bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of the deep convolutional neural network based magnetic resonance image scoring algorithm for differentiating between tuberculous and pyogenic spondylitis
Authors: Kim Kiwook , Kim Sungwon , Lee Young Han , Lee Seung Hyun , Lee Hye Sun , Kim Sungjun 
Published: August 2018

AbstractThe purpose of this study was to evaluate the performance of the deep convolutional neural network (DCNN) in differentiating between tuberculous and pyogenic spondylitis on magnetic resonance (MR) imaging, compared to the performance of three skilled radiologists. This clinical retrospective study used spine MR images of 80 patients with tuberculous spondylitis and 81 patients with pyogenic spondylitis that was bacteriologically and/or histologically confirmed from January 2007 to December 2016. Supervised training and validation of the DCNN classifier was performed with four-fold cross validation on a patient-level independent split. The object detection and classification model was implemented as a DCNN and was designed to calculate the deep-learning scores of individual patients to reach a conclusion. Three musculoskeletal radiologists blindly interpreted the images. The diagnostic performances of the DCNN classifier and of the three radiologists were expressed as receiver operating characteristic (ROC) curves, and the areas under the ROC curves (AUCs) were compared using a bootstrap resampling procedure. When comparing the AUC value of the DCNN classifier (0.802) with the pooled AUC value of the three readers (0.729), there was no significant difference (P = 0.079). In differentiating between tuberculous and pyogenic spondylitis using MR images, the performance of the DCNN classifier was comparable to that of three skilled radiologists.
Gene expression profiling during hibernation in the European hamster
Authors: Gautier Célia , Bothorel Béatrice , Ciocca Dominique , Valour Damien , Gaudeau Albane , Dupré Clémence , Lizzo Giulia , Brasseur Chantal , Riest-Fery Isabelle , Stephan Jean-Philippe , Nosjean Olivier , Boutin Jean A. , Guénin Sophie-Pénélope , Simonneaux Valérie 
Published: August 2018

AbstractHibernation is an exceptional physiological response to a hostile environment, characterized by a seasonal period of torpor cycles involving dramatic reductions of body temperature and metabolism, and arousal back to normothermia. As the mechanisms regulating hibernation are still poorly understood, here we analysed the expression of genes involved in energy homeostasis, torpor regulation, and daily or seasonal timing using digital droplet PCR in various central and peripheral tissues sampled at different stages of torpor/arousal cycles in the European hamster. During torpor, the hypothalamus exhibited strongly down-regulated gene expression, suggesting that hypothalamic functions were reduced during this period of low metabolic activity. During both torpor and arousal, many structures (notably the brown adipose tissue) exhibited altered expression of deiodinases, potentially leading to reduced tissular triiodothyronine availability. During the arousal phase, all analysed tissues showed increased expression of the core clock genes Per1 and Per2. Overall, our data indicated that the hypothalamus and brown adipose tissue were the tissues most affected during the torpor/arousal cycle, and that clock genes may play critical roles in resetting the body’s clocks at the beginning of the active period.
Macrophage mannose receptor, CD206, predict prognosis in patients with pulmonary tuberculosis
Authors: Suzuki Yuzo , Shirai Masahiro , Asada Kazuhiro , Yasui Hideki , Karayama Masato , Hozumi Hironao , Furuhashi Kazuki , Enomoto Noriyuki , Fujisawa Tomoyuki , Nakamura Yutaro , Inui Naoki , Shirai Toshihiro , Hayakawa Hiroshi , Suda Takafumi 
Published: August 2018

AbstractTuberculosis (TB) remains a leading cause of fatal infectious disease. Accumulations of macrophages are found in infected sites; thus, we hypothesized that a marker of activated macrophages may be related to prognosis of pulmonary TB (PTB). This study investigated serum soluble macrophage mannose receptor, sCD206, in PTB and examined its clinical significance. First, the concentration of sCD206 was measured in the sera of 96 patients with PTB (Tenryu cohort), and in pleural effusions from 29 patients with TB pleurisy. These were verified in another independent cohort (Shizuoka cohort). We found increased concentrations of sCD206 in sera, but not in pleural effusions of PTB patients. Notably, PTB patients with poor prognosis showed significantly higher levels of serum sCD206. At a cut-off value of 1,600 ng/mL in the Tenryu cohort, sCD206 predicted prognosis of PTB with area under the curve 0.847, sensitivity 77.3%, and specificity 86.5%. These results were validated in the Shizuoka cohort. Pathological analyses showed concordance of enhanced CD206 expression in lung and pleural tissues with caseating granuloma in TB. Serum sCD206 increased in PTB and was associated with prognosis. sCD206 is a potential biomarker for PTB.
Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls
Authors: Behravan Hamid , Hartikainen Jaana M. , Tengström Maria , Pylkäs Katri , Winqvist Robert , Kosma Veli–Matti , Mannermaa Arto 
Published: August 2018

