bluuebunny/crossref_metadata_2025 huggingface dataset:
A chalcogen-bonded complex H3N⋯S=C=S formed by ammonia and carbon disulfide characterised by chirped-pulse, broadband microwave spectroscopy
Authors: Gougoula Eva , Medcraft Chris , Alkorta Ibon , Walker Nicholas R. , Legon Anthony C.
Published: February 2019

Ground-state rotational spectra were observed for ten symmetric-top isotopologues H3N⋯S=C=S, H3N⋯34S=C=S, H3N⋯S=C=34S, H3N⋯S=13C=S, H315N⋯S=C=S, H315N⋯34S=C=S, H315N⋯S=C=34S, H315N⋯S=13C=S, H315N⋯33S=C=S, and H315N⋯S=C=33S, the first five in their natural abundance in a mixture of ammonia and carbon disulphide in argon and the second group with enriched 15NH3. The four asymmetric-rotor isotopomers H2DN⋯S=C=S, H2DN⋯34S=C=S, H2DN⋯S=C=34S, and HD2N⋯S=C=S were investigated by using a sample composed of ND3 mixed with CS2. Rotational constants, centrifugal distortion constants, and 33S nuclear quadrupole coupling constants were determined from spectral analyses and were interpreted with the aid of models of the complex to determine its symmetry, geometry, one measure of the strength of the intermolecular binding, and information about the subunit dynamics. The complex has C3v symmetry, with nuclei in the order H3N⋯S=C=S, thereby establishing that the non-covalent interaction is a chalcogen bond involving the non-bonding electron pair of ammonia as the nucleophile and the axial region near one of the S atoms as the electrophile. The small intermolecular stretching force constant kσ = 3.95(5) N m−1 indicates a weak interaction and suggests the assumption of unperturbed component geometries on complex formation. A simple model used to account for the contribution of the subunit angular oscillations to the zero-point motion leads to the intermolecular bond length r(N⋯S) = 3.338(10) Å.
An improved Ku-band TTO with compact solenoid and better plasma-suppressing collector
Authors: Xu Weili , He Juntao , Ling Junpu
Published: February 2019

A Ku-band transit-time oscillator (TTO) with compact magnetic coil and a novel collector structure is proposed. By utilizing the natural bending of the magnetic field, this TTO could decrease over 25% length of uniform magnetic field and the required energy of the solenoid. Besides, the larger radius and decreased magnetic field at the collector lead to larger collection area and less current density in collector surface, simulation shows that the energy deposition peak is 2.5 times less in this novel collector. That this novel collector also has evident advantages in suppressing the adverse effect of plasmas than traditional one in simulation, when hydrogen gas is preset on the collector surface. Particle-in-cell simulation shows that with a 2.4GW beam guided by a decreasing magnetic field of about 0.7T, 0.85GW microwave power pulse at 13.23GHz is generated in this TTO, yielding a conversion efficiency of about 35.4%.
Towards athermal Brillouin strain sensing based on heavily germania-doped core optical fibers
Authors: Deroh M. , Sylvestre T. , Chretien J. , Maillotte H. , Kibler B. , Beugnot J.-C.
Published: February 2019

Owing to their interesting linear and nonlinear optical properties, germania-based core optical fibers are being widely used in a wide range of applications ranging from nonlinear optics to optical sensing. We here examine both the strain and temperature coefficients of stimulated Brillouin scattering in heavily doped core optical fibers with ultrahigh GeO2 doping level up to 98-mol. %. Our results show that the temperature dependence of the Brillouin gain spectrum becomes almost negligible (CT = 0.07 MHz/°C) for high doping content, while its Brillouin strain coefficient remains significant (Cε = 21.4 kHz με−1) compared to that of standard single-mode optical fibers (Cε = 48.9 kHz με−1). It is further shown that the temperature coefficient tends to zero when removing the fiber coating, indicating that those athermal highly GeO2-doped-core optical fibers could advantageously be used for Brillouin fiber strain sensing.
Synthesis of large-scale few-layer PtS2 films by chemical vapor deposition
Authors: Zhao Donghui , Xie Sheng , Wang Yang , Zhu Hao , Chen Lin , Sun Qingqing , Zhang David Wei
Published: February 2019

PtS2, a group-10 transition metal dichalcogenide, has prominent layer-depended band structure, and can enable extremely high phonon-limited mobility at room temperature. Here, we demonstrate the theoretical study on the electronic band structures of PtS2 with different thickness by using density functional theory (DFT), as well as experimental realization of large-area synthesis of few-layer PtS2 film by direct sulfurization of pre-deposited Pt. The synthetic process suggested that the reaction pressure is a key factor in the formation of high-quality PtS2 semiconducting films. Characterizations with atomic force microscopy (AFM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS) have indicated that good film stoichiometry and uniformity have been achieved. Furthermore, field-effect transistor (FET) arrays were fabricated based on the large-scale PtS2 film, exhibiting well-uniform electrical performance with p-type transport behavior. These results can open up an attractive approach to promote the large-scale applications of PtS2 in advanced nanoelectronics and optoelectronics devices and systems.
Clinical application of bacteriophages in Europe
Authors: Pirnay Jean-Paul , De Vos Daniel , Verbeken Gilbert
Published: February 2019

