bluuebunny/crossref_metadata_2025_split huggingface dataset:
Qudaich: A smart sequence aligner
Authors: Akhter Sajia , Edwards Robert A 
Published: June 2016

AbstractNext generation sequencing (NGS) technology produces massive amounts of data in a reasonable time and low cost. Analyzing and annotating these data requires sequence alignments to compare them with genes, proteins and genomes in different databases. Sequence alignment is the first step in metagenomics analysis, and pairwise comparisons of sequence reads provide a measure of similarity between environments. Most of the current aligners focus on aligning NGS datasets against long reference sequences rather than comparing between datasets. As the number of metagenomes and other genomic data increases each year, there is a demand for more sophisticated, faster sequence alignment algorithms. Here, we introduce a novel sequence aligner, Qudaich, which can efficiently process large volumes of data and is suited to de novo comparisons of next generation reads datasets. Qudaich can handle both DNA and protein sequences and attempts to provide the best possible alignment for each query sequence. Qudaich can produce more useful alignments quicker than other contemporary alignment algorithms.Author SummaryThe recent developments in sequencing technology provides high throughput sequencing data and have resulted in large volumes of genomic and metagenomic data available in public databases. Sequence alignment is an important step for annotating these data. Many sequence aligners have been developed in last few years for efficient analysis of these data, however most of them are only able to align DNA sequences and mainly focus on aligning NGS data against long reference genomes. Therefore, in this study we have designed a new sequence aligner, qudaich, which can generate pairwise local sequence alignment (at both the DNA and protein level) between two NGS datasets and can efficiently handle the large volume of NGS datasets. In qudaich, we introduce a unique sequence alignment algorithm, which outperforms the traditional approaches. Qudaich not only takes less time to execute, but also finds more useful alignments than contemporary aligners.
The combination of the functionalities of feedback circuits is determinant for the number and size of attractors of molecular networks
Authors: Azpeitia Eugenio , Muñoz Stalin , González-Tokman Daniel , Martínez-Sánchez Mariana Esther , Weinstein Nathan , Naldi Aurélien , Álvarez-Buylla Elena R. , Rosenblueth David A , Mendoza Luis 
Published: June 2016

ABSTRACTMolecular regulation was initially assumed to follow both a unidirectional and a hierarchical organization forming pathways. Regulatory processes, however, form highly interlinked networks with non-hierarchical and non-unidirectional structures that contain statistically overrepresented circuits (motifs). Here, we analyze the behavior of pathways containing non-hierarchical and non-unidirectional interactions that create motifs. In comparison with unidirectional and hierarchical pathways, our pathways have a high diversity of behaviors, characterized by the size and number of attractors. Motifs have been studied individually showing that feedback circuit motifs regulate the number and size of attractors. It is less clear what happens in molecular networks that usually contain multiple feedbacks. Here, we find that the way feedback circuits couple to each other (i.e., the combination of the functionalities of feedback circuits) regulate both the precise number and size of the attractors. We show that the different sets of expected results of epistasis analysis (a method to infer regulatory interactions) are produced by many non-hierarchical and non-unidirectional structures. Thus, these structures cannot be correctly inferred by epistasis analysis. Finally, we show that the structures producing the epistasis results have remarkably similar sets of combinations of functionalities, that combined with other network properties could greatly improve epistasis analysis.
Calming Meditation Increases Altruism, Decreases Parochialism
Authors: Frost Karl 
Published: June 2016

AbstractIt has been proposed that cultivating calm will increase altruism and decrease parochialism, where altruism is defined as self-sacrifice in support of others, regardless of group affiliation or identity, and parochialism is defined as prosocial self-sacrifice restricted to fellow members of a group. Such could be the case with a calming meditation practice. An alternate hypothesis, coming from the study of ritual, proposes that shared practices lead to bonding, increasing parochialism, but not altruism generally. These contradictory hypotheses of the potential effects of shared cultural practices of calming meditation were explored via a formal behavioral experiment using a simple treatment and control format with a short, facilitated breath awareness practice known to produce calm. Altruism and parochialism were measured through anonymous play in Public Goods games performed with both in-group and out-group individuals. The sum of contributions of the two plays gave a measure of altruism, while the difference between the two gave a measure of parochialism. The analysis of the results using Bayesian AICc model comparison methods supports the first hypothesis that calming practices reduces parochialism and increases altruism. The hypothesis of intentional shared practice as parochialism inducing was not supported by the results in this case of a shared calming practice.
Gene-Culture Coevolution of Prosocial Rituals
Authors: Frost Karl 
Published: June 2016

