bluuebunny/crossref_metadata_2025_split huggingface dataset:
An improved constraint filtering technique for inferring hidden states and parameters of a biological model
Authors: Murtuza Baker Syed , Poskar C. Hart , Schreiber Falk , Junker Björn H. 
Published: February 2013

Abstract
Motivation: In systems biology, kinetic models represent the biological system using a set of ordinary differential equations (ODEs). The correct values of the parameters within these ODEs are critical for a reliable study of the dynamic behaviour of such systems. Typically, it is only possible to experimentally measure a fraction of these parameter values. The rest must be indirectly determined from measurements of other quantities. In this article, we propose a novel statistical inference technique to computationally estimate these unknown parameter values. By characterizing the ODEs with non-linear state-space equations, this inference technique models the unknown parameters as hidden states, which can then be estimated from noisy measurement data.
Results: Here we extended the square-root unscented Kalman filter SR-UKF proposed by Merwe and Wan to include constraints with the state estimation process. We developed the constrained square-root unscented Kalman filter (CSUKF) to estimate parameters of non-linear state-space models. This probabilistic inference technique was successfully used to estimate parameters of a glycolysis model in yeast and a gene regulatory network. We showed that our method is numerically stable and can reliably estimate parameters within a biologically meaningful parameter space from noisy observations. When compared with the two common non-linear extensions of Kalman filter in addition to four widely used global optimization algorithms, CSUKF is shown to be both accurate and computationally efficient. With CSUKF, statistical analysis is straightforward, as it directly provides the uncertainty on the estimation result.
Availability and implementation: Matlab code available upon request from the author.
Contact: baker@ipk-gatersleben.de
Supplementary information: Supplementary data are available at Bioinformatics online.
The Arabidopsis Elongator Complex Subunit2 Epigenetically Regulates Plant Immune Responses
Authors: Wang Yongsheng , An Chuanfu , Zhang Xudong , Yao Jiqiang , Zhang Yanping , Sun Yijun , Yu Fahong , Amador David Moraga , Mou Zhonglin 
Published: February 2013

Abstract
The Arabidopsis thaliana Elongator complex subunit2 (ELP2) genetically interacts with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1), a key transcription coactivator of plant immunity, and regulates the induction kinetics of defense genes. However, the mechanistic relationship between ELP2 and NPR1 and how ELP2 regulates the kinetics of defense gene induction are unclear. Here, we demonstrate that ELP2 is an epigenetic regulator required for pathogen-induced rapid transcriptome reprogramming. We show that ELP2 functions in a transcriptional feed-forward loop regulating both NPR1 and its target genes. An elp2 mutation increases the total methylcytosine number, reduces the average methylation levels of methylcytosines, and alters (increases or decreases) methylation levels of specific methylcytosines. Interestingly, infection of plants with the avirulent bacterial pathogen Pseudomonas syringae pv tomato DC3000/avrRpt2 induces biphasic changes in DNA methylation levels of NPR1 and PHYTOALEXIN DEFICIENT4 (PAD4), which encodes another key regulator of plant immunity. These dynamic changes are blocked by the elp2 mutation, which is correlated with delayed induction of NPR1 and PAD4. The elp2 mutation also reduces basal histone acetylation levels in the coding regions of several defense genes. Together, our data demonstrate a new role for Elongator in somatic DNA demethylation/methylation and suggest a function for Elongator-mediated chromatin regulation in pathogen-induced transcriptome reprogramming.
CD8+ Effector T Cells at the Fetal–Maternal Interface, Balancing Fetal Tolerance and Antiviral Immunity
Authors: Tilburgs Tamara , Strominger Jack L. 
Published: February 2013

During pregnancy CD8+ effector T cells need optimal immune regulation to prevent a detrimental response to allogeneic fetal cells while providing immune protection to infections. A significant proportion of (prospective) mothers carry naïve or memory CD8+ T cells with a TCR that can directly bind to paternal MHC molecules. In addition, a high percentage of pregnant women develop specific T cell responses to fetal minor histocompatibility antigens (mHags). Under normal conditions, fetal–maternal MHC and mHag mismatches lead to elevated lymphocyte activation but do not induce pregnancy failure. Furthermore, viral infections alter the maternal CD8+ T cell response by changing the CD8+ T cell repertoire and increasing the influx of CD8+ T cells to decidual tissue. The normally high T cell activation threshold at the fetal–maternal interface may prevent efficient clearance of viral infections. Conversely, the increased inflammatory response due to viral infections may break fetal–maternal tolerance and lead to pregnancy complications. The aim of this review is to discuss the recent studies of CD8+ T cells in pregnancy, identify potential mechanisms for antigen‐specific immune recognition of fetal extravillous trophoblast (EVT) cells by CD8+ T cells, and discuss the impact of viral infections and virus‐specific CD8+ T cells during pregnancy.
Von Willebrand disease‐associated angiodysplasia: a few answers, still many questions
Authors: Franchini Massimo , Mannucci Pier Mannuccio 
Published: February 2013

