bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rheumatoid Arthritis Patient's Journey
Authors: Rosa Javier E. , García María Victoria , Luissi Aurelia , Pierini Florencia , Sabelli Mirtha , Mollerach Florencia , Soriano Enrique R. 
Published: October 2019

Objectives
The aims of this study were to establish delay times from articular symptoms onset to first rheumatologist consultation, rheumatoid arthritis (RA) diagnosis, and treatment initiation with disease-modifying antirheumatic drug (DMARD) therapy and to assess the impact of delayed diagnosis on structural damage.

Methods
This was an observational cohort study. Rheumatoid arthritis adult patients treated in a private health system between January 1, 1996, and December 31, 2016, were included. Electronic medical records were reviewed to obtain clinical and demographic data, dates of first disease symptom, diagnosis, and date of first treatment with DMARDs. Physical function (Health Assessment Questionnaire) and structural damage (Sharp score modified by van der Heijde) were also assessed.

Results
Two hundred forty-six patients (81% female), with a mean age of 67.25 (standard deviation [SD], 14.53) years, were included. At the end of follow-up period, median Health Assessment Questionnaire (n = 145) and radiological scores (n = 171) were 0.125 (interquartile range, 0–0.87) and 15 (interquartile range, 6–33), respectively. A mean of 9.2 (SD, 20) months (median, 3 months) elapsed from the first disease symptom to rheumatologist consultation, 14.2 (SD, 24) months (median, 4.8 months) to RA diagnosis, and 16.9 (SD, 25.4) months (median, 7 months) to treatment initiation with DMARDs. Significantly greater structural damage was found in patients with a diagnosis delay of more than 12 months (n = 70) (p = 0.0325).

Conclusions
Despite good access to medical consultation in a private health system, there is still a delay to RA diagnosis and to start pharmacological therapy. A delay of more than 12 months was significantly associated with greater radiological damage after 5 years of follow-up.
A Very Rare Localization of Rhinolith: Fossa of Rosenmuller
Authors: Aksakal Ceyhun 
Published: October 2019

Abstract
Sixty-five-year old male patient applied to our clinic with nonspecific complaints such as tinnitus, otalgia, headache, halitosis, and persistent globus pharyngeus which had been continued for 5 years. His complaints persisted despite different extensive treatments. In nasoendoscopy, a yellow-colored mass with purulent discharge around was observed in eustachian tube opening in left fossa of Rosenmüller. Computed tomography scan showed a mass of 6 × 6 mm size in left fossa of Rosenmüller. After excision of the mass under local anesthesia, significant reductions were observed in patient's symptoms. Histopathology of the mass was reported as rhinolith. Although fossa of Rosenmüller is a quite rare localization for rhinoliths, it needs to be considered in differential diagnosis of patients with nonspecific symptoms such as halitosis, globus pharyngeus, and otalgia. This report represents a patient with rhinolith localized in fossa of Rosenmüller as the 2nd report in the literature.
Comparison of Lengthening Temporalis Myoplasty and Free-Gracilis Muscle Transfer for Facial Reanimation in Children
Authors: Nguyen Phuong D. , Faschan Kristin S. , Mazzaferro Daniel M. , Konieczny Tami , Jackson Oksana A. , Bartlett Scott P. 
Published: October 2019

Background:
Lengthening temporalis myoplasty (LTM) and cross-face nerve graft with free gracilis muscle transfer (CFNG-FGMT) are the 2 most common procedures used to restore dynamic facial animation and improve facial symmetry. There has not been direct comparison or consensus. Here, the authors compare our experience with respect to muscle activity, symmetry, and excursion.

Methods:
A retrospective review was performed of patients with facial palsy who had CFNG-FGMT or LTM from 2008 to 2016 at a single institution. Postoperative surface EMG was recorded at maximum open smile. Normal and paralyzed sides of the face were analyzed with Facial Assessment by Computer Evaluation software. Commissure excursion and symmetry was assessed.