Bacteriophages could help address the antibiotic resistance crisis that impacts health systems all over the world. In 2011, the European Commission formally confirmed that phage products used as therapeutics are medicinal products and thus manufacturers need to navigate the extremely arduous and enormously expensive medicine development and marketing pathway. However, up until now, not one therapeutic phage product has made it to the European market, and yet clinicians are under increasing pressure to use phages in the treatment of multidrug-resistant bacterial infections. While a handful of small European enterprises are struggling to squeeze therapeutic phage products through the conventional and centralised European medicinal products funnel, some clinicians and academics are exploring (European) national solutions to accelerate the availability of phages for the treatment of an increasing number of desperate patients. This mini-review summarises the actual status and perspectives of clinical phage application in Europe.
Elongin B is a binding partner of the male germ cell nuclear speckle protein sperm-associated antigen 16S (SPAG16S) and is regulated post-transcriptionally in the testis
Authors: Zhang Zhengang , Huang Qian , Wang Zhenyu , Zou Jie , Yu Zuoren , Strauss III Jerome F. , Zhang Zhibing
Published: February 2019

In this study we identified Elongin B, a regulatory subunit of the trimeric elongation factor Elongin ABC, which increases the overall rate of elongation by RNA polymerase II, as a major binding partner of sperm-associated antigen 16S (SPAG16S), a component of nuclear speckles. Nuclear speckles are nuclear subcompartments involved in RNA maturation. Previously, we showed that SPAG16S is essential for spermatogenesis. In the present study, a specific antibody against mouse Elongin B was generated and reacted with a protein with the predicted size of Elongin B in the testis; immunofluorescence staining revealed that the Elongin B was located in the nuclei and residual bodies. In round spermatids, Elongin B was colocalised with splicing factor SC35 (SC35), a marker of nuclear speckles. During the first wave of spermatogenesis, Elongin B transcripts were initially detected at Postnatal Day (PND) 8, and levels were greatly increased afterwards. However, Elongin B protein was only found from PND30, when germ cells progressed through spermiogenesis. Polysomal gradient analysis of Elongin B transcripts isolated from adult mouse testes revealed that most of the Elongin B mRNA was associated with translationally inactive, non-polysomal ribonucleoproteins. An RNA electrophoretic mobility shift assay demonstrated that the 3′ untranslated region of the Elongin B transcript was bound by proteins present in testis but not liver extracts. These findings suggest that post-transcriptional regulation of Elongin B occurs in the testis, which is a common phenomenon during male germ cell development. As a major binding partner of SPAG16S, Elongin B may play an important role in spermatogenesis by modulating RNA maturation.
An experimental investigation of differential object marking in Mexican Spanish
Authors: Bautista-Maldonado Salvador , Montrul Silvina
Published: February 2019

Differential Object Marking (DOM) is a phenomenon widely attested in Spanish. In two experimental studies using
production and acceptability judgments we examined the extent to which Mexican Spanish presents some variation among monolingual
speakers with respect to expansion of DOM. We tested whether DOM with animate and specific objects is categorical in this variety,
and whether DOM is expanding to inanimate definite and indefinite objects as observed by diachronic studies of Mexican and other
Latin American varieties. We also tested DOM with other constructions: bare plurals, the verbs like tener and
haber, small clauses and causative and perception verbs. Our study contributes new data documenting
linguistic variation in native speakers and confirms synchronic and diachronic analyses of DOM in Spanish.
Subjectivity in Spanish causal connectives
Authors: Cárcamo Morales Benjamín
Published: February 2019

Recent literature has focused on specifying the nature of causal relations. Although the identification of whether connectives prototypically convey objective or subjective relations has been carried out for languages such as French, Dutch and English, the same has not occurred in the case of Spanish. The present study examines frequently used connectives and lexical cue phrases in terms of domain, propositional attitude, and presence of a Subject of Consciousness (SoC) in order to determine the degrees of subjectivity conveyed by the connectives. The findings show thatdebido a (que)is a highly specific connective used in objective causal relations about facts which do not involve SoC. On the contrary, the connectivesporqueandya quepresent similar flexibility that result in both being used to convey subjective and objective causal relations. This study supports the assumption of subjectivity being a cognitive mechanism that shows across different languages.
Antigen-presenting ILC3 regulate T cell–dependent IgA responses to colonic mucosal bacteria
Authors: Melo-Gonzalez Felipe , Kammoun Hana , Evren Elza , Dutton Emma E. , Papadopoulou Markella , Bradford Barry M. , Tanes Ceylan , Fardus-Reid Fahmina , Swann Jonathan R. , Bittinger Kyle , Mabbott Neil A. , Vallance Bruce A. , Willinger Tim , Withers David R. , Hepworth Matthew R.
Published: February 2019

Intestinal immune homeostasis is dependent upon tightly regulated and dynamic host interactions with the commensal microbiota. Immunoglobulin A (IgA) produced by mucosal B cells dictates the composition of commensal bacteria residing within the intestine. While emerging evidence suggests the majority of IgA is produced innately and may be polyreactive, mucosal-dwelling species can also elicit IgA via T cell–dependent mechanisms. However, the mechanisms that modulate the magnitude and quality of T cell–dependent IgA responses remain incompletely understood. Here we demonstrate that group 3 innate lymphoid cells (ILC3) regulate steady state interactions between T follicular helper cells (TfH) and B cells to limit mucosal IgA responses. ILC3 used conserved migratory cues to establish residence within the interfollicular regions of the intestinal draining lymph nodes, where they act to limit TfH responses and B cell class switching through antigen presentation. The absence of ILC3-intrinsic antigen presentation resulted in increased and selective IgA coating of bacteria residing within the colonic mucosa. Together these findings implicate lymph node resident, antigen-presenting ILC3 as a critical regulatory checkpoint in the generation of T cell–dependent colonic IgA and suggest ILC3 act to maintain tissue homeostasis and mutualism with the mucosal-dwelling commensal microbiota.
Nucleophilic substitution at di- and triphosphates: leaving group ability of phosphate versus diphosphate
Authors: van Beek Bas , van Bochove Marc A , Hamlin Trevor A , Bickelhaupt F Matthias
Published: February 2019