SummaryThe association between angiodysplasia and von Willebrand disease (VWD) has been known for more than 40 years. Bleeding in the gastrointestinal tract associated with angiodysplasia worsens the clinical course of this inherited haemorrhagic disorder and management may become difficult and challenging. Angiodysplasia associated with acquired defects or dysfunctions of von Willebrand factor (VWF) has also been reported in a variety of conditions such as monoclonal gammopathies, Heyde syndrome and in carriers of ventricular assist devices. The most recent advances concerning the mechanistic, clinical and therapeutic aspects of VWD‐associated angiodysplasia are summarized in this review, together with the limitations of our knowledge that warrant further research in the frame of international cooperation.
A comparison of rural and urban Indian children's visual detection of threatening and nonthreatening animals
Authors: Penkunas Michael J. , Coss Richard G. 
Published: February 2013

AbstractRecent studies indicate that young children preferentially attend to snakes, spiders, and lions compared with nondangerous species, but these results have yet to be replicated in populations that actually experience dangerous animals in nature. This multi‐site study investigated the visual‐detection biases of southern Indian children towards two potentially dangerous taxa, snakes and lions, that constituted major threats during human evolution. Three‐ to 8‐year‐old children from two distinct populations were presented with visual‐search tasks containing one target image embedded in matrices of eight distractor images. Children living in Bangalore city, an urban setting in which exposure to dangerous animals would only occur occasionally during family outings to zoos and forest areas, were compared with children living in and around National Parks where exposure to dangerous species is frequent. In the first two experiments, children from both locations detected snake and lion images more rapidly than nonthreatening lizard and antelope images, respectively. Neither urban nor rural children displayed a bias for detecting horses versus cows, the latter constituting a familiar animal with strong religious significance. For all three experiments, the reaction times of urban and rural children were very similar, indicating that periodic exposure to dangerous animals early in life, coupled with adult cautioning, did not facilitate better snake and lion detection. This consistency of urban and rural children with different exposure to dangerous animals suggests that detection of some dangerous species may reflect both experience in nature and visual biases shaped by natural selection.
The ability of the Reciproc R25 instrument to reach the full root canal working length without a glide path
Authors: De‐Deus G. , Arruda T. E. P. , Souza E. M. , Neves A. , Magalhães K. , Thuanne E. , Fidel R. A. S. 
Published: February 2013

AbstractAimTo assess the frequency in which the Reciproc instrument reaches the full working length (FWL) of mandibular molar canals without a glide path.MethodologyFrom a pool of mandibular molars, 253 root canals were classified as straight (G1) and, 249 root canals as moderately curved (G2) following Schneider's method. A R25 Reciproc instrument (VDW, Munich, Germany) was advanced in the canals without any previous glide path. All cases where Reciproc instruments reached the FWL were classified as ‘Reaching the FWL’ (RFWL). When the FWL was not reached by the R25, the root canals were classified as ‘Not Reaching the FWL’ (NRFWL). Pearson's χ2 test compared (i) the frequency distributions of root canals classified as RFWL and NRFWL for each group and (ii) the frequency distributions of NRFWL canals between the groups.ResultsIn G1, 9 cases (3.56%) and in G2, 23 canals (9.34%) were classified as NRFWL. The difference between NRFWL and RFWL was significant in both groups (P = 0.00, χ 2 = 217.2 for G1; P = 0.00, χ 2 = 167.8 for G2). The frequency of NRFWL was significantly higher for G2 (P = 0.02, χ 2 = 5.452).ConclusionThe R25 Reciproc instrument is able to reach the FWL of straight‐ and moderate‐curved mandibular molar canals without a glide path in a large proportion of cases.
Susceptibility of kiwifruit (Actinidia spp.) cultivars to Ceratitis capitata (Diptera: Tephritidae) infestation
Authors: Papachristos D. P. , Papadopoulos N. T. , Maglaras E. , Michaelakis A. , Antonatos S. Α. 
Published: February 2013