Results:
Six patients with LTM and 10 with CFNG-FGMT met inclusion criteria. Muscle activity was 1st identified in LTM patients after 3 months (47.42 mV, P < 0.001) and CFNG-FGMT patients after 3 months (28.30 mV, P < 0.001) compared to immediate postoperative period. Relative to preoperative excursion, there was significant increase of 3.33 mm in commissure excursion seen at the 0 to 3 month period for LTM patients (P = 0.04). Commisure excursion for CFNG-FGMT was seen later, in the 3- to 6-month postoperative period (4.01, P = 0.024). During smile, CFNG-FGMT patients had better symmetry than unilateral LTM patients. In bilateral LTM patients, there was no significant change in symmetry.

Conclusion:
Dynamic facial animation improved in both surgical groups. The LTM demonstrates a faster rate of muscle recruitment compared to CFNG-FGMT. After 3 months, both LTM and CFNG-FGMT groups had comparable excursions. A decision-making algorithm is presented.
Catastrophic Allergic Fungal Sinusitis: A Report of Two Cases
Authors: Walter Eyal , McKean Erin L. , Camelo-Piragua Sandra I. , Parmar Hemant A. , Trobe Jonathan D. 
Published: October 2019

Background:
Allergic fungal rhinosinusitis (AFRS) is a common condition in which sinusitis develops as an IgE-mediated response to common sinonasal fungal organisms. If that response leads to blockage of sinus ostia, bone expansion and erosion by expansive cysts containing dense inspissated debris may occur with the potential for critical neurovascular compression including damage to the anterior visual pathway.

Methods:
Review of clinical and imaging features of 2 patients who sustained catastrophic clinical outcomes.

Results:
The first patient had pansinusitis with massive mucocele-like cysts expanding the sphenoid sinus and cranial base and causing compression of the anterior visual pathway that led to persistent severe vision loss despite extensive sinus surgery. The second patient developed sphenoethmoidal expansion with a marked inflammatory response and presumed conversion to invasive fungal sinusitis that caused anterior visual pathway vision loss, bilateral ocular motor palsies from extension into the cavernous sinuses, and death from a large middle cerebral artery stroke.

Conclusions:
Although AFRS is most often benign and treatable, it may rarely produce catastrophic outcomes, especially if the sphenoid sinus is involved. Irreversible vision loss may occur from compression, and ocular motor palsies and death from conversion to invasive fungal disease. Close ophthalmologic and imaging monitoring is necessary in patients with expanded sinuses, and prophylactic sinus surgery may be indicated in certain cases.
Analysis of online information available for treatment of depression
Authors: Clarke Zachary , Ghezzi Pietro 
Published: October 2019

AbstractThe Internet has become a prime source of health information available to the public. Our aims were to assess the content and quality of online information for the treatment of depression.We searched, “How to cure depression” on Google and analysed the first 200 websites according to the website typology and a standard health information assessment tool, the Journal of the American Medical Association (JAMA) criteria (presence of authorship, date, disclosure, and references). We also analyzed content in terms of treatments mentioned and developed a Quality Indicator Score (QIS) based on the guidelines for treating depression from the UK National Institute for Health and Care Excellence (NICE).News websites were the most frequent typology followed by health portals, non-profit, professional and government; commercial websites were the least represented. In the top ten websites, news and health portals remained first and second respectively. Antidepressants were the most mentioned treatment, followed by psychotherapy, lifestyle & exercise, social support, diet. The least mentioned interventions were sunlight & light therapy, routine, and ketamine & psychedelics. Commercial websites preferentially mentioned supplements, while ketamine and psychedelic drugs were the most covered by news outlets. Analysing webpages according to our QIS showed the median of NICE recommended treatments was 2.5 out of 5 possible treatments: antidepressants, lifestyle & exercise, psychotherapy, social support and ECT. Government websites had the highest QIS, news and commercial websites the lowest. Webpages with high QIS ranked higher in Google.
Real-time Continuous Hand Motion Myoelectric Decoding by Automated Data Labeling
Authors: Hu Xuhui , Zeng Hong , Chen Dapeng , Zhu Jiahang , Song Aiguo 
Published: October 2019

