bluuebunny/crossref_metadata_2025_split huggingface dataset:
FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human
Authors: Xie Gui-Yan , Xia Mengxuan , Miao Ya-Ru , Luo Mei , Zhang Qiong , Guo An-Yuan 
Published: December 2019

Abstract

Summary
Transcription factors (TFs) and microRNAs (miRNAs) are two kinds of important regulators for transcriptional and post-transcriptional regulations. Understanding cross-talks between the two regulators and their targets is critical to reveal complex molecular regulatory mechanisms. Here, we developed FFLtool, a web server for detecting potential feed forward loop (FFL) of TF-miRNA-target regulation in human. In FFLtool, we integrated comprehensive regulations of TF-target and miRNA-target, and developed two functional modules: (i) The ‘FFL Analysis’ module can detect potential FFLs and internal regulatory networks in a user-defined gene set. FFLtool also provides three levels of evidence to illustrate the reliability for each FFL and enrichment functions for co-target genes of the same TF and miRNA; (ii) The ‘Browse FFLs’ module displays FFLs comprised of differentially or specifically expressed TFs and miRNAs and their target genes in cancers. FFLtool is a valuable resource for investigating gene expression regulation and mechanism study in biological processes and diseases.

Availability and implementation
FFLtool is available on http://bioinfo.life.hust.edu.cn/FFLtool/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Neural Systems for Own-body Processing Align with Gender Identity Rather Than Birth-assigned Sex
Authors: Majid D S Adnan , Burke Sarah M , Manzouri Amirhossein , Moody Teena D , Dhejne Cecilia , Feusner Jamie D , Savic Ivanka 
Published: December 2019

Abstract
Gender identity is a core aspect of self-identity and is usually congruent with birth-assigned sex and own body sex-perception. The neuronal circuits underlying gender identity are unknown, but greater awareness of transgenderism has sparked interest in studying these circuits. We did this by comparing brain activation and connectivity in transgender individuals (for whom gender identity and birth-assigned sex are incongruent) with that in cisgender controls (for whom they are congruent) when performing a body self-identification task during functional magnetic resonance imaging. Thirty transgender and 30 cisgender participants viewed images of their own bodies and bodies morphed in sex toward or opposite to birth-assigned sex, rating each image to the degree they identified with it. While controls identified with images of themselves, transgender individuals identified with images morphed “opposite” to their birth-assigned sex. After covarying out the effect of self-similarity ratings, both groups activated similar self- and body-processing systems when viewing bodies that aligned with their gender identity rather than birth-assigned sex. Additionally, transgender participants had greater limbic involvement when viewing ambiguous, androgynous images of themselves morphed toward their gender identity. These results shed light on underlying self-processing networks specific to gender identity and uncover additional involvement of emotional processing in transgender individuals.
Emergence of an Invariant Representation of Texture in Primate Somatosensory Cortex
Authors: Lieber Justin D , Bensmaia Sliman J 
Published: December 2019

Abstract
A major function of sensory processing is to achieve neural representations of objects that are stable across changes in context and perspective. Small changes in exploratory behavior can lead to large changes in signals at the sensory periphery, thus resulting in ambiguous neural representations of objects. Overcoming this ambiguity is a hallmark of human object recognition across sensory modalities. Here, we investigate how the perception of tactile texture remains stable across exploratory movements of the hand, including changes in scanning speed, despite the concomitant changes in afferent responses. To this end, we scanned a wide range of everyday textures across the fingertips of rhesus macaques at multiple speeds and recorded the responses evoked in tactile nerve fibers and somatosensory cortical neurons (from Brodmann areas 3b, 1, and 2). We found that individual cortical neurons exhibit a wider range of speed-sensitivities than do nerve fibers. The resulting representations of speed and texture in cortex are more independent than are their counterparts in the nerve and account for speed-invariant perception of texture. We demonstrate that this separation of speed and texture information is a natural consequence of previously described cortical computations.
Wildcat bankers or political failure? The Irish financial pantomime, 1797–1826
Authors: Kenny Seán , Turner John D 
Published: December 2019