Adenosine triphosphate (ATP) is the universal energy carrier in biochemical processes. Herein, we aim for a better understanding of the origin of the high-energy content of the triphosphate moiety involved, the influence of various physicochemical factors thereon, and implication for the actual SN2@P-induced hydrolysis, which drives uphill biochemical processes, such as, DNA replication. To this end, we have investigated the SN2@P-induced hydrolysis of triphosphate (PPP) versus that of diphosphate (PP) using density functional theory (DFT) at COSMO(H2O)-ZORA-OLYP/TZ2P. We find that SN2@P-induced hydrolysis of PPP is favored over that of PP, both kinetically and thermodynamically. The energetic advantage of PPP over PP is slightly diminished by the coordination of Mg2+ counterions. Our activation strain and energy decomposition analyses reveal that the activation barrier for PPP hydrolysis is lower compared to that for PP due to a weaker P
α
–O leaving group bond.
A Model of the Teichmüller space of genus-zero bordered surfaces by period maps
Authors: Radnell David , Schippers Eric , Staubach Wolfgang
Published: February 2019

We consider Riemann surfaces

Σ
\Sigma

with

n
n

borders homeomorphic to

S

1

\mathbb {S}^1

and no handles. Using generalized Grunsky operators, we define a period mapping from the infinite-dimensional Teichmüller space of surfaces of this type into the unit ball in the linear space of operators on an

n
n

-fold direct sum of Bergman spaces of the disk. We show that this period mapping is holomorphic and injective.
Syntaxin 11 regulates the stimulus-dependent transport of Toll-like receptor 4 to the plasma membrane by cooperating with SNAP-23 in macrophages
Authors: Kinoshita Daiki , Sakurai Chiye , Morita Maya , Tsunematsu Masashi , Hori Naohiro , Hatsuzawa Kiyotaka
Published: February 2019

Syntaxin 11 (stx11) is a soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) that is selectively expressed in immune cells; however, its precise role in macrophages is unclear. We showed that stx11 knockdown reduces the phagocytosis of Escherichia coli in interferon-γ–activated macrophages. stx11 knockdown decreased Toll-like receptor 4 (TLR4) localization on the plasma membrane without affecting total expression. Plasma membrane–localized TLR4 was primarily endocytosed within 1 h by lipopolysaccharide (LPS) stimulation and gradually relocalized 4 h after removal of LPS. This relocalization was significantly impaired by stx11 knockdown. The lack of TLR4 transport to the plasma membrane is presumably related to TLR4 degradation in acidic endosomal organelles. Additionally, an immunoprecipitation experiment suggested that stx11 interacts with SNAP-23, a plasma membrane–localized SNARE protein, whose depletion also inhibits TLR4 replenishment in LPS-stimulated cells. Using an intramolecular Förster resonance energy transfer (FRET) probe for SNAP-23, we showed that the high FRET efficiency caused by LPS stimulation is reduced by stx11 knockdown. These findings suggest that stx11 regulates the stimulus-dependent transport of TLR4 to the plasma membrane by cooperating with SNAP-23 in macrophages. Our results clarify the regulatory mechanisms underlying intracellular transport of TLR4 and have implications for microbial pathogenesis and immune responses.
Analysis and Interpretation of Google Trends Data on Public Interest in Cosmetic Body Procedures
Authors: Tijerina Jonathan D , Morrison Shane D , Nolan Ian T , Vail Daniel G , Lee Gordon K , Nazerali Rahim
Published: February 2019

Background

Several online resources such as Google Trends (GT) enable plastic surgeons to track search volume trends for cosmetic procedures. Understanding these data may allow surgeons to better anticipate patients’ interests and meet their needs.

Objectives

The authors sought to evaluate the correlation between GT search volumes and annual surgery volumes.

Methods

Search terms were generated using the “related queries” feature of GT. Data were obtained for the terms breast augmentation, buttock augmentation, buttock implants, buttock lift, calf augmentation, liposuction, lower body lift, thighplasty, abdominoplasty, and brachioplasty from January 2004 to November 2017. Annual volumes for respective procedures were obtained from statistics reports of the American Society of Plastic Surgeons (ASPS) from 2006 to 2017 and American Society of Aesthetic Plastic Surgery (ASAPS) from 2004 to 2017. Correlations were evaluated applying univariate linear regression of GT data to both ASPS and ASAPS data.

Results

Geographical and temporal variations in search volume were detected during the study. Search volume trends that correlated significantly with both ASPS and ASAPS surgery volume trends were: “butt implants surgery” (ASPS: R2 = 0.366, P = 0.049; ASAPS: R2 = 0.380, P = 0.019); “liposuction” (ASPS: R2 = 0.690, P = 0.002; ASAPS: R2 = 0.578, P = 0.002); and “liposuction surgery” (ASPS: R2 = 0.672, P = 0.002; ASAPS: R2 = 0.476, P = 0.006). Several search terms demonstrated no significant relationships, negative correlations, or were significant with only one database.