AbstractIn this paper an automated data labeling (ADL) neural network was proposed to streamline dataset collecting for real-time predicting the continuous motion of hand and wrist, these gestures are only decoded from a surface electromyography (sEMG) array of eight channels. Unlike collecting both the bio-signals and hand motion signals as samples and labels in supervised learning, this algorithm only collects the unlabeled sEMG into an unsupervised neural network, in which the hand motion labels are auto-generated. The coefficient of determination (r2) for three DOFs, i.e. wrist flex/extension, wrist pro/supination, hand open/close, was 0.86, and 0.87 respectively. The comparison between real motion labels and auto-generated labels shows that the latter has earlier response than former. The results of Fitts’ law test indicate that ADL has capability of controlling multi-DOFs simultaneously even though the training set only contains sEMG data from single DOF gesture. Moreover, no more hand motion measurement needed which greatly helps upper-limb amputee imagine the gesture of residual limb to control a dexterous prosthesis.
L1 and B1 repeats blueprint the spatial organization of chromatin
Authors: Lu J. Yuyang , Chang Lei , Li Tong , Wang Ting , Yin Yafei , Zhan Ge , Zhang Ke , Percharde Michelle , Wang Liang , Peng Qi , Yan Pixi , Zhang Hui , Han Xue , Bi Xianju , Shao Wen , Hong Yantao , Wu Zhongyang , Wang Peizhe , Li Wenzhi , Zhang Jing , Chang Zai , Hou Yingping , Li Pilong , Ramalho-Santos Miguel , Na Jie , Xie Wei , Sun Yujie , Shen Xiaohua 
Published: October 2019

SUMMARYDespite extensive mapping of three-dimensional (3D) chromatin structures, the basic principles underlying genome folding remain unknown. Here, we report a fundamental role for L1 and B1 retrotransposons in shaping the macroscopic 3D genome structure. Homotypic clustering of B1 and L1 repeats in the nuclear interior or at the nuclear and nucleolar peripheries, respectively, segregates the genome into mutually exclusive nuclear compartments. This spatial segregation of L1 and B1 is conserved in mouse and human cells, and occurs dynamically during establishment of the 3D chromatin structure in early embryogenesis and the cell cycle. Depletion of L1 transcripts drastically disrupts the spatial distributions of L1- and B1-rich compartments. L1 transcripts are strongly associated with L1 DNA sequences and induce phase separation of the heterochromatin protein HP1α. Our results suggest that genomic repeats act as the blueprint of chromatin macrostructure, thus explaining the conserved higher-order structure of chromatin across mammalian cells.
DDIA: data dependent-independent acquisition proteomics - DDA and DIA in a single LC-MS/MS run
Authors: Guan Shenheng , Taylor Paul P. , Han Ziwei , Moran Michael F. , Ma Bin 
Published: October 2019

ABSTRACTData dependent acquisition (DDA) and data independent acquisition (DIA) are traditionally separate experimental paradigms in bottom-up proteomics. In this work, we developed a strategy combining the two experimental methods into a single LC-MS/MS run. We call the novel strategy, data dependent-independent acquisition proteomics, or DDIA for short. Peptides identified by conventional and robust DDA identification workflow provide useful information for interrogation of DIA scans. Deep learning based LC-MS/MS property prediction tools, developed previously can be used repeatedly to produce spectral libraries facilitating DIA scan extraction. A complete DDIA data processing pipeline, including modules for iRT vs RT calibration curve generation, DIA extraction classifier training, FDR control has been developed. A key advantage of the DDIA method is that it requires minimal information for processing its data.GRAPHIC ABSTRACT
Intercellular adhesion stiffness moderates cell decoupling on stiff substrates
Authors: Vargas D. A. , Heck T. , Smeets B. , Ramon H. , Parameswaran H. , Van Oosterwyck H. 
Published: October 2019

