bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters
Authors: Shafiee Kamalabad Mahdi , Grzegorczyk Marco 
Published: September 2019

Abstract

Motivation
Non-homogeneous dynamic Bayesian networks (NH-DBNs) are a popular tool for learning networks with time-varying interaction parameters. A multiple changepoint process is used to divide the data into disjoint segments and the network interaction parameters are assumed to be segment-specific. The objective is to infer the network structure along with the segmentation and the segment-specific parameters from the data. The conventional (uncoupled) NH-DBNs do not allow for information exchange among segments, and the interaction parameters have to be learned separately for each segment. More advanced coupled NH-DBN models allow the interaction parameters to vary but enforce them to stay similar over time. As the enforced similarity of the network parameters can have counter-productive effects, we propose a new consensus NH-DBN model that combines features of the uncoupled and the coupled NH-DBN. The new model infers for each individual edge whether its interaction parameter stays similar over time (and should be coupled) or if it changes from segment to segment (and should stay uncoupled).

Results
Our new model yields higher network reconstruction accuracies than state-of-the-art models for synthetic and yeast network data. For gene expression data from A.thaliana our new model infers a plausible network topology and yields hypotheses about the light-dependencies of the gene interactions.

Availability and implementation
Data are available from earlier publications. Matlab code is available at Bioinformatics online.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Recovery Illusion: What Is Delaying the Rescue of Imperiled Species?
Authors: Ferreira Catarina C , Hossie Thomas J , Jenkins Deborah A , Wehtje Morgan , Austin Cayla E , Boudreau Melanie R , Chan Kevin , Clement Amy , Hrynyk Morgan , Longhi Jessica , MacFarlane Shawn , Majchrzak Yasmine N , Otis Josée-Anne , Peers Michael J L , Rae Jason , Seguin Jacob L , Walker Spencer , Watt Cristen , Murray Dennis L 
Published: September 2019

AbstractWith unprecedented losses in biodiversity, the need for stronger environmental policy has emerged as a conservation priority. Yet recovery planning for imperiled species remains a cumbersome, slow legislative process. In the present article, we examine features of recovery planning for species listed under Canada's Species at Risk Act to determine those influencing recovery planning duration. We found that the time to completion of recovery strategies increases with the number of jurisdictions concurrently listing the species, greater land tenure diversity, species population size, and road density. Species at risk in Canada with no listing status in the United States also suffered longer delays. To achieve a more efficient, timely, and defensible implementation of recovery planning, we recommend that governments prioritize recovery planning on the basis of risk level, promote transjurisdictional collaboration among listing agencies, anticipate and mitigate conservation challenges associated with multitenured and developed landscapes, and adopt procedures that enhance compliance with legislated timelines for recovery planning.
Exacerbation of C1q dysregulation, synaptic loss and memory deficits in tau pathology linked to neuronal adenosine A2A receptor
Authors: Carvalho Kevin , Faivre Emilie , Pietrowski Marie J , Marques Xavier , Gomez-Murcia Victoria , Deleau Aude , Huin Vincent , Hansen Jan N , Kozlov Stanislav , Danis Clément , Temido-Ferreira Mariana , Coelho Joana E , Mériaux Céline , Eddarkaoui Sabiha , Gras Stéphanie Le , Dumoulin Mélanie , Cellai Lucrezia ,   NeuroCEB Brain Bank, Landrieu Isabelle , Chern Yijuang , Hamdane Malika , Buée Luc , Boutillier Anne-Laurence , Levi Sabine , Halle Annett , Lopes Luisa V , Blum David 
Published: September 2019

See Cunha (doi:10.1093/brain/awz335) for a scientific commentary on this article.Carvalho et al. provide clues to the onset of immune dysregulation underlying early synaptic loss in Alzheimer’s disease and tauopathies, by linking overactivation of adenosine A2A receptors in tau pathology to a particular microglial signature (upregulation of C1q and TREM2) allied to the loss of glutamatergic synapses and cognitive deficits.
Ceftolozane/Tazobactam vs Polymyxin or Aminoglycoside-based Regimens for the Treatment of Drug-resistant Pseudomonas aeruginosa
Authors: Pogue Jason M , Kaye Keith S , Veve Michael P , Patel Twisha S , Gerlach Anthony T , Davis Susan L , Puzniak Laura A , File Tom M , Olson Shannon , Dhar Sorabh , Bonomo Robert A , Perez Federico 
Published: September 2019