AbstractWe propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree boosting method followed by an adaptive iterative SNP search to capture complex non-linear SNP-SNP interactions and consequently, obtain group of interacting SNPs with high BC risk-predictive potential. We also propose a support vector machine formed by the identified SNPs to classify BC cases and controls. Our approach achieves mean average precision (mAP) of 72.66, 67.24 and 69.25 in discriminating BC cases and controls in KBCP, OBCS and merged KBCP-OBCS sample sets, respectively. These results are better than the mAP of 70.08, 63.61 and 66.41 obtained by using a polygenic risk score model derived from 51 known BC-associated SNPs, respectively, in KBCP, OBCS and merged KBCP-OBCS sample sets. BC subtype analysis further reveals that the 200 identified KBCP SNPs from the proposed method performs favorably in classifying estrogen receptor positive (ER+) and negative (ER−) BC cases both in KBCP and OBCS data. Further, a biological analysis of the identified SNPs reveals genes related to important BC-related mechanisms, estrogen metabolism and apoptosis.
Eye movement characteristics reflected fatigue development in both young and elderly individuals
Authors: Zargari Marandi Ramtin , Madeleine Pascal , Omland Øyvind , Vuillerme Nicolas , Samani Afshin 
Published: August 2018

AbstractFatigue can develop during prolonged computer work, particularly in elderly individuals. This study investigated eye movement characteristics in relation to fatigue development. Twenty young and 18 elderly healthy adults were recruited to perform a prolonged functional computer task while their eye movements were recorded. The task lasted 40 minutes involving 240 cycles divided into 12 segments. Each cycle consisted of a sequence involving memorization of a pattern, a washout period, and replication of the pattern using a computer mouse. The participants rated their perceived fatigue after each segment. The mean values of blink duration (BD) and frequency (BF), saccade duration (SCD) and peak velocity (SPV), pupil dilation range (PDR), and fixation duration (FD) along with the task performance based on clicking speed and accuracy, were computed for each task segment. An increased subjective evaluation of fatigue suggested the development of fatigue. BD, BF, and PDR increased whereas SPV and SCD decreased over time in the young and elderly groups. Longer FD, shorter SCD, and lower task performance were observed in the elderly compared with the young group. The present findings provide a viable approach to develop a computational model based on oculometrics to track fatigue development during computer work.
Independent modes of disease repair by AIM protein distinguished in AIM-felinized mice
Authors: Sugisawa Ryoichi , Komatsu Ginga , Hiramoto Emiri , Takeda Naoki , Yamamura Ken-ichi , Arai Satoko , Miyazaki Toru 
Published: August 2018

