishmania infection among all the three tests: saliva, buffy coat and DAT results. Using nucleotide sequencing, at least three species of Leishmania infection were identified in saliva, i.e., L. siamensis (n=28), L. martiniquensis (n=9), and L. donovani complex (n=1). As a result, buffy coat still appears to be a better specimen to diagnose asymptomatic VL infection among individuals with HIV. However, the use of both buffy coat and saliva together as clinical specimens would increase the sensitivity of Leishmania detection.