AbstractBackgroundCeftolozane/tazobactam is a novel cephalosporin/beta-lactamase inhibitor combination that often retains activity against resistant Pseudomonas aeruginosa. The comparative safety and efficacy vs polymyxins or aminoglycosides in this setting remains unknown.MethodsA retrospective, multicenter, observational cohort study was performed. Patients who received ceftolozane/tazobactam were compared with those treated with either polymyxin or aminoglycoside-based regimens for infections due to drug-resistant P. aeruginosa. Multivariate logistic regression was performed controlling for factors associated with treatment to assess the independent impact of ceftolozane/tazobactam on clinical cure, acute kidney injury (AKI), and in-hospital mortality.ResultsA total of 200 patients were included (100 in each treatment arm). The cohort represented an ill population with 69% in the intensive care unit, 63% mechanically ventilated, and 42% in severe sepsis or septic shock at infection onset. The most common infection type was ventilator-associated pneumonia (52%); 7% of patients were bacteremic. Combination therapy was more commonly used in polymyxin/aminoglycoside patients than those who received ceftolozane/tazobactam (72% vs 15%, P &lt; .001). After adjusting for differences between groups, receipt of ceftolozane/tazobactam was independently associated with clinical cure (adjusted odds ratio [aOR], 2.63; 95% confidence interval [CI], 1.31–5.30) and protective against AKI (aOR, 0.08; 95% CI, 0.03–0.22). There was no difference in in-hospital mortality. The number needed to treat for a clinical cure with ceftolozane/tazobactam was 5, and the number needed to harm with AKI with a polymyxin/aminoglycoside was 4.ConclusionsThese data support the preferential use of ceftolozane/tazobactam over polymyxins or aminoglycosides for drug-resistant P. aeruginosa infections.
In Vitro Activity of Cefiderocol Against a Broad Range of Clinically Important Gram-negative Bacteria
Authors: Yamano Yoshinori 
Published: September 2019

AbstractCarbapenem-resistant gram-negative bacteria including Enterobacteriaceae as well as nonfermenters, such as Pseudomonas aeruginosa and Acinetobacter baumannii, have emerged as significant global clinical threats. Although new agents have recently been approved, none are active across the entire range of resistance mechanisms presented by carbapenem-resistant gram-negative bacteria. Cefiderocol, a novel siderophore cephalosporin, has been shown in large surveillance programs and independent in vitro studies to be highly active against all key gram-negative causative pathogens isolated from patients with hospital-acquired or ventilator-associated pneumonia, bloodstream infections, or complicated urinary tract infections. The improved structure, the novel mode of entry into bacteria, and its stability against carbapenemases enables cefiderocol to exhibit high potency against isolates that produce carbapenemases of all classes or are resistant due to porin channel mutations and/or efflux pump overexpression. Resistance to cefiderocol is uncommon and appears to be multifactorial.
Kidney transplantation for active multiple myeloma or smoldering myeloma: a case–control study
Authors: Kormann Raphaël , Pouteil-Noble Claire , Muller Clotilde , Arnulf Bertrand , Viglietti Denis , Sberro Rebecca , Sayegh Johnny , Durrbach Antoine , Dantal Jacques , Girerd Sophie , Pernin Vincent , Albano Laetitia , Rondeau Eric , Peltier Julie 
Published: September 2019