AbstractTissue macrophage-derived apoptosis inhibitor of macrophage (AIM, encoded bycd5lgene) is a circulating protein that has suppressive functions in a broad range of diseases including obesity, liver steatosis, hepatocellular carcinoma (HCC), and acute kidney injury (AKI). In healthy states, high levels of AIM circulate in the inactivated state by associating with the immunoglobulin M (IgM) pentamer in the blood, whereas during AKI, AIM dissociates from IgM and gains disease repair activity. Here, we assessed whether AIM activation via its release from IgM is required to ameliorate other diseases. To this end, we employed a mouse line in which mouse AIM was replaced with feline AIM (AIM-felinized mice). Because feline AIM rarely dissociates from IgM due to its extremely high binding affinity for IgM, these mice exhibited deficient AKI repair as in cats. When fed a high-fat diet (HFD), similar to AIM-deficient (AIM−/−) mice, AIM-felinized mice exhibited enhanced triacylglycerol deposition in visceral adipocytes and hepatocytes, resulting in more prominent obesity and fatty liver than in wild-type mice. In contrast, the incidence of HCC after a 1-year HFD was remarkably lower in AIM-felinized mice than inAIM−/−mice, suggesting that AIM produced by liver Kupffer macrophages might directly facilitate the elimination of HCC cells. Accordingly, the marked deposition of AIM accompanied by accumulation of Kupffer cells was obvious during HCC tumour development in AIM-felinized mice. Δsµ mice, which harbour almost no circulating AIM due to the lack of secreted IgM, showed a phenotype comparable with that of AIM-felinized mice in prevention of those diseases. Thus, blood AIM released from IgM contributes to suppression of obesity and fatty liver as in AKI, whereas macrophage-derived noncirculating AIM mainly prevents HCC development. Our study depicted two different modes of disease prevention/repair facilitated by AIM, which could be the basis for HCC therapy that works by increasing AIM expression in macrophages.
Gulf war illness-related chemicals increase CD11b/c+ monocyte infiltration into the liver and aggravate hepatic cholestasis in a rodent model
Authors: Petrescu Anca D. , Grant Stephanie , Frampton Gabriel , McMillin Matthew , Kain Jessica , Kodali Maheedhar , Shetty Ashok K. , DeMorrow Sharon 
Published: August 2018

AbstractGulf War Illness (GWI) is a chronic multisymptom disorder affecting veterans of the 1990–91 Gulf war. GWI was linked with exposure to chemicals including the nerve gas prophylactic drug pyridostigmine-bromide (PB) and pesticides (DEET, permethrin). Veterans with GWI exhibit prolonged, low-level systemic inflammation, though whether this impacts the liver is unknown. While no evidence exists that GWI-related chemicals are hepatotoxic, the prolonged inflammation may alter the liver’s response to insults such as cholestatic injury. We assessed the effects of GWI-related chemicals on macrophage infiltration and its subsequent influence on hepatic cholestasis. Sprague Dawley rats were treated daily with PB, DEET and permethrin followed by 15 minutes of restraint stress for 28 days. Ten weeks afterward, GWI rats or naïve age-matched controls underwent bile duct ligation (BDL) or sham surgeries. Exposure to GWI-related chemicals alone increased IL-6, and CD11b+F4/80− macrophages in the liver, with no effect on biliary mass or hepatic fibrosis. However, pre-exposure to GWI-related chemicals enhanced biliary hyperplasia and fibrogenesis caused by BDL, compared to naïve rats undergoing the same surgery. These data suggest that GWI patients could be predisposed to developing worse liver pathology due to sustained low-level inflammation of the liver when compared to patients without GWI.
A novel cell-based screening assay for small-molecule MYB inhibitors identifies podophyllotoxins teniposide and etoposide as inhibitors of MYB activity
Authors: Yusenko Maria , Jakobs Anke , Klempnauer Karl-Heinz 
Published: August 2018

AbstractThe transcription factor MYB plays key roles in hematopoietic cells and has been implicated the development of leukemia. MYB has therefore emerged as an attractive target for drug development. Recent work has suggested that targeting MYB by small-molecule inhibitors is feasible and that inhibition of MYB has potential as a therapeutic approach against acute myeloid leukemia. To facilitate the identification of small-molecule MYB inhibitors we have re-designed and improved a previously established cell-based screening assay and have employed it to screen a natural product library for potential inhibitors. Our work shows that teniposide and etoposide, chemotherapeutic agents causing DNA-damage by inhibiting topoisomerase II, potently inhibit MYB activity and induce degradation of MYB in AML cell lines. MYB inhibition is suppressed by caffeine, suggesting that MYB is inhibited indirectly via DNA-damage signalling. Importantly, ectopic expression of an activated version of MYB in pro-myelocytic NB4 cells diminished the anti-proliferative effects of teniposide, suggesting that podophyllotoxins disrupt the proliferation of leukemia cells not simply by inducing general DNA-damage but that their anti-proliferative effects are boosted by inhibition of MYB. Teniposide and etoposide therefore act like double-edged swords that might be particularly effective to inhibit tumor cells with deregulated MYB.
An iPhone Application for Blood Pressure Monitoring via the Oscillometric Finger Pressing Method
Authors: Chandrasekhar Anand , Natarajan Keerthana , Yavarimanesh Mohammad , Mukkamala Ramakrishna 
Published: August 2018

