bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semi-supervised learning of Hidden Markov Models for biological sequence analysis
Authors: Tamposis Ioannis A , Tsirigos Konstantinos D , Theodoropoulou Margarita C , Kontou Panagiota I , Bagos Pantelis G 
Published: November 2018

AbstractMotivationHidden Markov Models (HMMs) are probabilistic models widely used in applications in computational sequence analysis. HMMs are basically unsupervised models. However, in the most important applications, they are trained in a supervised manner. Training examples accompanied by labels corresponding to different classes are given as input and the set of parameters that maximize the joint probability of sequences and labels is estimated. A main problem with this approach is that, in the majority of the cases, labels are hard to find and thus the amount of training data is limited. On the other hand, there are plenty of unclassified (unlabeled) sequences deposited in the public databases that could potentially contribute to the training procedure. This approach is called semi-supervised learning and could be very helpful in many applications.ResultsWe propose here, a method for semi-supervised learning of HMMs that can incorporate labeled, unlabeled and partially labeled data in a straightforward manner. The algorithm is based on a variant of the Expectation-Maximization (EM) algorithm, where the missing labels of the unlabeled or partially labeled data are considered as the missing data. We apply the algorithm to several biological problems, namely, for the prediction of transmembrane protein topology for alpha-helical and beta-barrel membrane proteins and for the prediction of archaeal signal peptides. The results are very promising, since the algorithms presented here can significantly improve the prediction performance of even the top-scoring classifiers.Supplementary informationSupplementary data are available at Bioinformatics online.
GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
Authors: Moerman Thomas , Aibar Santos Sara , Bravo González-Blas Carmen , Simm Jaak , Moreau Yves , Aerts Jan , Aerts Stein 
Published: November 2018

Abstract

Summary
Inferring a Gene Regulatory Network (GRN) from gene expression data is a computationally expensive task, exacerbated by increasing data sizes due to advances in high-throughput gene profiling technology, such as single-cell RNA-seq. To equip researchers with a toolset to infer GRNs from large expression datasets, we propose GRNBoost2 and the Arboreto framework. GRNBoost2 is an efficient algorithm for regulatory network inference using gradient boosting, based on the GENIE3 architecture. Arboreto is a computational framework that scales up GRN inference algorithms complying with this architecture. Arboreto includes both GRNBoost2 and an improved implementation of GENIE3, as a user-friendly open source Python package.

Availability and implementation
Arboreto is available under the 3-Clause BSD license at http://arboreto.readthedocs.io.

Supplementary information
Supplementary data are available at Bioinformatics online.
Detection of Structural Defects in Fabric Parts Using a Novel Edge Detection Method
Authors: Dhivya M , Renuka Devi M 
Published: November 2018

Abstract
A fabric fault detection scheme is implemented in this work using frame harmonizing-based approach. Many recent research works deliver the fabric defect detection techniques. But in the textiles industry, the fast process of fabric cutting and sewing, lots of auxiliary imperfections have emerged. Particularly these defects cannot be identified easily by experts as well as an automated system. In our system, a novel frame extraction technique is used to find the defects in the fabric production pipeline. The input fabric image frame is pre-processed by transformation and filtering techniques. In this work,a novel multi-directional and multi-scale outline extraction method is proposed to extract the edge map. Contour-based features are extracted and classified by K-nearest neighbor classifier. The experimentation with real-time dataset produced the outstanding performance results when compared with state of the art methods.
A Molecular Targeted Immunotherapeutic Strategy for Ulcerative Colitis via Dual-targeting Nanoparticles Delivering miR-146b to Intestinal Macrophages
Authors: Deng Feihong , He Shuying , Cui Shudan , Shi Yanqiang , Tan Yuyong , Li Zhijun , Huang Chongyang , Liu Deliang , Zhi Fachao , Peng Liang 
Published: November 2018

Abstract

Background and Aims
Macrophages are a promising therapeutic target for intestinal mucosal repair. MiR-146b appears to control macrophage activation and cell proliferation.