AbstractBackgroundThe increased survival of patients with multiple myeloma (MM) raises the question of kidney transplantation (KT) in patients with end-stage renal disease (ESRD).MethodsWe included 13 patients with MM or smoldering myeloma (SMM) and ESRD transplanted between 2007 and 2015, including 7 MM with cast nephropathy, 3 with MM-associated amyloid light chain amyloidosis or light chain deposition disease and 3 SMM and compared them with 65 control-matched kidney-transplanted patients. Nine of the MM patients with KT were also compared with 63 matched MM patients on haemodialysis.ResultsPre-transplantation parameters were comparable, except for the duration of renal replacement therapy (57.8 versus 37.0 months; P = 0.029) in MM versus control patients, respectively. The median follow-up post-KT was 44.4 versus 36.4 months (P = 0.40). The median MM graft and patient survival were 80.1 and 117.2 months, respectively, and were not significantly different from control patients, although mortality tended to be higher in the 10 symptomatic MM patients (P = 0.059). MM patients had significantly more viral and fungal infections and immunosuppressive maintenance therapy modifications while they received lower induction therapy. Two MM patients relapsed and two SMM cases evolved to MM after KT. Three cast nephropathies occurred, two of them leading to ESRD. Moreover, survival of MM with KT increased relative to control haemodialysed patients (P = 0.002).ConclusionsSelected MM patients may benefit from KT but need careful surveillance in the case of KT complications and MM evolution.
Clinical parameters predicting complications in native kidney biopsies
Authors: Peters Björn , Nasic Salmir , Segelmark Mårten 
Published: September 2019

Abstract

Background
Renal biopsies are essential in nephrology but they are invasive and complications can occur. The aim of this study was to explore clinical parameters that can be used as predictors for biopsy complications.

Methods
Clinical parameters such as demographics, biopsy indications, serology, comorbidities and clinical chemistry were retrieved from a regional biopsy registry between 2006 and 2015 and from a nationwide registry between 2015 and 2017. Clinical data before biopsy were compared with data on major biopsy complications. Fisher’s exact and χ2 tests were used and odds ratios (ORs) with 95% confidence intervals (CIs) were presented. Univariate and multiple binary logistic regression analyses were performed with complications as outcome. A two-sided P-value &lt;0.05 was considered significant.

Results
In total, 2835 consecutive native kidney biopsies were analysed (39% women and 61% men, median age 57 years). No death and nephrectomy due to biopsy complications were registered. The frequency of major biopsy complications was 5.65%. In the multiple logistic regression, the risk for complications increased in women [OR 1.51 (95% CI 1.08–2.11)] and decreased with age: 45–64 years age group [OR 0.66 (95% CI 0.44–0.99)] and &gt;74 years age group [OR 0.51 (95% CI 0.27–0.96)]. Among comorbidities, patients with diabetes mellitus type 2 [OR 2.07 (95% CI 1.15–3.72)] and non-ischaemic heart disease [OR 3.20 (95% CI 1.64–6.25)] had a higher risk for major biopsy complications.

Conclusions
Female gender, younger age (≤44 years), diabetes mellitus type 2 and non-ischaemic heart disease were found as risk factors for major biopsy complications.
Updatable Lossy Trapdoor Functions Under Consecutive Leakage
Authors: Huang Meijuan , Yang Bo , Zhang Mingwu , Zhang Lina , Hou Hongxia 
Published: September 2019

Abstract
Lossy trapdoor functions (LTFs), introduced by Peikert and Waters (STOC’08), have already been found to be a very useful tool in constructing complex cryptographic primitives in a black-box manner, such as one-way trapdoor functions, deterministic public-key encryption, CCA-secure public-key encryption, etc. Due to the existence of the side-channel attack, the leakage of trapdoor information in lossy trapdoor function systems can lead to the impossibility of provable security. Recently, Zhang et al. introduced a model of consecutive and continual leakage-resilient and updatable lossy trapdoor functions (ULTFs) and provided a concrete construction to achieve the security. Meanwhile, they proposed a consecutive and continual leakage-resilient public-key encryption scheme. However, in this paper, we demonstrate that the correctness of injective function can not be satisfied. Furthermore, the attacker can easily distinguish the evaluation key of ULTFs generated by the challenger according to the security model. Finally, we show two new constructions based on the continual leakage-resilient public-key encryption scheme of Brakerski et al. (FOCS 2010) and demonstrate the security of our scheme in the consecutive and continual leakage model.
Do zealots increase or decrease the polarization of social networks?
Authors: Shekatkar Snehal M 
Published: September 2019