AbstractUsing a new biography of banks, we examine the stability of Irish banking from 1797 to 1826 by constructing a failure rate series. We find that the ultimate cause of the frequent and severe banking crises was the crisis-prone structure of the banking system, which was designed to benefit the political elite. There is little evidence to suggest that wildcat banking or the failure of the Bank of Ireland to act as a lender of last resort were to blame. We also find that the main economic effect of the episodic crises was major diminutions in the money supply.
Some Kinds of Home: Home, Transnationality and Belonging in Noviolet Bulawayo’s We Need New Names
Authors: Nyambi Oliver , Makombe Rodwell , Motahane Nonki 
Published: December 2019

Abstract
Over the years, the notion of home has permeated disciplinary, inter- and cross-disciplinary enquiries into the human condition. In recent years, ideas, constructions and perceptions of ‘homes’ have been further complicated by constant shifts in conceptions and practices of transnational mobilities that have informed and disrupted ways of seeing, making and re-making homes at home and away from ‘home’. In this article, we draw from Sara Ahmed’s idea of home as ‘a space within us’ to read the novel We Need New Names (2013) by the transnational Zimbabwean writer NoViolet Bulawayo as a text that interrogates the intertwined and complicated relationship between home, transnational identity and belonging. Focusing on the protagonist’s experiences in both Zimbabwe and America, this article examines the idea of home as it refracts uniquely twenty-first-century experiences, perceptions and notions of transnational spaces, and shapes certain notions of identity, transnationality and belonging in We Need New Names.
IQ motif-containing GTPase-activating protein 1 is essential for the optimal maintenance of lung ILC2s
Authors: Tayama Shunichi , Okuyama Yuko , Phung Hai The , Asao Atsuko , Kobayashi Shuhei , Musha Tomomi , Machiyama Tomoaki , Sakurai Tsuyoshi , Zhang Chengming , Ushio-Fukai Masuko , Kawabe Takeshi , So Takanori , Ishii Naoto 
Published: December 2019

AbstractGroup 2 innate lymphoid cells (ILC2s) play critical roles in type 2 immunity and are crucial for pathogenesis of various types of inflammatory disease. IQ motif-containing GTPase-activating protein 1 (IQGAP1) is a ubiquitously expressed scaffold protein that is involved in multiple cellular functions such as cell survival and trafficking. While the roles for IQGAP1 in T and B lymphocytes have been uncovered, the physiological significance of IQGAP1 in innate lymphocytes remains to be elucidated. In the current study, we demonstrate that using bone marrow chimeras, the deficiency of IQGAP1 caused an impaired survival of lung ILC2s in a cell-intrinsic manner and that Iqgap1−/− mice displayed decreased accumulation of ILC2s after administration of papain and thereby reduced the pathology of the disease. Moreover, Iqgap1−/− ILC2s showed a significantly enhanced apoptosis as compared to wild-type ILC2s under both steady-state and inflammatory conditions. Together these results identify for the first time that IQGAP1 is essential for homeostasis of ILC2s in the lung.
Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Campylobacter jejuni and Campylobacter coli isolated from cases of diarrhoeal disease in England and Wales, 2015–16
Authors: Painset Anaïs , Day Martin , Doumith Michel , Rigby Jonathan , Jenkins Claire , Grant Kathie , Dallman Timothy J , Godbole Gauri , Swift Craig 
Published: December 2019

Abstract

Objectives
To compare and evaluate phenotypic and genotypic methods for the detection of antimicrobial resistance (AMR) in Campylobacter jejuni and Campylobacter coli in England and Wales.

Methods
WGS data from 528 isolates of Campylobacter spp. (452 C. jejuni and 76 C. coli) from human (494), food (21) and environmental (2) sources, collected between January 2015 and December 2016, and from the PHE culture collection (11) were mapped to genes known to be associated with phenotypic resistance to antimicrobials in the genus. Phenotypic antibiotic susceptibility (erythromycin, ciprofloxacin, tetracycline, gentamicin and streptomycin) testing using an in-agar dilution method was performed on all isolates.