Methods
By loading miR-146b mimic on mannose-modified trimethyl chitosan [MTC]-conjugated nanoparticles [NPs] [MTC-miR146b], a molecular targeted immunotherapeutic approach was developed to selectively target intestinal macrophages for mucosal regeneration and tumourigenesis in mouse models.

Results
We first confirmed that miR-146b expression was significantly enhanced during mucosal regeneration in a murine colitis model. Moreover， after mucosal damage, MTC-miR146b mimic-treated wild-type mice had dramatically restored body weight and mucosal barrier function compared with MTC-NC treated mice. Strikingly, MTC-miR146b mimic oral administration protected miR-146b-deficient mice from dextran sodium sulphate [DSS] injury and the colitis-associated cancer process. Mechanistically, miR-146b strongly inhibited M1 macrophage activation by suppressing the Toll-like receptor 4 [TLR4] signalling pathway, resulting in the repression of the induction of pro-inflammatory cytokines including TNF-α, IL-6, and IL-1β. More importantly, miR-146b overexpression in bone marrow-derived macrophages [BMDMs] in M1 differentiation conditions induced a phenotype similar to M2 macrophages and improved the proliferation of co-cultured colonic epithelial cells via STAT3-dependent IL-10 production.

Conclusions
MTC-miR146b should be regarded as an effective candidate for oral delivery and could improve the efficacy of immunotherapies for ulcerative colitis and colitis-associated cancer.
Does long-term use of pain relievers have an impact on the rate of orthodontic tooth movement? A systematic review of animal studies
Authors: Makrygiannakis Miltiadis A , Kaklamanos Eleftherios G , Athanasiou Athanasios E 
Published: November 2018

SummaryBackgroundPain relief drugs are used and misused widely and may theoretically affect the events leading to orthodontic tooth movement.ObjectiveTo systematically investigate and appraise the quality of the available evidence regarding the effect of pain relief medications on the rate of orthodontic tooth movement.Search methodsSearch without restrictions in eight databases (including grey literature) and hand searching until October 2018.Selection criteriaAnimal controlled studies investigating the effect of pain relievers on the rate of orthodontic tooth movement.Data collection and analysisFollowing study retrieval and selection, relevant data were extracted and the risk of bias was assessed using the SYRCLE’s risk of bias tool.ResultsFourteen studies were finally identified, most of which at unclear risk of bias. Ibuprofen and loxoprofen did not show any significant effects on the rate of orthodontic tooth movement, whereas indomethacin, ketorolac, morphine, and high doses of etoricoxib were found to decrease it. Inconsistent or conflicting effects were noted after the administration of acetaminophen, acetylsalicylic acid, celecoxib, meloxicam, and tramadol. The quality of the available evidence was considered at best as low.ConclusionsLong-term consumption of pain relievers may affect the rate of orthodontic tooth movement. The orthodontist should be capable of identifying patients taking pain relievers independently of orthodontic treatment and consider the possible implications.Trial registrationPROSPERO (CRD42017078208).
Body Flexibility Enhances Maneuverability in the World’s Largest Predator
Authors: Segre P S , Cade D E , Calambokidis J , Fish F E , Friedlaender A S , Potvin J , Goldbogen J A 
Published: November 2018