Conclusions

This study characterizes GT as a convenient and informative data set for plastic surgeons to analyze patient interest in cosmetic body-sculpting procedures. GT represents a useful instrument for tailoring marketing strategies and addressing the needs of our patient population.
Management of Recurrent Symptomatic Macromastia: A Single Surgeon’s Experience
Authors: Qureshi Ali A , Stevens W Grant
Published: February 2019

Background

Breast reduction for symptomatic macromastia can have excellent long-term results and relief of symptoms. However, patients may require a re-reduction for recurrent symptoms. Previous reports of re-reduction after a primary inferior pedicle reduction have called into question the safety of blood supply to the nipple-areola complex with re-reduction.

Objectives

To examine a single surgeon’s experience and management of recurrent symptomatic macromastia after inferior pedicle breast reduction.

Methods

A retrospective review was performed of a single surgeon’s breast reduction experience using billing data to identify cases of breast re-reduction from January 2003 and January 2018. Breast re-reduction was performed either with a Wise pattern, inferior pedicle or with a smile reduction with an inferior pedicle. Liposuction was used in re-reductions only.

Results

In 15 years, 3530 breast reductions were performed in 1758 patients. In 7 patients, 14 total re-reductions were performed, including 13 secondary breast re-reductions (12 bilateral, 1 unilateral) and 1 tertiary, unilateral breast re-reduction. Seven Wise pattern, inferior pedicle and 7 smile reductions with inferior pedicle procedures were done at the breast level. This translates to a re-reduction incidence of 1 in 250 or 0.4% rate of re-reduction at the patient level in our practice. The minor complication rate was 14% (1 seroma), and the major complication rate was 0%. There were no instances of partial or complete nipple areola necrosis.

Conclusions

Recurrent symptomatic macromastia can be managed with re-reduction with re-creation of the inferior pedicle or a smile breast reduction as we describe without increased risk to nipple-areolar complex viability.

Level of Evidence: 4
MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers
Authors: Koohi-Moghadam Mohamad , Borad Mitesh J , Tran Nhan L , Swanson Kristin R , Boardman Lisa A , Sun Hongzhe , Wang Junwen
Published: February 2019

We present MetaMarker, a pipeline for discovering metagenomic biomarkers from whole-metagenome sequencing samples. Different from existing methods, MetaMarker is based on a de novo approach that does not require mapping raw reads to a reference database. We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool samples from France to discover CRC specific metagenomic biomarkers. We showed robustness of the discovered biomarkers by validating in independent samples from Hong Kong, Austria, Germany and Denmark. We further demonstrated these biomarkers could be used to build a machine learning classifier for CRC prediction.

Availability and implementation

MetaMarker is freely available at https://bitbucket.org/mkoohim/metamarker under GPLv3 license.

Supplementary information

Supplementary data are available at Bioinformatics online.
RECAP reveals the true statistical significance of ChIP-seq peak calls
Authors: Chitpin Justin G , Awdeh Aseel , Perkins Theodore J
Published: February 2019

Motivation

Chromatin Immunopreciptation (ChIP)-seq is used extensively to identify sites of transcription factor binding or regions of epigenetic modifications to the genome. A key step in ChIP-seq analysis is peak calling, where genomic regions enriched for ChIP versus control reads are identified. Many programs have been designed to solve this task, but nearly all fall into the statistical trap of using the data twice—once to determine candidate enriched regions, and again to assess enrichment by classical statistical hypothesis testing. This double use of the data invalidates the statistical significance assigned to enriched regions, thus the true significance or reliability of peak calls remains unknown.

Results

Using simulated and real ChIP-seq data, we show that three well-known peak callers, MACS, SICER and diffReps, output biased P-values and false discovery rate estimates that can be many orders of magnitude too optimistic. We propose a wrapper algorithm, RECAP, that uses resampling of ChIP-seq and control data to estimate a monotone transform correcting for biases built into peak calling algorithms. When applied to null hypothesis data, where there is no enrichment between ChIP-seq and control, P-values recalibrated by RECAP are approximately uniformly distributed. On data where there is genuine enrichment, RECAP P-values give a better estimate of the true statistical significance of candidate peaks and better false discovery rate estimates, which correlate better with empirical reproducibility. RECAP is a powerful new tool for assessing the true statistical significance of ChIP-seq peak calls.

Availability and implementation

The RECAP software is available through www.perkinslab.ca or on github at https://github.com/theodorejperkins/RECAP.

Supplementary information

Supplementary data are available at Bioinformatics online.
VHost-Classifier: virus-host classification using natural language processing
Authors: Kitson Ezra , Suttle Curtis A
Published: February 2019

Motivation

When analyzing viral metagenomic sequences, it is often desired to filter the results of a BLAST analysis by the host species of the virus. VHost-Classifier automates this procedure using a natural language processing algorithm written in Python 3, which takes a list of taxonomic identifiers (taxids) returned from a BLAST query using viral sequences as input. The taxid output is binned by the evolutionary lineage of their host, based on string matching the words in their English names. If VHost-Classifier cannot identify a host, it attempts to bin the sequences by the environment from which the sample originated. VHost-Classifier predicts the evolutionary lineage of the host from the virus name and does not rely on referencing taxids against a database; therefore, it is not constrained by the size of a database and can host classify newly characterized viruses.

Results

Benchmarked on a test dataset of 1000 randomly selected viral taxids on the NCBI taxonomy database, VHost-Classifier assigned, with 100% accuracy, a host to the rank of Class for >93% of viruses, and to the rank of Family for >37% of viruses.