AbstractLaboratory no‐choice tests were conducted to determine whether the kiwifruit cultivars Hayward, Tsechelidis (Actinidia deliciosa) and Soreli (A. chinensis) are hosts of the Mediterranean fruit fly, Ceratitis capitata. Kiwifruits were exposed to gravid females for 24 h, and the number of eggs laid as well as larval developmental rates and survival rates of immatures' was determined. Moreover, oviposition and survival rates were recorded for adults obtained from the above three cultivars. Similar experimental procedures were followed using nectarines (Prunus persica), a favourable host for C. capitata. Furthermore, using McPhail‐type traps loaded with food attractants, we compared adult population densities in four kiwifruits and adjacent citrus orchards. Infestation rates were also determined in kiwifruits collected from the above kiwifruit orchards. The results demonstrate that C. capitata, under laboratory conditions, oviposit on all three kiwifruit cultivars tested. The numbers of eggs laid and survival rates of immatures were significantly lower for the two cultivars of A. deliciosa compared with nectarines. On the other hand, oviposition rates were much higher in the cultivar Soreli (A. chinensis) compared with nectarines; however, none of the immatures reached adulthood. Adults obtained from the Hayward and Tsechelidis cultivars had shorter longevity and females were less fecund than those obtained from nectarines. Adult Mediterranean fruit flies were captured in all four kiwifruit orchards, but at significantly lower numbers compared with citrus orchards. Fruit sampling from the Hayward and Tsechelidis cultivars indicated a minimal infestation of the Hayward fruits only (0.41%), which, however, resulted in no adult emergence. Removal of the fruit surface hairs of Hayward cultivar increased dramatically the oviposition rates of C. capitata in laboratory conditions, suggesting significant oviposition‐deterrent properties. The importance of our findings for determining a non‐host status for kiwifruits is discussed.
Morphological and functional events associated to weaning in rabbits
Authors: Bivolarski B. L. , Vachkova E. G. 
Published: February 2013

SummaryIt is acknowledged that the most critical period of rabbit post natal development comprises the first 10–15 days after weaning, when the animals are most susceptible to gastrointestinal infections and at greatest risk of a fatal outcome. Detailed information on rabbits' weaning is provided. The advantages and disadvantages of early weaning (under 23 days of age) are summarised. Regardless of the numerous reports, the effects of early weaning on the growth and development of bunnies and the physiological status of rabbit does are contradictory. The morphological changes in rabbit digestive tract related to weaning – development of intestinal mucosa, height of villi, crypt depth and villus height to crypt depth ratio – are described in detail. The review also goes over several functional changes in rabbits' organism during weaning: blood cholesterol, triglycerides, α‐amylase, lysozyme, complement, triiodothyronine and thyroxine concentrations, and the time course of epidermal growth factor in the milk of lactating does. Based on published research reports, both ours and of other authors, we suggest that from a physiological point of view, the early weaning of rabbits is not fully justified at present. Nevertheless, the increasing market demand for rabbit meat makes early weaning an attractive alternative for farmers and necessitates further studies on the optimisation of weaning in this species.
Rural Considerations in Establishing Network Adequacy Standards for Qualified Health Plans in State and Regional Health Insurance Exchanges
Authors: Talbot Jean A. , Coburn Andrew , Croll Zach , Ziller Erika 
Published: February 2013

AbstractPurposeThe Affordable Care Act (ACA) requires Health Insurance Exchanges (HIEs) to specify network adequacy standards for the Qualified Health Plans (QHPs) they offer to consumers. This article examines rural issues surrounding network adequacy standards, and offers recommendations for crafting standards that optimize rural access.MethodThis policy analysis reviews ACA requirements for QHP network adequacy standards, considering Medicaid managed care and Medicare Advantage (MA) standards as models. We analyze the implications of stringent vs flexible access standards in terms of how choices might affect health plans' participation in rural markets and rural enrollees' access to care. Finally, we propose strategies for designing standards with the degree of flexibility most likely to benefit rural consumers.FindingsA traditional approach to safeguarding rural access is to impose strict network adequacy standards on plans in rural areas. However, if strict standards prove difficult to meet due to rural provider scarcity, they might diminish QHPs' willingness to serve rural areas. Thus, they could exacerbate rather than alleviate rural access problems.ConclusionsTo benefit rural communities, network adequacy standards must be strong enough to provide real protections for beneficiaries, yet flexible enough to accommodate rural delivery system constraints and remain attainable for QHPs. Useful strategies to achieve this balance might include: adjusting standards according to degrees of rurality and rural utilization norms; counting midlevel clinicians toward fulfillment of patient‐provider ratios; and allowing plans to ensure rural access through delivery system innovations such as telehealth.
Is All Punishment Local? The Effects of Jurisdictional Context on Sentence Length*
Authors: Chen Elsa Y. 
Published: February 2013