Results
Concordance between phenotypic resistance and the presence of corresponding AMR determinants was 97.5% (515/528 isolates). Only 13 out of 528 isolates (10 C. jejuni and 3 C. coli) had discordant interpretations for at least one of the five antibiotics tested, equating to a total of 15 (0.6%) discrepancies out of 2640 isolate/antimicrobial combinations. Seven discrepant results were genotypically resistant but phenotypically susceptible (major errors) and eight discrepant results were genotypically susceptible but phenotypically resistant (very major errors).

Conclusions
The use of this bioinformatics approach for predicting AMR from WGS data for routine public health surveillance is a reliable method for real-time monitoring of changing AMR patterns in isolates of C. jejuni and C. coli.
Breast Cancer Mortality After Implementation of Organized Population-Based Breast Cancer Screening in Norway
Authors: Sebuødegård Sofie , Botteri Edoardo , Hofvind Solveig 
Published: December 2019

Abstract

Background
We estimated breast cancer (BC) mortality reduction associated with invitations to a nationwide population-based screening program and with changes in treatment.

Materials and methods
BreastScreen Norway started in 1996 and became nationwide in 2005. It invites women aged 50–69 years to biennial mammographic screening. We retrieved individual-level data for 1 340 333 women from national registries. During 1996–2014 (screening window), women contributed person-years in noninvited and invited periods. We created comparable periods for 1977–1995 (prescreening window) by dividing the follow-up time for each woman into pseudo-noninvited and pseudo-invited periods. We estimated BC mortality for the four periods, using the so-called evaluation model: counting BC deaths in each period for all women diagnosed within the period and counting BC deaths and person-years after screening-age for those diagnosed within screening age. We used a multivariable flexible parametric survival model to estimate hazard ratio (HR) for the effect of invitation and improved treatment.

Results
Using the regression approach, we found 5818 BC deaths across 16 533 281 person-years. Invitations to screening reduced BC mortality by 20% (HR = 0.80, 95% confidence interval [CI] = 0.70 to 0.91) among women 50 years and older and by 25% (HR = 0.75, 95% CI = 0.65 to 0.86) among screening-aged women. The treatment effect was 23% (HR = 0.77, 95% CI = 0.65 to 0.92) for women 50 years and older and 17% (HR = 0.83, 95% CI = 0.74 to 0.94) for screening-aged women.

Conclusion
We observed a similar reduction in BC mortality associated with invitations to screening and improvements in treatment during 1977–2014, among women 50 years and older.
Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs
Authors: Arvola René M , Chang Chung-Te , Buytendorp Joseph P , Levdansky Yevgen , Valkov Eugene , Freddolino Lydia , Goldstrohm Aaron C 
Published: December 2019

Abstract
Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility and neurological functions in Drosophila. We sought to identify the mechanism of Pumilio-mediated repression and find that it accelerates degradation of target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique to Pumilio orthologs. We show that the repressive activities of the Pumilio RDs depend on specific subunits of the Ccr4–Not (CNOT) deadenylase complex. Depletion of Pop2, Not1, Not2, or Not3 subunits alleviates Pumilio RD-mediated repression of protein expression and mRNA decay, whereas depletion of other CNOT components had little or no effect. Moreover, the catalytic activity of Pop2 deadenylase is important for Pumilio RD activity. Further, we show that the Pumilio RDs directly bind to the CNOT complex. We also report that the decapping enzyme, Dcp2, participates in repression by the N-terminus of Pumilio. These results support a model wherein Pumilio utilizes CNOT deadenylase and decapping complexes to accelerate destruction of target mRNAs. Because the N-terminal RDs are conserved in mammalian Pumilio orthologs, the results of this work broadly enhance our understanding of Pumilio function and roles in diseases including cancer, neurodegeneration and epilepsy.
Resonance width for a particle–core coupling model with a square-well potential
Authors: Hagino K , Sagawa H , Kanaya S , Odahara A 
Published: December 2019