AbstractBlue whales are often characterized as highly stable, open-ocean swimmers who sacrifice maneuverability for long-distance cruising performance. However, recent studies have revealed that blue whales actually exhibit surprisingly complex underwater behaviors, yet little is known about the performance and control of these maneuvers. Here, we use multi-sensor biologgers equipped with cameras to quantify the locomotor dynamics and the movement of the control surfaces used by foraging blue whales. Our results revealed that simple maneuvers (rolls, turns, and pitch changes) are performed using distinct combinations of control and power provided by the flippers, the flukes, and bending of the body, while complex trajectories are structured by combining sequences of simple maneuvers. Furthermore, blue whales improve their turning performance by using complex banked turns to take advantage of their substantial dorso-ventral flexibility. These results illustrate the important role body flexibility plays in enhancing control and performance of maneuvers, even in the largest of animals. The use of the body to supplement the performance of the hydrodynamically active surfaces may represent a new mechanism in the control of aquatic locomotion.
Direct detection of quasar feedback via the Sunyaev–Zeldovich effect
Authors: Lacy Mark , Mason Brian , Sarazin Craig , Chatterjee Suchetana , Nyland Kristina , Kimball Amy , Rocha Graca , Rowe Barnaby , Surace Jason 
Published: November 2018

ABSTRACT
The nature and energetics of feedback from thermal winds in quasars can be constrained via observations of the Sunyaev–Zeldovich Effect (SZE) induced by the bubble of thermal plasma blown into the intergalactic medium by the quasar wind. In this letter, we present evidence that we have made the first detection of such a bubble, associated with the hyperluminous quasar HE 0515-4414. The SZE detection is corroborated by the presence of extended emission line gas at the same position angle as the wind. Our detection appears on only one side of the quasar, consistent with the SZE signal arising from a combination of thermal and kinetic contributions. Estimates of the energy in the wind allow us to constrain the wind luminosity to the lower end of theoretical predictions, ∼0.01 per cent of the bolometric luminosity of the quasar. However, the age we estimate for the bubble, ∼0.1 Gyr, and the long cooling time, ∼0.6 Gyr, means that such bubbles may be effective at providing feedback between bursts of quasar activity.
Very long baseline interferometry radio structure and radio brightening of the high-energy neutrino emitting blazar TXS 0506+056
Authors: Kun E , Biermann P L , Gergely L Á 
Published: November 2018

ABSTRACT
We report on the radio brightening of the blazar TXS 0506+056 (at z = 0.3365), and we support its identification by the IceCube Neutrino Observatory as a source of the high-energy (HE) neutrino IC-170922A. Data from the Monitoring Of Jets in AGN with VLBA Experiments (MOJAVE)/Very Long Baseline Array (VLBA) survey indicate that its radio brightness has abruptly increased since 2016 January. When decomposing the total radio flux density curve (in the period 2008 January to 2018 July), provided by the Owens Valley Radio Observatory, into eight Gaussian flares, the peak time of the largest flare overlaps with the HE neutrino detection, while the total flux density has exhibited a threefold increase since 2016 January. We reveal the radio structure of TXS 0506+056 by analysing very long baseline interferometry (VLBI) data from the MOJAVE/VLBA survey. The jet components maintain quasi-stationary core separations. The structure of the ridge line is indicative of a jet curve in the region 0.5–2 mas (2.5–9.9 pc projected) from the VLBI core. The brightness temperature of the core and the pc-scale radio morphology support a helical jet structure at small inclination angle (&lt;8${^{\circ}_{.}}$2). The jet pointing towards the Earth is a key property facilitating multimessenger observations (HE neutrinos, γ-rays and radio flares). The radio brightening preceding the detection of a HE neutrino is similar to the one reported for the blazar PKS 0723–008 and IceCube event ID5.
Utility of Columbia classification in focal segmental glomerulosclerosis: renal prognosis and treatment response among the pathological variants
Authors: Tsuchimoto Akihiro , Matsukuma Yuta , Ueki Kenji , Tanaka Shigeru , Masutani Kosuke , Nakagawa Kaneyasu , Mitsuiki Koji , Uesugi Noriko , Katafuchi Ritsuko , Tsuruya Kazuhiko , Nakano Toshiaki , Kitazono Takanari 
Published: November 2018

Abstract

Background
The utility of the Columbia classification (Col-class) for focal segmental glomerulosclerosis (FSGS) has not yet been fully proven.