Availability and implementation

For more information about VHost-Classifier as well as implementation instructions, visit https://github.com/Kzra/VHost-Classifier.

Supplementary information

Supplementary data are available at Bioinformatics online.
Enhancing the prediction of disease–gene associations with multimodal deep learning
Authors: Luo Ping , Li Yuanyuan , Tian Li-Ping , Wu Fang-Xiang
Published: February 2019

Motivation

Computationally predicting disease genes helps scientists optimize the in-depth experimental validation and accelerates the identification of real disease-associated genes. Modern high-throughput technologies have generated a vast amount of omics data, and integrating them is expected to improve the accuracy of computational prediction. As an integrative model, multimodal deep belief net (DBN) can capture cross-modality features from heterogeneous datasets to model a complex system. Studies have shown its power in image classification and tumor subtype prediction. However, multimodal DBN has not been used in predicting disease–gene associations.

Results

In this study, we propose a method to predict disease–gene associations by multimodal DBN (dgMDL). Specifically, latent representations of protein-protein interaction networks and gene ontology terms are first learned by two DBNs independently. Then, a joint DBN is used to learn cross-modality representations from the two sub-models by taking the concatenation of their obtained latent representations as the multimodal input. Finally, disease–gene associations are predicted with the learned cross-modality representations. The proposed method is compared with two state-of-the-art algorithms in terms of 5-fold cross-validation on a set of curated disease–gene associations. dgMDL achieves an AUC of 0.969 which is superior to the competing algorithms. Further analysis of the top-10 unknown disease–gene pairs also demonstrates the ability of dgMDL in predicting new disease–gene associations.

Availability and implementation

Prediction results and a reference implementation of dgMDL in Python is available on https://github.com/luoping1004/dgMDL.

Supplementary information

Supplementary data are available at Bioinformatics online.
Unraveling UCA1 lncRNA prognostic utility in urothelial bladder cancer
Authors: Avgeris Margaritis , Tsilimantou Anastasia , Levis Panagiotis K , Rampias Theodoros , Papadimitriou Maria-Alexandra , Panoutsopoulou Konstantina , Stravodimos Konstantinos , Scorilas Andreas
Published: February 2019

In the era of precision oncology, bladder cancer (BlCa) is characterized by generic patient management and lack of personalized prognosis and surveillance. Herein, we have studied the clinical significance of urothelial cancer associated 1 (UCA1) lncRNA in improving patients’ risk stratification and prognosis. A screening cohort of 176 BlCa patients was used for UCA1 quantification. The Hedegaard et al. (n = 476) and The Cancer Genome Atlas (TCGA) provisional (n = 413) were analyzed as validation cohorts for non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (MIBC), respectively. Patients’ survival outcome was assessed using recurrence and progression for NMIBC or death for MIBC as clinical endpoint events. Bootstrap analysis was performed for internal validation of Cox regression analysis, whereas the clinical benefit of disease prognosis was assessed by decision curve analysis. UCA1 was significantly overexpressed in bladder tumors compared with normal urothelium, which was confirmed only in the case of NMIBC. Interestingly, reduced expression of UCA1 was correlated with muscle-invasive disease as well as with tumors of higher stage and grade. UCA1 loss was strongly associated with higher risk of short-term relapse [hazard ratio (HR) = 1.974; P = 0.032] and progression to invasive stages (HR = 3.476; P = 0.023) in NMIBC. In this regard, Hedegaard et al. and TCGA validation cohorts confirmed the unfavorable prognostic nature of UCA1 loss in BlCa. Finally, prognosis prediction models integrating UCA1 underexpression and established clinical disease markers contributed to improved stratification specificity and superior clinical benefit for NMIBC prognosis. Underexpression of UCA1 correlates with worse disease outcome in NMIBC and contributes to superior prediction of disease early relapse and progression as well as improved patient stratification specificity.
FMRP Modulates Activity-Dependent Spine Plasticity by Binding Cofilin1 mRNA and Regulating Localization and Local Translation
Authors: Feuge Jonas , Scharkowski Franziska , Michaelsen-Preusse Kristin , Korte Martin
Published: February 2019

Multiple variants of intellectual disability, e.g., the Fragile X Syndrome are associated with alterations in dendritic spine morphology, thereby pointing to dysregulated actin dynamics during development and processes of synaptic plasticity. Surprisingly, although the necessity of spine actin remodeling was demonstrated repeatedly, the importance and precise role of actin regulators is often undervalued. Here, we provide evidence that structural and functional plasticity are severely impaired after NMDAR-dependent LTP in the hippocampus of Fmr1 KO mice. We can link these defects to an aberrant activity-dependent regulation of Cofilin 1 (cof1) as activity-dependent modulations of local cof1 mRNA availability, local cof1 translation as well as total cof1 expression are impaired in the absence of FMRP. Finally, we can rescue activity-dependent structural plasticity in KO neurons by mimicking the regulation of cof1 observed in WT cells, thereby illustrating the potential of actin modulators to provide novel treatment strategies for the Fragile X Syndrome.
Derivation and Validation of a Clinical Decision Guideline for Influenza Testing in 4 US Emergency Departments
Authors: Dugas Andrea F , Hsieh Yu-Hsiang , LoVecchio Frank , Moran Gregory J , Steele Mark T , Talan David A , Rothman Richard E ,   Emergency Department National Influenza Network Investigators, Stubbs Amy , Kemble Laurie , Beckham Danielle , Neal Niccole , Mulrow Mary , Krishnadasan Anusha , Pathmarajah Kavitha , Pathmarajah Kavitha , Torrez Raquel , Gonzalez Eva , Martin Gabina , Urzagaste Noemi Quinteros , Furoy Jacklyn , Hernandez Mayra , Collison Claire , Duval Anna , Beard Raphaelle , Avornu Ama , Medina Rebecca , McBryde Breana
Published: February 2019