Abstract
We derive a compact formula for the width of a multi-channel resonance state. To this end, we use a deformed square-well potential and solve the coupled-channels equations. We obtain the $S$-matrix in the Breit–Wigner form, from which partial widths can be extracted. We apply the resultant formula to a deformed nucleus and discuss the behavior of partial width for an $s$-wave channel.
Serological testing in small vessel vasculitis
Authors: Segelmark Mårten 
Published: December 2019

Abstract
Serological analysis has a central role in the diagnostic work-up of patients with suspected small vessel vasculitis, both for establishing a specific diagnosis and for the monitoring of response to therapy. Autoantibodies can be detected in all forms of primary small vessel vasculitis as well as in the most common forms of secondary vasculitis. For primary vasculitis the most important serological test is for ANCA. ANCA can be found in 75–95% of patients with pauci-immune small vessel vasculitis leading to this subgroup of vasculitides being named ANCA associated vasculitis. ANCA levels often follow this disease course, but the value of serial ANCA testing is controversial. Other important autoantibodies in primary small vessel vasculitis are anti-glomerular basement membrane antibodies, anti-C1q, anti-galactose deficient IgA and cryoglobulins. A wide variety of systemic inflammatory diseases and infections can be complicated by small vessel vasculitis and detected by serological testing. Important examples are SLE, rheumatoid arthritis, Hepatitis C and HIV.
Nerve Growth Factor Protects Against Pyrethroid-Induced Endoplasmic Reticulum (ER) Stress in Primary Hippocampal Neurons
Authors: Hossain Muhammad M , Richardson Jason R 
Published: December 2019

Abstract
Neurotrophins are a family of growth factors crucial for growth and survival of neurons in the developing and adult brain. Reduction in neurotrophin levels is associated with reduced neurogenesis and cognitive deficits in rodents. Recently, we demonstrated that long-term exposure to low levels of the pyrethroid pesticide deltamethrin causes hippocampal endoplasmic reticulum (ER) stress and learning deficits in mice. Here, we found that nerve growth factor (NGF) mRNA and protein were selectively reduced in the hippocampus of deltamethrin-treated mice. To explore potential mechanisms responsible for this observation, we employed mouse primary hippocampal neurons. Exposure of neurons to deltamethrin (1–5 μM) caused ER stress as indicated by increased levels of C/EBP-homologous protein (CHOP) and glucose-regulated protein 78 (GRP78). These changes were accompanied by increased levels of caspase-12, activated caspase-3, and decreased levels of NGF. Inhibition of ER stress with the eukaryotic initiation factor 2 alpha (eIF2α) inhibitor salubrinal abolished deltamethrin-induced activation of caspase-12 and caspase-3, and restored NGF levels. Furthermore, deltamethrin decreased Akt (protein kinase B) phosphorylation, which was significantly prevented by co-treatment with NGF or SC-79 in cells. Collectively, these results demonstrate that the loss of NGF following ER stress may contribute to deltamethrin-induced apoptosis in the hippocampus through the Akt signaling pathway, and that this may provide a plausible mechanism for impaired learning and memory observed following exposure of mice to deltamethrin.
Patients with left ventricle assist devices presenting for thoracic surgery and lung resection: tips, tricks and evidence
Authors: Hayes Tim , Charlesworth Mike , Garcia Miguel 
Published: December 2019

Purpose of review
Over a thousand left ventricular-assist device (LVAD) implants were performed for heart failure destination therapy in 2017. With increasing survival, we are seeing increasing numbers of patients present for noncardiac surgery, including resections for cancer. This article will review the relevant literature and guidelines for patients with LVADs undergoing thoracic surgery, including lung resection.

Recent findings
The International Society for Heart and Lung Transplant Mechanically Assisted Circulatory Support Registry has received data on more than 16 000 patients with LVADs. Four-year survival is more than 60% for centrifugal devices. There are increasing case reports, summaries and recommendations for patients with LVADs undergoing noncardiac surgery. However, data on thoracic surgery is restricted to case reports.