Methods
We extracted 201 FSGS patients from 10 nephrology centers in Japan and investigated the difference of a composite renal endpoint, defined as doubling of serum creatinine and/or development of end-stage renal disease, in pathological variants. Sensitivity analysis was used to prove the utility of the Col-class to predict renal outcomes. Additionally, the renal protective effects of steroids and/or immunosuppression (steroid/IS) were investigated in patients stratified according to the Col-class.

Results
The patients were classified into the following variants: not otherwise specified [NOS; n = 121 (60.1%)], perihilar [n = 31 (15.4%)], cellular [n = 19 (9.5%)], tip [n = 17 (8.5%)] and collapsing [n = 13 (6.5%)]. No tip variant patients reached the renal endpoint. The renal outcome in the collapsing variant was significantly poorer than that in the NOS [hazard ratio (HR) 3.71; P = 0.005]. In the sensitivity analysis, the area under the receiver operating characteristic curve for the renal endpoint was increased by adding Col-class to a model including common risk factors (P = 0.021). In a subgroup treated without steroid/IS, the outcome in the cellular variant was worse than that in the NOS (HR 5.10; P = 0.040) but the difference was not observed in the subgroup with steroid/IS (HR 0.54; P = 0.539).

Conclusions
The Col-class is useful to predict renal prognosis in Japanese patients with FSGS. In addition to good prognosis in the tip variant and poor in the collapsing variant, good clinical course in the cellular variant treated with steroid/IS was suggested.
Effects of low-moisture, sugarcane molasses-based block supplementation on growth, physiological parameters, and liver trace mineral status of growing beef heifers fed low-quality, warm-season forage
Authors: Moriel Philipe , Artioli Luís F A , Piccolo Matheus B , Miranda Miguel , Ranches Juliana , Ferreira Vitor S M , Antunes Lorenzo Q , Bega Amanda M , Miranda Victor F B , Vieira José F R L , Vasconcelos José L M 
Published: November 2018

Abstract
The objectives of the study were to evaluate the growth, physiological parameters, and liver trace mineral status of beef heifers provided low-quality warm-season forage and different forms (meal vs. block) of trace mineral-fortified supplementation. One hundred yearling Nellore heifers were blocked by initial body weight (BW) (184 ± 2.5 kg) and randomly assigned into 1 of 20 drylot pens (5 heifers/pen). Treatments were randomly assigned to pens (5 pens/treatment) and consisted of heifers receiving: 1) a loose meal trace mineral supplement (TM; De Heus Animal Nutrition Industry); 2) free choice access to a low-moisture, cooked sugarcane molasses-based protein block (LMB); 3) isocaloric and isonitrogenous, loose meal protein supplement pair-fed to LMB supplement dry matter (DM) intake (PSPF); and (4) loose meal protein supplement offered at 0.2% of BW (PS). Supplements were formulated to achieve same daily intake of supplemental trace mineral among treatments. Hence, TM supplement was offered at 66.6% of the supplement DMI of LMB heifers. Heifers were offered free choice access to water and ground brachiaria (Brachiaria brizantha) hay from day 0 to 45. Overall average daily gain from day 0 to 45 was the least for TM heifers (P ≤ 0.05) and did not differ among LMB, PSPF, and PS heifers (P ≥ 0.60). Daily hay DMI did not differ among treatments (P ≥ 0.63). Total intake of DM and TDN were least for TM heifers (P ≤ 0.03) and did not differ (P ≥ 0.66) among LMB, PSPF, and PS heifers. Total supplemental intake of crude protein (CP) and rumen degradable protein (RDP) and total intake of CP and RDP (supplement + hay) were least for TM and greatest for PS heifers (P ≤ 0.05), and intermediate for LMB and PSPF heifers (P ≥ 0.70). Effects of treatment × day and treatment were not detected (P ≥ 0.61) for plasma concentrations of insulin-like growth factor 1 (IGF-1), and non-esterified fatty acids (NEFA). Effects of treatment were detected for plasma concentrations of PUN (P = 0.005) and tended to be detected for plasma concentrations of glucose (P = 0.08), which were least for TM heifers (P ≤ 0.03) and did not differ (P ≥ 0.17) among LMB, PSPF, and PS heifers. Trace mineral intake and liver concentrations of all trace minerals did not differ (P ≥ 0.13) among treatments. Hence, the use of LMB supplementation resulted in positive effects on growth without impacting trace mineral status compared to a loose meal trace mineral salt, and similar growth performance and trace mineral status compared to a conventional protein supplementation offered at 0.2% of body weight.
Implications of Failure to Achieve a Result From Prenatal Maternal Serum Cell-Free DNA Testing: A Historical Cohort Study
Authors: Chan N. , Smet M.-E. , Sandow R. , da Silva Costa F. , McLennan A. 
Published: November 2018