Background

An accurate diagnosis of influenza is essential for appropriate antiviral treatment, in accordance with Centers for Disease Control and Prevention (CDC) guidelines. However, no clear guidance exists on which patients should be tested. We sought to develop a clinical decision guideline (CDG) to inform influenza testing decisions for those adult emergency department (ED) patients deemed appropriate for antiviral treatment by CDC guidelines.

Methods

A prospective cohort study was performed at 4 US EDs. From November 2013 to April 2014, we enrolled adult ED patients with fever or respiratory symptoms who met criteria for antiviral treatment, per 2013 CDC guidelines. All patients were tested for influenza using polymerase chain reaction. Data were randomly split into derivation (80%) and validation (20%) data sets. A discrete set of independent variables was selected by logistic regression, using the derivation set to create a scoring system, with a target sensitivity of at least 90%. The derived CDG was then validated.

Results

Of 1941 enrolled participants, 183 (9.4%) had influenza. The derived CDG included new or increased cough (2 points), headache (1 point), subjective fever (1 point), and triage temperature >100.4°C (1 point), with a score of ≥3 indicating influenza testing was warranted. The CDG had a sensitivity and specificity of 94.1% and 36.6%, respectively, in the derivation set and of 91.5% and 34.6%, respectively, in the validation set.

Conclusions

A CDG with high sensitivity was derived and validated. Incorporation into practice could standardize testing for high-risk patients in adult EDs during influenza seasons, potentially improving diagnoses and treatment.

Clinical Trial Registration

NCT01947049.
Psychosocial Barriers to Viral Suppression in a Community-based Sample of Human Immunodeficiency Virus–infected Men Who Have Sex With Men and People Who Inject Drugs in India
Authors: Prabhu Sandeep , McFall Allison M , Mehta Shruti H , Srikrishnan Aylur K , Kumar Muniratnam Suresh , Anand Santhanam , Shanmugam Saravanan , Celentano David D , Lucas Gregory M , Solomon Sunil S
Published: February 2019

Background

Little is known about the impact of psychosocial factors and substance use on viral suppression among human immunodeficiency virus (HIV)–infected key populations in resource-limited settings. Accordingly, we examined the association and interactions between depression, alcohol use, and recreational drug use on viral suppression among men who have sex with men (MSM) and people who inject drugs (PWID) in India.

Methods

MSM and PWID were recruited across India using respondent-driven sampling (RDS). Correlates of viral suppression were determined using Poisson regression models incorporating RDS-II weights. Two-way multiplicative interactions were assessed with separate models of all combinations of the 3 variables of interest using interaction terms; 3-way interactions were evaluated by stratifying 2-way interactions by the third variable.

Results

Among 1454 treatment-eligible HIV-infected MSM and 1939 PWID, older age (adjusted prevalence ratio [aPR], 1.14 for MSM; 1.41 for PWID) and higher HIV treatment literacy (aPR, 1.58 for MSM; 3.04 for PWID) were positively associated with viral suppression. Among MSM, there was evidence of a synergistic negative association between severe depression and recreational drug use (aPR, 0.37 [95% confidence interval {CI}, .16–.84]), alcohol dependence and recreational drug use (aPR, 0.45 [95% CI, .20–.99]), and severe depression, alcohol dependence, and recreational drug use (aPR, 0.23 [95% CI, .09–.57]). Among PWID, daily injection (aPR, 0.51 [95% CI, .31–.82]) was the primary barrier to suppression.

Conclusions

Incorporating psychosocial and harm-reduction services into differentiated care models targeting MSM and PWID in low-resource settings is critical to achieving the 90-90-90 HIV/AIDS targets.
Assessment of left ventricular outflow tract and aortic root: comparison of 2D and 3D transthoracic echocardiography with multidetector computed tomography
Authors: Visby Lasse , Kristensen Charlotte Burup , Pedersen Frederik Holm Grund , Sigvardsen Per Ejlstrup , Kofoed Klaus Fuglsang , Hassager Christian , Møgelvang Rasmus
Published: February 2019

Aims

Accurate echocardiographic assessment of left ventricular outflow tract (LVOT) and the aortic root is necessary for risk stratification and choice of appropriate treatment in patients with pathologies of the aortic valve and aortic root. Conventional 2D transthoracic echocardiographic (TTE) assessment is based on the assumption of a circular shaped LVOT and aortic root, although previous studies have indicated a more ellipsoid shape. 3D TTE and multidetector computed tomography (MDCT) applies planimetry and are not dependent on geometrical assumptions. The aim was to test accuracy, feasibility, and reproducibility of 3D TTE compared to 2D TTE assessment of LVOT and aortic root areas, with MDCT as reference.