Summary
Successful thoracic surgery requires understanding of the LVAD physiology. Modern devices are preload dependent and afterload sensitive. The effects of one-lung ventilation, including hypoxia and hypercapnia, may increase pulmonary vascular resistance and impair the right ventricle. Successful surgery necessitates a multidisciplinary approach, including thorough preoperative assessment; optimization and planning of intraoperative management strategies; and approaches to anticoagulation, right ventricular failure and LVAD flow optimization. This article discusses recent evidence on these topics.
Cochlear Implant Data Logs Predict Children’s Receptive Vocabulary
Authors: Busch Tobias , Vermeulen Anneke , Langereis Margreet , Vanpoucke Filiep , van Wieringen Astrid 
Published: December 2019

Objectives:
The data logs of Cochlear Nucleus cochlear implant (CI) sound processors show large interindividual variation in children’s daily CI use and auditory environments. This study explored whether these differences are associated with differences in the receptive vocabulary of young implanted children.

Design:
Data of 52 prelingually deaf children, who had received a CI before 3 years of age, were obtained from their clinical records. In total, 73 Peabody Picture Vocabulary tests and CI data logs for 1 year preceding each test were collected. The data logs were used to determine the children’s average daily amount of CI use and exposure to speech, speech in noise, noise, music, and quiet. In addition, information was collected about other potential predictors of language abilities, namely gender, age, age at implantation, etiology of deafness, educational placement, and implantation mode (unilateral, bilateral). Model selection with Akaike’s information criterion was used to determine which data-logging metrics, other variables, and combinations of both best predict receptive vocabulary scores.

Results:
The data showed a strong positive association between receptive vocabulary and daily CI use, and a negative association between receptive vocabulary and daily exposure to music. Associations with the data logs’ speech and noise metrics were less clear. The most important other variable was educational placement. The best model performance was achieved when data logs and other information were combined.

Conclusions:
The results emphasize the importance of consistent CI use and a rich auditory environment for the early language development of young CI users. The study also shows that CI data logs capture information about children’s environment and CI use that are related to language performance and can help to detect and address problems and improve the auditory rehabilitation after cochlear implantation.
Spectral Contrast Effects Reveal Different Acoustic Cues for Vowel Recognition in Cochlear-Implant Users
Authors: Feng Lei , Oxenham Andrew J. 
Published: December 2019

Objectives:
The identity of a speech sound can be affected by the spectrum of a preceding stimulus in a contrastive manner. Although such aftereffects are often reduced in people with hearing loss and cochlear implants (CIs), one recent study demonstrated larger spectral contrast effects in CI users than in normal-hearing (NH) listeners. The present study aimed to shed light on this puzzling finding. We hypothesized that poorer spectral resolution leads CI users to rely on different acoustic cues not only to identify speech sounds but also to adapt to the context.

Design:
Thirteen postlingually deafened adult CI users and 33 NH participants (listening to either vocoded or unprocessed speech) participated in this study. Psychometric functions were estimated in a vowel categorization task along the /i/ to /ε/ (as in “bit” and “bet”) continuum following a context sentence, the long-term average spectrum of which was manipulated at the level of either fine-grained local spectral cues or coarser global spectral cues.

Results:
In NH listeners with unprocessed speech, the aftereffect was determined solely by the fine-grained local spectral cues, resulting in a surprising insensitivity to the larger, global spectral cues utilized by CI users. Restricting the spectral resolution available to NH listeners via vocoding resulted in patterns of responses more similar to those found in CI users. However, the size of the contrast aftereffect remained smaller in NH listeners than in CI users.

Conclusions:
Only the spectral contrasts used by listeners contributed to the spectral contrast effects in vowel identification. These results explain why CI users can experience larger-than-normal context effects under specific conditions. The results also suggest that adaptation to new spectral cues can be very rapid for vowel discrimination, but may follow a longer time course to influence spectral contrast effects.