(Abstracted from BJOG 2018;125:848–855)
Noninvasive prenatal testing (NIPT) involves the analysis of cell-free DNA fragments in maternal serum. During pregnancy, cell-free DNA consists of both maternal fragments, primarily from hematopoietic cells, and fetal fragments, released from trophoblasts during apoptosis.
Cannabis Use During the Perinatal Period in a State With Legalized Recreational and Medical Marijuana: The Association Between Maternal Characteristics, Breastfeeding Patterns, and Neonatal Outcomes
Authors: Crume Tessa L. , Juhl Ashley L. , Brooks-Russell Ashley , Hall Katelyn E. , Wymore Erica , Borgelt Laura M. 
Published: November 2018

(Abstracted from J Pediatr 2018;197:90–96)
Cannabis is the most commonly used psychoactive substance in the United States, and recent estimates of the prevalence of cannabis use among pregnant women in the United States range between 3% and 16%. Population-based surveillance data from the National Survey on Drug Use and Health suggests that cannabis use among pregnant women in the United States has increased as much as 62% between 2002 and 2014.
Vitamin D and Risk of Pregnancy-Related Hypertensive Disorders: Mendelian Randomization Study
Authors: Magnus Maria C. , Miliku Kozeta , Bauer Anna , Engel Stephanie M. , Felix Janine F. , Jaddoe Vincent W. V. , Lawlor Debbie A. , London Stephanie J. , Magnus Per , McGinnis Ralph , Nystad Wenche , Page Christian M. , Rivadeneira Fernando , Stene Lars C. , Tapia German , Williams Nicholas , Bonilla Carolina , Fraser Abigail 
Published: November 2018

(Abstracted from BMJ 2018;361:k2167)
Observational studies have found that women with lower levels of 25-hydroxyvitamin D are at greater risk of preeclampsia. Although some small trials of vitamin D supplementation in pregnancy have suggested a potential benefit of supplementation, a recent meta-analysis found no impact on preeclampsia from vitamin D supplementation.
A 17β-Estradiol–Progesterone Oral Capsule for Vasomotor Symptoms in Postmenopausal Women: A Randomized Controlled Trial
Authors: Lobo Rogerio A. , Archer David F. , Kagan Risa , Kaunitz Andrew M. , Constantine Ginger D. , Pickar James H. , Graham Shelli , Bernick Brian , Mirkin Sebastian 
Published: November 2018

(Abstracted from Obstet Gynecol 2018;132:161–170)
After the first publication of Women's Health Initiative findings in 2002, many women stopped taking US Food and Drug Administration (FDA)–approved, hormone therapy (HT) and started using non–FDA-approved, “natural” compounded HT believing that it was a safer option. In 2015, it was estimated that 1 million to 2.5 million US women used the unapproved, compounded HT.
Obesity in relation to serum persistent organic pollutant concentrations in CHAMACOS women
Authors: Warner Marcella , Rauch Stephen , Coker Eric S. , Harley Kim , Kogut Katherine , Sjödin Andreas , Eskenazi Brenda 
Published: November 2018

Background:
Environmental exposure to endocrine-disrupting chemicals (EDCs), including persistent organic pollutants (POPs), has been hypothesized to increase risk of obesity. Using data from the Center for Health Assessment of Mothers and Children of Salinas (CHAMACOS) study, we examined the longitudinal relationship between serum concentrations of a POPs mixture and several obesity measures.