Methods and results

We examined 51 patients with 2D/3D TTE and MDCT at the same day. All patients were re-examined with 2D/3D TTE on a different day to evaluate 2D and 3D re-test variability. Areas of LVOT, aortic annulus, and sinus were assessed using 2D, 3D TTE, and MDCT. Both 2D/3D TTE underestimated the areas compared to MDCT; however, 3D TTE areas were significantly closer to MDCT-areas. 2D vs. 3D mean MDCT-differences: LVOT 1.61 vs. 1.15 cm2, P = 0.019; aortic annulus 1.96 vs. 1.06 cm2, P < 0.001; aortic sinus 1.66 vs. 1.08 cm2, P = 0.015. Feasibility was 3D 76–79% and 2D 88–90%. LVOT and aortic annulus areas by 3D TTE had lowest variabilities; intraobserver coefficient of variation (CV) 9%, re-test variation CV 18–20%.

Conclusion

Estimation of LVOT and aortic root areas using 3D TTE is feasible, more precise and more accurate than 2D TTE.
Is low serum albumin associated with postoperative bronchopleural fistula in patients undergoing pulmonary resections?
Authors: Zhang Wenbiao , Li Shuangjiang , Chen Longqi , Zhou Qinghua
Published: February 2019

A best evidence topic in thoracic surgery was written according to a structured protocol. The question addressed was whether low serum albumin (sAlb) was associated with postoperative bronchopleural fistula (BPF) in patients undergoing pulmonary resections. Altogether 660 papers were found using the reported search, of which 5 retrospective cohort studies represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Four of the 5 cohort studies showed that the preoperative sAlb level in patients who experience a BPF was significantly lower than that in patients who did not experience a BPF. One of the 5 studies also reported that the incidence of BPF in patients with a lower sAlb (13.6%) was found to be significantly higher than that in patients with a higher sAlb (7.0%). The level of hypoalbuminaemia is not defined, but it may be <3.5 g/dl. This cut-off value of sAlb is assumed from the currently available retrospective data. No prospective study has been reported to address this issue. In summary, low preoperative sAlb can serve as a significant risk factor for postoperative BPF in patients undergoing pulmonary resections.
Are cities good for health? A study of the impacts of planned urbanization in China
Authors: Hou Bo , Nazroo James , Banks James , Marshall Alan
Published: February 2019

Background

Urbanization in developing countries is usually accompanied by migration to cities, making it a challenge to unpack the independent relationships between migration, urbanization and health, particularly in the presence of health-selective migration. Since 1978, unprecedented planned urbanization has taken place in China and further increases to the urban population are expected. This paper explored the impacts of urbanization in China through a comparative study of in situ urbanized population.

Methods

Using the China Health and Retirement Longitudinal Study (CHARLS), a nationally representative dataset for people aged 45 years or older, we compared self-assessed general health, depressive symptoms and waist circumference among three groups: (i) in situ urbanized-rural residents; (ii) rural residents; and (iii) urban residents. Using a model informed by the literature on the social determinants of health in later life, we investigated the patterning and drivers of differences in health outcomes between these three groups, in order to explore the impact of urbanization independent of the impact of migration.

Results

There are consistent advantages in health and less depression among urbanized-rural residents compared with the rural group; and this group has even better health outcomes than the urban group after adjusting for early life differences. However, this relationship is reversed for waist circumference. Socioeconomic circumstances and factors related to a planned urbanization partly explain these effects.

Conclusions

Urbanization in China has, on average, had an independent and positive effect on health and well-being. Planned urbanization could benefit people’s health in developing countries. It is likely that improved infrastructure is a key driver.
Analysis of hard-thresholding for distributed compressed sensing with one-bit measurements
Authors: Maly Johannes , Palzer Lars
Published: February 2019

A simple hard-thresholding operation is shown to be able to uniformly recover $L$ signals $\textbf{x}_1,...,\textbf{x}_L \in{\mathbb{R}}^n$ that share a common support of size $s$ from $m = \mathscr{O}(s)$ one-bit measurements per signal if $L \geqslant \ln (en/s)$. This result improves the single signal recovery bounds with $m = \mathscr{O}(s\ln (en/s))$ measurements in the sense that asymptotically fewer measurements per non-zero entry are needed. Numerical evidence supports the theoretical considerations.
Twist Automorphisms on Quantum Unipotent Cells and Dual Canonical Bases
Authors: Kimura Yoshiyuki , Oya Hironori
Published: February 2019

In this paper, we construct twist automorphisms on quantum unipotent cells, which are quantum analogues of the Berenstein–Fomin–Zelevinsky twist automorphisms on unipotent cells. We show that those quantum twist automorphisms preserve the dual canonical bases of quantum unipotent cells. Moreover, we prove that quantum twist automorphisms are described by the syzygy functors for representations of preprojective algebras in the symmetric case. This is the quantum analogue of Geiß–Leclerc–Schröer’s description, and Geiß–Leclerc–Schröer’s results are essential in our proof. As a consequence, we show that quantum twist automorphisms are compatible with quantum cluster monomials. The 6-periodicity of specific quantum twist automorphisms is also verified.
Towards the Finite Slope Part for GLn
Authors: Breuil Christophe , Herzig Florian
Published: February 2019

Let $L$ be a finite extension of ${\mathbb{Q}}_p$ and $n\geq 2$. We associate to a crystabelline $n$-dimensional representation of ${\operatorname{Gal}}(\overline L/L)$ satisfying mild genericity assumptions a finite length locally ${\mathbb{Q}}_p$-analytic representation of ${\operatorname{GL}}_n(L)$. In the crystalline case and in a global context, using the recent results on the locally analytic socle from [6], we prove that this representation indeed occurs in spaces of $p$-adic automorphic forms. We then use this latter result in the ordinary case to show that certain “ordinary” $p$-adic Banach space representations constructed in our previous work appear in spaces of $p$-adic automorphic forms. This gives strong new evidence to our previous conjecture in the $p$-adic case.
Tied Labour, Savings and Rural Labour Market Wages: Evidence from a Framed Field Experiment
Authors: Nanyiti Aisha , Pamuk Haki , Bulte Erwin
Published: February 2019