AbstractWe developed an iPhone X application to measure blood pressure (BP) via the “oscillometric finger pressing method”. The user presses her fingertip on both the front camera and screen to increase the external pressure of the underlying artery, while the application measures the resulting variable-amplitude blood volume oscillations via the camera and applied pressure via the strain gauge array under the screen. The application also visually guides the fingertip placement and actuation and then computes BP from the measurements just like many automatic cuff devices. We tested the application, along with a finger cuff device, against a standard cuff device. The application yielded bias and precision errors of −4.0 and 11.4 mmHg for systolic BP and −9.4 and 9.7 mmHg for diastolic BP (n = 18). These errors were near the finger cuff device errors. This proof-of-concept study surprisingly indicates that cuff-less and calibration-free BP monitoring may be feasible with many existing and forthcoming smartphones.
Origin of cancer-associated fibroblasts and tumor-associated macrophages in humans after sex-mismatched bone marrow transplantation
Authors: Kurashige Masako , Kohara Masaharu , Ohshima Kenji , Tahara Shinichiro , Hori Yumiko , Nojima Satoshi , Wada Naoki , Ikeda Jun-ichiro , Miyamura Koichi , Ito Masafumi , Morii Eiichi 
Published: August 2018

AbstractCancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) in tumor stroma play a key role in disease progression. Recent studies using mice models suggest that CAFs are partly derived from bone marrow and TAMs primarily originate from bone marrow-derived inflammatory monocytes. However, the origin of these cells in humans remains unclear. Hence, we investigated their human origin, using specimens from human secondary tumors that developed after sex-mismatched bone marrow transplantation, by modified immunofluorescent in situ hybridization analysis and triple immunostaining. We observed that most of the α-smooth muscle actin (αSMA)-positive CAFs in the mammary gland, liver, and oral mucosa specimens obtained 3–19 years after bone marrow transplantation are recipient-derived cells. In contrast, the majority of the peritumoral αSMA-negative fibroblast-like cells are actually bone marrow-derived HLA-DR-positive myeloid cells, such as macrophages and dendritic cells. Furthermore, almost all CD163-positive TAMs and macrophages present in the non-tumor areas are derived from bone marrow.
Regional-scale management maps for forested areas of the Southeastern United States and the US Pacific Northwest
Authors: Marsik Matthew , Staub Caroline G. , Kleindl William J. , Hall Jaclyn M. , Fu Chiung-Shiuan , Yang Di , Stevens Forrest R. , Binford Michael W. 
Published: August 2018

AbstractForests in the United States are managed by multiple public and private entities making harmonization of available data and subsequent mapping of management challenging. We mapped four important types of forest management, production, ecological, passive, and preservation, at 250-meter spatial resolution in the Southeastern (SEUS) and Pacific Northwest (PNW) USA. Both ecologically and socio-economically dynamic regions, the SEUS and PNW forests represent, respectively, 22.0% and 10.4% of forests in the coterminous US. We built a random forest classifier using seasonal time-series analysis of 16 years of MODIS 16-day composite Enhanced Vegetation Index, and ancillary data containing forest ownership, roads, US Forest Service wilderness and forestry areas, proportion conifer and proportion riparian. The map accuracies for SEUS are 89% (10-fold cross-validation) and 67% (external validation) and PNW are 91% and 70% respectively with the same validation. The now publicly available forest management maps, probability surfaces for each management class and uncertainty layer for each region can be viewed and analysed in commercial and open-source GIS and remote sensing software.
Kernel-nulling for a robust direct interferometric detection of extrasolar planets
Authors: Martinache Frantz , Ireland Michael J. 
Published: August 2018