Methods:
Concentrations of 17 POPs were measured in serum collected in 2009–2011 from 468 CHAMACOS women. Anthropometry measurements and personal interviews were completed at up to three study visits between 2009 and 2014. We assessed the relationship of serum POPs concentrations with adiposity measures longitudinally using generalized estimation equation (GEE) models. We implemented Bayesian Kernel Machine Regression (BKMR) to elucidate the effects of joint exposure to the POPs mixture.

Results:
In GEE models, positive associations with body mass index were found for dichlorodiphenyltrichloroethane (Q4 vs. Q1: adjusted β = 3.2 kg/m2; 95% CI = 1.5, 4.9), β-hexachlorocyclohexane (Q4 vs. Q1: adjusted β = 3.6 kg/m2; 95% CI = 2.0, 5.2), and polybrominated diphenyl ether (PBDE)-47 (Q4 vs. Q1: adjusted β = 1.9 kg/m2; 95% CI = 0.3, 3.5), while PBDE-153 was inversely associated (Q4 vs. Q1: adjusted β = −2.8 kg/m2; 95% CI = −4.4, −1.2). BKMR results, while largely consistent with single pollutant models, revealed the shape and direction of the exposure–response relationships, as well as interactions among pollutants within the mixture, that could not be discovered by single-pollutant models.

Conclusion:
In summary, we found significant associations of serum POPs with several adiposity measures using both conventional regressions and BKMR. Our results provide support for the chemical obesogen hypothesis, that exposure to EDCs may alter risk for later obesity.
An Orally Available NLRP3 Inflammasome Inhibitor Prevents Western Diet–Induced Cardiac Dysfunction in Mice
Authors: Carbone Salvatore , Mauro Adolfo G. , Prestamburgo Andrea , Halquist Matthew S. , Narayan Pratush , Potere Nicola , Mezzaroma Eleonora , Van Tassell Benjamin W. , Abbate Antonio , Toldo Stefano 
Published: November 2018

Background:
A diet rich in saturated fat and sugars (Western diet, WD) induces myocardial expression of the NLRP3 inflammasome and dysfunction in mice. We therefore hypothesized that a diet enriched with an orally available NLRP3 inflammasome inhibitor could prevent WD-induced cardiac dysfunction in mice.

Methods:
Ten-week-old CD-1 male mice were fed WD or standard diet (SD) for 8 weeks. The compound 16673-34-0, an orally active NLRP3 inhibitor, was added to the diet at a concentration of 100 mg/Kg. The plasmatic levels of the NLRP3 inflammasome inhibitor were measured. Food intake, body weight, and glucose tolerance were assessed. Cardiac systolic and diastolic functions were measured by Doppler echocardiography at baseline, 4 weeks, and 8 weeks.

Results:
WD induced a significant increase in body weight (+14%, P = 0.02), impaired glucose tolerance (+34%, P = 0.03), and a significant increase in isovolumetric relaxation time (+129%, P = 0.03) and reduction in left ventricular ejection fraction (−10%, P = 0.03), as compared to standard chow diet (SD). The treatment with NLRP3 inhibitor in the diet prevented cardiac systolic and diastolic dysfunction (P < 0.05 for left ventricular ejection fraction, isovolumetric relaxation time, and myocardial performance index in WD with drug vs. WD without drug), without significant changes in heart rate and metabolic parameters.

Conclusions:
An orally available NLRP3 inhibitor prevented WD-induced cardiac dysfunction in obese mice.