How does the introduction of tied labour or a saving product affect labour market decisions and wages in rural agricultural labour markets? We develop a theoretical model of labour tying that incorporates diminishing marginal returns to consumption and inequality (behindness) aversion in the context of a rural agricultural labour market with seasonally fluctuating demand for labour, and test model predictions using a framed field experiment (modified ultimatum game) in rural Uganda. Our main findings are that (1) wages fluctuate with productivity, (2) access to tied contracts decreases wages for casual labour and (3) access to a saving technology does not improve wages for tied labour. Consistent with model predictions and earlier theory, we empirically find that income for workers goes down (and income for landlords goes up) if an institutional innovation enables consumption smoothing by workers (tied contracts or a saving technology).
A Novel Liquid Chromatography Tandem Mass Spectrometry Technique using Multi-Period-Multi-Experiment of MRM-EPI-MRM3 with Library Matching for Simultaneous Determination of Amphetamine Type Stimulants Related Drugs in Whole Blood, Urine and Dried Blood Stain (DBS)—Application to Forensic Toxicology Cases in Malaysia
Authors: Zubaidi Fathiah A , Choo Yeun-Mun , Tan Guan-Huat , Hamid Hamimah Abd , Choy Yap Ken
Published: February 2019

A novel mass spectrometry detection technique based on a multi-period and multi- experiment (MRM-EPI-MRM3) with library matching in a single run for fast and rapid screening and identification of amphetamine type stimulants (ATS) related drugs in whole blood, urine and dried blood stain was developed and validated. The ATS-related drugs analyzed in this study include ephedrine, pseudoephedrine, amphetamine, methamphetamine, MDMA (3,4-Methylenedioxymethamphetamine), MDA (3,4-Methylenedioxyamphetamine), MDEA (3,4-Methylenedioxy-N-ethylamphetamine) and phentermine. The relative standard deviation for inter and intraday was less than 15% while recoveries ranged from 80% to 120% for all three matrices, i.e., whole blood, urine and dried blood stain. All compounds gave library matching percentage of more than 85% based on the purity. This method was proven to be simple and robust, and provide high confident results complemented with library matching confirmation.
Shipping Fools: Foucault’s Wandering Madman and Civic Responsibility in Late Medieval Germany
Authors: Koenig Anne M
Published: February 2019

Few aspects of Michel Foucault’s seminal study The History of Madness have been more widely derided and debunked than Foucault’s assertion that medieval mad persons sailed the rivers of Europe as a kind of real-world counterpart to the literary and artistic trope of the ship of fools. But while Foucault was not correct in many of his assumptions, he also was not entirely wrong to draw attention to the river. Based on archival research in Nuremberg, Munich, and Frankfurt, this article offers a critical insight into how some medieval cities managed their problematic mad. In particular, it uncovers the widespread and little-understood practice of expelling the mad from late medieval German towns. It argues that the practice of expulsion was multilayered, ranging from relatively benign trips to convey a mad person back home, to official banishments of criminal mad men and women. It finds that most of the expelled mad, however, were simply sent away, out of the city walls and away from municipal responsibility. These expulsions appear frequently in fifteenth-century records and reveal that one particular kind of route was preferred by cities in Southern Germany: the river. In fact, municipal leaders routinely used the Danube, the Isar, and the Main rivers as the best way to rid their towns of difficult or friendless mad persons. While such river journeys did not take place on “ships of fools,” the river was thus a critical and meaningful part of the geographic and cultural landscapes of madness.
Spatio-temporal expression of phytoglobin: a determining factor in the NO specification of cell fate
Authors: Stasolla Claudio , Huang Shuanglong , Hill Robert D , Igamberdiev Abir U
Published: February 2019

Plant growth and development rely on the orchestration of cell proliferation, differentiation, and ultimately death. After varying rounds of divisions, cells respond to positional cues by acquiring a specific fate and embarking upon distinct developmental pathways which might differ significantly from those of adjacent cells exposed to diverse cues. Differential cell behavior is most apparent in response to stress, when some cells might be more vulnerable than others to the same stress condition. This appears to be the case for stem cells which show abnormal features of differentiation and ultimately signs of deterioration at the onset of specific types of stress such as hypoxia and water deficit. A determining factor influencing cell behavior during growth and development, and cell response during conditions of stress is nitric oxide (NO), the level of which can be regulated by phytoglobins (Pgbs), known scavengers of NO. The modulation of NO by Pgbs can be cell, tissue, and/or organ specific, as revealed by the expression patterns of Pgbs dictated by the presence of distinct cis-regulatory elements in their promoters. This review discusses how the temporal and spatial Pgb expression pattern influences NO-mediated responses and ultimately cell fate acquisition in plant developmental processes.
Facultative crassulacean acid metabolism in a C3–C4 intermediate
Authors: Winter Klaus , Sage Rowan F , Edwards Erika J , Virgo Aurelio , Holtum Joseph A M
Published: February 2019

Portulaca cryptopetala is a C3–C4 intermediate species that exhibits facultative CAM suggesting that in Portulaca facultative CAM is ancestral to C4.