AbstractThe interplay between cell-cell and cell-substrate interactions is complex yet necessary for the formation and well-functioning of tissues. The same mechanosensing mechanisms used by the cell to sense its extracellular matrix, also play a role in intercellular interactions. We used the discrete element method to develop a computational model of a deformable cell that includes subcellular components responsible for mechanosensing. We modeled a cell pair in 3D on a patterned substrate, a simple laboratory setup to study intercellular interactions. We explicitly modeled focal adhesions between the cells and the substrate, and adherens junctions between cells. These mechanosensing adhesions matured; their disassembly rate was dictated by the force they carry. We also modeled stress fibers which bind the discrete adhesions and contract. The mechanosensing fibers strengthened upon stalling and exerted higher forces. Traction exerted on the substrate was used to generate maps displaying the magnitude of the tractions along the cell-substrate interface. Simulated traction maps are compared to experimental maps obtained via traction force microscopy. The model recreates the dependence on substrate stiffness of the tractions’ spatial distribution across the cell-substrate interface, the contractile moment of the cell pair, the intercellular force, and the number of focal adhesions. It also recreates the phenomenon of cell decoupling, in which cells exert forces separately when substrate stiffness increases. More importantly, the model provides viable molecular explanations for decoupling. It shows that the implemented mechanosensing mechanisms are responsible for competition between different fiber-adhesion configurations present in the cell pair. The point at which an increasing substrate stiffness becomes as high as that of the cell-cell interface is the tipping point at which configurations that favor cell-substrate adhesion dominate over those favoring cell-cell adhesion. This competition is responsible for decoupling. Additionally, we learn that extent of decoupling is modulated by adherens junction maturation.Statement of SignificanceCells are sensitive to mechanical factors of their extracellular matrix while simultaneously in contact with other cells. This creates complex intercellular interactions that depend on substrate stiffness and play a role in processes such as development and diseases like cardiac arrhythmia, asthma, and cancer. The simplest cell collective system in vitro is a cell pair on a patterned substrate. We developed a computational model of this system which explains the role of molecular adhesions and contractile fibers in the dynamics of cell-cell interactions on substrates with different stiffness. It is one of the first models of a deformable cell collective based on mechanical principles. It recreates cellular decoupling, a phenomenon in which cells exert forces separately, when substrate stiffness increases.
Ambiguity coding allows accurate inference of evolutionary parameters from alignments in an aggregated state-space
Authors: Weber Claudia C. , Perron Umberto , Casey Dearbhaile , Yang Ziheng , Goldman Nick 
Published: October 2019

How can we best learn the history of a protein’s evolution? Ideally, a model of sequence evolution should capture both the process that generates genetic variation and the functional constraints determining which changes are fixed. However, in practical terms the most suitable approach may simply be the one that combines the convenience of easily available input data with the ability to return useful parameter estimates. For example, we might be interested in a measure of the strength of selection (typically obtained using a codon model) or an ancestral structure (obtained using structural modelling based on inferred amino acid sequence and side chain configuration).But what if data in the relevant state-space are not readily available? We show that it is possible to obtain accurate estimates of the outputs of interest using an established method for handling missing data. Encoding observed characters in an alignment as ambiguous representations of characters in a larger state-space allows the application of models with the desired features to data that lack the resolution that is normally required. This strategy is viable because the evolutionary path taken through the observed space contains information about states that were likely visited in the “unseen” state-space. To illustrate this, we consider two examples with amino acid sequences as input.We show thatω, a parameter describing the relative strength of selection on non-synonymous and synonymous changes, can be estimated in an unbiased manner using an adapted version of a standard 61-state codon model. Using simulated and empirical data, we find that ancestral amino acid side chain configuration can be inferred by applying a 55-state empirical model to 20-state amino acid data. Where feasible, combining inputs from both ambiguity-coded and fully resolved data improves accuracy. Adding structural information to as few as 12.5% of the sequences in an amino acid alignment results in remarkable ancestral reconstruction performance compared to a benchmark that considers the full rotamer state information. These examples show that our methods permit the recovery of evolutionary information from sequences where it has previously been inaccessible.
The effects of polydisperse crowders on the compaction of the Escherichia coli nucleoid
Authors: Yang Da , Männik Jaana , Retterer Scott T. , Männik Jaan 
Published: October 2019

ABSTRACTDNA binding proteins, supercoiling, macromolecular crowders, and transient DNA attachments to the cell membrane have all been implicated in the organization of the bacterial chromosome. However, it is unclear what role these factors play in compacting the bacterial DNA into a distinct organelle-like entity, the nucleoid. By analyzing the effects of osmotic shock and mechanical squeezing on Escherichia coli, we show that macromolecular crowders play a dominant role in the compaction of the DNA into the nucleoid. We find that a 30% increase in the crowder concentration from physiological levels leads to a 3-fold decrease in the nucleoid’s volume. The compaction is anisotropic, being higher along the long axes of the cell at low crowding levels. At higher crowding levels the compression becomes isotropic, implying that E. coli nucleoids lack a well-defined backbone. We furthermore show that the compressibility of the nucleoid is not significantly affected by cell growth rates and by prior treatment with rifampicin. The latter results point out that in addition to poly-ribosomes, soluble cytoplasmic proteins have a significant contribution in determining the size of the nucleoid.
Contributions of the conserved insect carbon dioxide receptor subunits to odor detection
Authors: Kumar Arun , Tauxe Genevieve M. , Perry Sarah , Scott Christi A. , Dahanukar Anupama , Ray Anandasankar 
Published: October 2019