Context. Combining the resolving power of long-baseline interferometry with the high-dynamic range capability of nulling still remains the only technique that can directly sense the presence of structures in the innermost regions of extrasolar planetary systems.
Aims. Ultimately, the performance of any nuller architecture is constrained by the partial resolution of the on-axis star whose light it attempts to cancel out. However from the ground, the effective performance of nulling is dominated by residual time-varying instrumental phase and background errors that keep the instrument off the null. Our work investigates robustness against instrumental phase.
Methods. We introduce a modified nuller architecture that enables the extraction of information that is robust against piston excursions. Our method generalizes the concept of kernel, now applied to the outputs of the modified nuller so as to make them robust to second order pupil phase error. We present the general method to determine these kernel-outputs and highlight the benefits of this novel approach.
Results. We present the properties of VIKiNG: the VLTI Infrared Kernel NullinG, an instrument concept within the Hi-5 framework for the 4-UT VLTI infrastructure that takes advantage of the proposed architecture, to produce three self-calibrating nulled outputs.
Conclusions. Stabilized by a fringe-tracker that would bring piston-excursions down to 50 nm, this instrument would be able to directly detect more than a dozen extrasolar planets so-far detected by radial velocity only, as well as many hot transiting planets and a significant number of very young exoplanets.
Warped disks during type II outbursts in Be/X-ray binaries: evidence from optical polarimetry
Authors: Reig P. , Blinov D. 
Published: August 2018

Context. Current models that explain giant (type II) X-ray outbursts in Be/X-ray binaries (BeXB), are based on the idea of highly distorted disks. They are believed to occur when a misaligned and warped disk becomes eccentric, allowing the neutron star to capture a large amount of material. The BeXB 4U 0115+63 underwent two major outbursts in 2015 and 2017.
Aims. Our aim is to investigate whether the structural changes in the disk expected during type II outbursts can be detected through optical polarimetry.
Methods. We present the first optical polarimetric observations and new optical spectra of the BeXB 4U 0115+63 covering the period 2013–2017. We study in detail the shape of the Hα line profile and the polarization parameters before, during, and after the occurrence of a type II X-ray outburst.
Results. We find significant changes in polarization degree and polarization angle and highly distorted line profiles during the 2017 X-ray outburst. The degree of polarization decreased by ∼1%, while the polarization angle, which is supposed to be related with the disk orientation, first increased by ∼10° in about two months and then decreased by a similar amount and on a similar timescale once the X-ray activity ceased.
Conclusions. We interpret the polarimetric and spectroscopic variability as evidence for the presence of a warped disk.
Spectroscopic classification and Gaia DR2 parallaxes of new nearby white dwarfs among selected blue proper motion stars
Authors: Scholz R.-D. , Meusinger H. , Schwope A. , Jahreiß H. , Pelisoli I. 
Published: August 2018

Aims. With our low-resolution spectroscopic observing programme for selected blue proper motion stars, we tried to find new white dwarfs (WDs) in the solar neighbourhood.
Methods. We used the Lépine & Shara Proper Motion (LSPM) catalogue with a lower proper motion limit of 150 mas yr−1 and the Second US Naval Observatory CCD Astrograph Catalog (UCAC2) for proper motions down to about 90 mas yr−1. The LSPM and UCAC2 photometry was combined with Two Micron All Sky Survey (2MASS) near-infrared (NIR) photometry. Targets selected according to their blue optical-to-NIR and NIR colours were observed mainly at Calar Alto. The spectra were classified by comparison with a large number of already known comparison objects, including WDs, simultaneously observed within our programme. Gaia DR2 parallaxes and colours were used to confirm or reject spectroscopic WD candidates and to derive improved effective temperatures.
Results. We found ten new WDs at distances between 24.4 pc and 79.8 pc, including six hot DA WDs: GD 221 (DA2.0), HD 166435 B (DA2.2), GD 277 (DA2.2), 2MASS J19293865+1117523 (DA2.4), 2MASS J05280449+4105253 (DA3.6), and 2MASS J05005185-0930549 (DA4.2). The latter is rather bright (G ≍ 12.6) and with its Gaia DR2 parallax of ≍14 mas it appears overluminous by about 3 mag compared to the WD sequence in the Gaia DR2 colour-magnitude diagram. It may be the closest extremely low mass (ELM) WD to the Sun. We further classified 2MASS J07035743+2534184 as DB4.1. With its distance of 25.6 pc it is the second nearest known representative of its class. With GD 28 (DA6.1), LP 740-47 (DA7.5), and LSPM J1919+4527 (DC10.3) three additional cool WDs were found. Gaia DR2 parallaxes show that four of our candidates, but also two previously supposed WDs (WD 1004+665 and LSPM J1445+2527) are in fact distant Galactic halo stars with high tangential velocities. Among our rejected WD candidates, we identified a bright (G = 13.4 mag) G-type carbon dwarf, LSPM J0937+2803, at a distance of 272 pc.