ObjectivesThis article investigates the extent to which contextual and individual factors influence the length of prison sentences in California.MethodsThe analysis applies a hierarchical linear model to individual and county‐level data.ResultsSome characteristics of the racial, organizational, and public safety environments are found to influence the length of prison terms.ConclusionsThe findings support the organizational maintenance perspective and the idea of minority incarceration as a response to a perceived crime threat. Political environment is not found to have a significant effect on sentence lengths, and the findings do not support the racial threat hypothesis. The effects of contextual factors are more modest than those of individual attributes, including legally relevant variables, such as offense severity, prior record, parole status, and three strikes eligibility. African‐American and younger offenders receive longer sentences, but this effect is not found for Latinos. Substantive, methodological, and policy implications are discussed.
Values, Beliefs, Attitudes: An Empirical Study on the Structure of Environmental Concern and Recycling Participation
Authors: Best Henning , Mayerl Jochen 
Published: February 2013

ObjectivesEmpirical studies on environmental behavior have been using a multitude of different operationalizations of environmental concern, which complicates cumulative research. In this article, we empirically explore the dimensionality of four environmental scales of different specificity, their interrelatedness, and their partial contribution to the explanation of recycling behavior. To facilitate the comparison of different studies, we integrate the scales into a hierarchical model.MethodsIn a German mail survey (n= 1,330), we queried participation in household waste recycling, Inglehart's postmaterialism scale, the new environmental paradigm scale, and a general and specific attitude scale. Using traditional path analysis and latent structural equation modeling, we test the hierarchical structure of environmental values, beliefs, and attitudes and their contribution to explaining recycling behavior.ResultsWe find direct effects of specific attitudes on behavior, but no direct effects of higher‐level cognitions. Rather, values and primitive beliefs influence general attitudes, which in turn determine specific attitudes. The empirical analyses confirm the proposed hierarchical structure.ConclusionsOur research reaffirms Ajzen and Fishbein's postulate of correspondence. Comparison of different studies is only meaningful when the hierarchical position of the respective scales is taken into account properly. To facilitate cumulative research, we propose to use standardized general scales such as the NEP in addition to more specific operationalizations.
Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales
Authors: Shanks Orin C. , Newton Ryan J. , Kelty Catherine A. , Huse Susan M. , Sogin Mitchell L. , McLellan Sandra L. 
Published: February 2013

ABSTRACT

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within
Firmicutes
,
Bacteroidetes
,
Actinobacteria
, and
Proteobacteria
. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States.
No Protective Effects of High-Dosage Dietary Zinc Oxide on Weaned Pigs Infected with Salmonella enterica Serovar Typhimurium DT104
Authors: Janczyk Pawel , Kreuzer Susanne , Assmus Jens , Nöckler Karsten , Brockmann Gudrun A. 
Published: February 2013

ABSTRACT

Twenty-eight-day-old weaned pigs were fed diets with a low (LZn), medium (MZn), or high (MZn) Zn concentration (50 to 80, 150, or 2,500 mg Zn/kg of diet, respectively) provided as zinc oxide (ZnO)(24 pigs per group). They were infected orally with
Salmonella enterica
serovar Typhimurium DT104 on day 32. Salmonellae were cultivated from feces (up to 42 days postinfection [dpi]) and organs (2 and 42 dpi). Activation of the adaptive systemic and mucosal immune systems was investigated by recording anti-
Salmonella
IgG levels and levels of B and T lymphocyte subpopulations in blood and gut-associated lymphatic tissue. Growth performance was recorded as well. Salmonellae were shed at higher levels and for longer periods in the HZn group (
P
< 0.05), with no differences in the tissues. At 2 dpi, the relative percentages of CD4
+
T helper cells (
P
< 0.01) and of CD2
+
T and NK cells (
P
< 0.01) in blood were reduced from the relative cell counts obtained at 0 dpi, irrespective of the Zn group. The lowest percentage of cytotoxic T cells was found 14 dpi in the HZn group relative to the MZn (
P
< 0.05) and LZn (
P
< 0.01) groups. Supplementation of the feed with 2,500 mg Zn/kg of diet immediately after weaning could positively affect the immune responses of piglets infected with
Salmonella
Typhimurium, but for a short period only. After 2 weeks, all positive effects disappeared, and rather negative effects, such as higher shedding of salmonellae, lower T cell frequencies, and worse performance, occurred. Thus, supplementation with ZnO at high levels in the pig industry should be limited to 2 to 3 weeks.