AbstractThe CO2 receptor in mosquitoes is broadly tuned to detect many diverse odorants. The receptor consists of three 7-TM subunits (Gr1, Gr2, and Gr3) in mosquitoes but only two subunits in Drosophila: Gr21a (Gr1 ortholog) and Gr63a (Gr3 ortholog). We demonstrate that Gr21a is required for CO2 responses in Drosophila as has been shown for Gr63a. Next, we generate a Drosophila double mutant for Gr21a and Gr63a, and in this background we functionally express combinations of Aedes Gr1, 2, and 3 genes in the “CO2 empty neuron.” Only two subunits, Gr2 and Gr3, suffice for response to CO2. Addition of Gr1 increases sensitivity to CO2 while it decreases the response to pyridine. The inhibitory effect of the antagonist isobutyric acid is observed upon addition of Gr1. Gr1 therefore increases the diversity of ligands of the receptor, and also modulates the response of the receptor complex.
Coincidence of cholinergic pauses, dopaminergic activation and depolarization drives synaptic plasticity in the striatum
Authors: Zhang Yan-Feng , Fisher Simon D. , Oswald Manfred , Wickens Jeffery R. , Reynolds John N. J. 
Published: October 2019

AbstractPauses in the firing of tonically-active cholinergic interneurons (ChIs) in the striatum coincide with phasic activation of dopamine neurons during reinforcement learning. However, how this pause influences cellular substrates of learning is unclear. Using two in vivo paradigms, we report that long-term potentiation (LTP) at corticostriatal synapses with spiny projection neurons (SPNs) is dependent on the temporal coincidence of ChI pause and dopamine phasic activation, critically accompanied by SPN depolarization.
Genetic interaction of mammalian IFT-A paralogs regulates cilia disassembly, ciliary protein trafficking, Hedgehog signaling and embryogenesis
Authors: Wang Wei , Allard Bailey A. , Pottorf Tana S. , Vivian Jay L. , Tran Pamela V. 
Published: October 2019

AbstractPrimary cilia are sensory organelles that are essential for eukaryotic development and health. These antenna-like structures are synthesized by intraflagellar transport protein complexes, IFT-B and IFT-A, which mediate bi-directional protein trafficking along the ciliary axoneme. Here using mouse embryonic fibroblasts (MEF), we investigate the ciliary roles of two mammalian orthologues ofChlamydomonasIFT-A gene,IFT139, namelyThm1(also known asTtc21b) andThm2 (Ttc21a). Thm1loss causes perinatal lethality, andThm2loss allows survival into adulthood. At E14.5, the number ofThm1;Thm2double mutant embryos is lower than that for a Mendelian ratio, indicating deletion ofThm1andThm2causes mid-gestational lethality. We examined the ciliary phenotypes of mutant MEF.Thm1-mutant MEF show decreased cilia assembly, shortened primary cilia, a retrograde IFT defect for IFT and BBS proteins, and reduced ciliary entry of membrane-associated proteins.Thm1-mutant cilia also show a retrograde transport defect for the Hedgehog transducer, Smoothened, and an impaired response to Smoothened agonist, SAG.Thm2-null MEF show normal ciliary dynamics and Hedgehog signaling, but additional loss of aThm1allele impairs response to SAG. Further,Thm1;Thm2double mutant MEF show enhanced cilia disassembly, and relative toThm1-null MEF, increased impairment of IFT81 retrograde transport and of INPP5E ciliary import. Thus,Thm1andThm2have unique and redundant roles in MEF.Thm1regulates cilia assembly, and together withThm2, cilia disassembly. Moreover,Thm1alone and together withThm2, regulates ciliary protein trafficking, Hedgehog signaling, and embryogenesis. These findings shed light on mechanisms underlyingThm1-,Thm2- or IFT-A-mediated ciliopathies.