AbstractZealots are the vertices in a social network who do not change their opinions under social pressure and are crucial to the study of opinion dynamics on complex networks. In this article, we study the effect of zealots on the polarization dynamics of a deterministic majority rule model using the configuration model as a substrate. To this end, we propose a novel quantifier, called ‘correlated polarization’, for measuring the amount of polarization in the network when vertices can exist in two opposite states. The quantifier takes into account not only the fraction of vertices with each opinion but also how they are connected to each other. We then show that the presence of zealots does not have a fixed effect on the polarization, and can change it in positive, negative or neutral way depending upon their topological characteristics like degree, their total fraction in the network, density and degree heterogeneity of the network and the type of initial conditions of the dynamics. Our results particularly highlight the importance of the role played by the initial conditions in drifting the polarization towards lower or higher values as the total number of zealots is increased.
Effects of odors on behaviors of captive Amur leopards Panthera pardus orientalis
Authors: Yu Shuangying , Jiang Zhigang , Zhu Hui , Li Chunwang , Zhang Enquan , Zhang Jinguo , Harrington Carin 
Published: September 2019

Abstract
Captive environments often fail to resemble the wild environment in respects of limited space, unchanging habitat, lack of stimulus and contingency. Common animal welfare problems which occur in captive animals include low behavioral diversity, abnormal behavior and excessive inactivity. Environmental enrichment, as an effective strategy to tackle these problems and promote mental health of captive animals, has been recognized as an important principal for captive animal management. Among all the enrichment techniques, olfactory enrichment is a simple and effective method for improving the well-being of the olfactory sensitive felids. Behavioral problems were observed in six Amur leopards Panthera pardus orientalis at Beijing Zoological Garden. These were held in the older type exhibits which have now been rebuilt. These behaviors include stereotypic behavior and excessive inactivity caused by the spatially limited enclosures with low levels of stimuli. To determine the effects of predator, prey, and herb odors as potential enrichment materials for captive leopards, we conducted olfactory enrichment experiments for the leopards and tested the effects of nutmeg Myristica fragrans, feces of roe deer Capreolus capreolus and urine of Amur tiger Panthera tigris altaica to test for an increase in behavioral repertoire and activity. Odors provided in this study were also believed to improve the psychological and physiological health of individuals. To standardize the method of presentation the odors were introduced to the enclosures by rubbing or spraying onto a clean towel. Our results show that the selected three odors effectively increased the behavioral diversity. Ten new behavior types were observed in the nutmeg experiment, eight in the feces of roe deer experiment and six in the tiger urine experiment. Among the three odors, cats responded to nutmeg for the longest duration, followed by tiger urine and feces of roe deer. Leopards showed more play behavior in presence of nutmeg while more investigatory behavior in presences of feces of roe deer and tiger urine. Providing novel odors increased the spatial use of the exhibit and the animal’s increased use of the logs, sleeping platforms and bars in the cages. Novel odors also significantly increased the overall activity of the leopards, but the effects were diminished in about three hours.
Effect of motilin on the contractility of gastric smooth muscle via NO pathway in guinea pigs
Authors: Wang Zhiming , Xu Luo , Lu Jiang 
Published: September 2019

Abstract
This study investigates the gastroprokinetic effects of motilin and erythromycin A (EM-A) and its potential mechanism in guinea pigs Cavia porcellus in vitro. Guinea pig stomach strips were mounted under organ baths containing Krebs solution. Motilin, EM-A, Nω-Nitro-L-arginine (L-NNA), L-arginine (L-AA) were added to the bathing solution in a non-cumulative way. Then the effects of motilin and EM-A was studied during electrical field stimulation (EFS) in the absence and presence of L-NNA and L-AA in the gastric anturm and fundus of guinea pigs. In addition, we observed the co-expression of motilin receptors and neuronal nitric oxide synthase (nNOS) in the gastric myenteric plexus of guinea pigs by fluo-immunohistochemistry. The results showed that the circular muscle tissues of the gastric fundus generated on-relaxations and off-contractions with the frequency of 1 - 16 Hz. The on-responses induced a relaxation' partially mediated by the release of nitric oxide (NO) because addition of L-NNA turned the relaxations into cholinergically mediated contractions. The off- contractions were also cholinergically mediated as they disappeared under non-adrenergic, non-cholinergic (NANC) conditions using atropine and guanethidine. In fundic strips, motilin and EM-A induced on-relaxation and off- contraction and both motilin (1 µmol/L) and EM-A (100 µmol/L) may significantly increased on- response and reduced off-response (P < 0.05). And the effects of motilin on strip responses were significantly enhanced compared with EM-A. The on-responses could be reversed into a cholinergically mediated contraction by addition of NOS inhibitors L-NNA. In contrast, administration of substrate of NOS, L-AA, significantly increased on-relaxations and reduced cholinergic motor responses which were induced by motilin or EM-A. However D-arginine (D-AA) did not change the above response induced by motilin or EM-A. In the antral strips, motilin and EM-A only increased off-contractions. The response to motilin and EM-A in the presence of L-NNA did differ from that obtained with L-NNA alone. It showed that both motilin and EM-A could enhance off-contractions induced by L-NNA (P < 0.05). Immunohistochemistry study showed that motilin receptor immunoreactive positive neurons were co-localized with nNOS positive neurons in the gastric myenteric plexus of the guinea pigs. These results suggested that motilin or EM-A modulates gastrointestinal motility which was mediated by activating gastric nervous and NO pathways in guinea pigs gastro-intestinal tract.
Optimal escape theory predicts escape behaviors beyond flight initiation distance: risk assessment and escape by striped plateau lizards Sceloporus virgatus
Authors: Cooper William E. 
Published: September 2019

Abstract
Escape theory predicts that flight initiation distance (FID = distance between predator and prey when escape begins) is longer when risk is greater and shorter when escape is more costly. A few tests suggest that escape theory applies to distance fled. Escape models have not addressed stochastic variables, such as probability of fleeing and of entering refuge, but their economic logic might be applicable. Experiments on several risk factors in the lizard Sceloporus virgatus confirmed all predictions for the above escape variables. FID was greater when approach was faster and more direct, for lizards on ground than on trees, for lizards rarely exposed to humans, for the second of two approaches, and when the predator turned toward lizards rather than away. Lizards fled further during rapid and second consecutive approaches. They were more likely to flee when approached directly, when a predator turned toward them, and during second approaches. They were more likely to enter refuge when approached rapidly. A novel finding is that perch height in trees was unrelated to FID because lizards escaped by moving out of sight, then moving up or down unpredictably. These findings add to a growing body of evidence supporting predictions of escape theory for FID and distance fled. They show that two probabilistic aspects of escape are predictable based on relative predation risk levels. Because individuals differ in boldness, the assessed optimal FID and threshold risks for fleeing and entering refuge are exceeded for an increasing proportion of individuals as risk increases.
Identifying Chinese species of Gammarus (Crustacea: Amphipoda) using DNA barcoding
Authors: Hou Zhong-e , Li Zhu , Li Shu-qiang 
Published: September 2019

Abstract
Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21. 9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.
Terrestrial behavior and use of forest strata in a group of black-and-white snub-nosed monkeys Rhinopithecus bieti at Xiaochangdu, Tibet
Authors: Xiang Zuofu , Huo Sheng , Xiao Wen , Quan Ruichang , Grueter Cyril C. 
Published: September 2019

Abstract
Food distribution and predation pressure are considered to be the main ecological factors that influence the use of forest strata (basically arboreality vs. terrestriality) in non-human primates. Here, we investigate ground use of wild, unprovisioned black-and-white snub-nosed monkeys Rhinopithecus bieti by means of the scan sampling method. The results show that the monkeys spent 15.0% of the day time on the ground; 16.6%, 12.7%, and 15.6% for adult males, adult females and juveniles, respectively. Adult males and juveniles of both sexes showed significantly higher rates of terrestrial time than adult females. Females without clinging infants spent significantly more time on the ground than expected, while females with clinging infants spent significantly less time on the ground than expected. These results suggest that the higher degree of terrestrial behavior for males and juveniles may be due to their higher agility in comparison with females. Our study showed that the monkeys fed more on lichens relative to other food items when in the trees, but more on buds/leaves, flowers, fruits/nuts, resin/bark, and herbs when on the ground. According to our investigation, the ecological significance of the species’ terrestriality lies mainly in the utilization of terrestrial food resources.