AbstractIt has been argued that costly socially learned rituals have the potential to generate prosocial emotional responses arising from genetically based behavioral dispositions, hijacking these behavioral dispositions to solve otherwise intractable cooperation problems. An example is the innovation of synchronous movement rituals which seem to engage the same altruistic response as instinctual mimicry. Arguments against this hypothesis are based in the idea that cheap markers of altruistic intent (“Green Beards“)are vulnerable to manipulation from non-cooperating free-riders that are similarly marked. This paper formally models the gene-culture coevolutionary dynamics of a system in which a costly socially learned ritual practice coevolves with the genes underpinning the prosocial response. This takes a ‘genetic mismatch’ hypothesis (where fast evolution of socially learned behaviors create a temporary mismatch with the coevolving genes, which take longer to evolve to equilibrium) and models it dynamically. The genetic and cultural fitness equations are first analyzed for equilibrium and then simulations are used to predicting trajectories for both the socially learned behavior and the hijacked genetic trait over time. Relying on fast culture and slow genes, it demonstrates how high levels of ritual efficacy may be established, at least temporarily, through gene culture interaction. It also shows how longer term feedbacks on the genes from culture may lead to decreases in the prosocial gene in the population and reduced overall population mean fitness, despite high levels of altruism in the population.
Bottom-up ecology of the human microbiome: from metagenomes to metabolomes
Authors: Garza Daniel R. , Van Verk Marcel C. , Huynen Martijn A. , Dutilh Bas E. 
Published: June 2016

AbstractThe environmental metabolome is a dominant and essential factor shaping microbial communities. Thus, we hypothesized that metagenomic datasets could reveal the quantitative metabolic status of a given sample. Using a newly developed bottom-up ecology algorithm, we predicted high-resolution metabolomes of hundreds of metagenomic datasets from the human microbiome, revealing body-site specific metabolomes consistent with known metabolomics data, and suggesting that common cosmetics ingredients are some of the major metabolites shaping the human skin microbiome.
Disorder Atlas: web-based software for the proteome-based interpretation of intrinsic disorder predictions
Authors: Vincent Michael , Schnell Santiago 
Published: June 2016

AbstractIntrinsically disordered proteins lack a stable three-dimensional structure under physiological conditions. While this property has gained considerable interest within the past two decades, disorder poses substantial challenges to experimental characterization efforts. In effect, numerous computational tools have been developed to predict disorder from primary sequences, however, interpreting the output of these algorithms remains a challenge. To begin to bridge this gap, we present Disorder Atlas, web-based software that facilitates the interpretation of intrinsic disorder predictions using proteome-based descriptive statistics. This service is also equipped to facilitate large-scale systematic exploratory searches for proteins encompassing disorder features of interest, and further allows users to browse the prevalence of multiple disorder features at the proteome level. As a result, Disorder Atlas provides a user-friendly tool that places algorithm-generated disorder predictions in the context of the proteome, thereby providing an instrument to compare the results of a query protein against predictions made for an entire population. Disorder Atlas currently supports ten eukaryotic proteomes and is freely available for non-commercial users athttp://www.disorderatlas.org.
Disrupting dorsolateral prefrontal cortex by rTMS reduces the P300 based marker of deception
Authors: Karton Inga , Kitt Anni-Bessie , Bachmann Talis 
Published: June 2016

AbstractIt is well known that electroencephalographic event related potential component P300 is sensitive to perception of critical items in a concealed information test. However, it is not known whether the relative level of expression of P300 as a neural marker of deception can be manipulated by means of non-invasive neuromodulation. Here, we show that while P300 exhibited systematic amplitude differences in response to the more as well as the less significant stimuli items encountered at the “crime scene” compared to neutral items, offline rTMS to dorsolateral prefrontal cortex attenuated P300 amplitude in response to the critical items. Yet, the individual subjects showed different sensitivity of the P300 as the marker of concealment. We conclude that rTMS can be used for subduing electrophysiological markers of deception, but this effect depends on whether the subject belongs to the group of CIT-sensitive individuals.
Impact of opportunistic salpingectomy on anti‐Müllerian hormone in patients undergoing laparoscopic hysterectomy: a multicentre randomised controlled trial
Authors: Song T , Kim MK , Kim M‐L , Jung YW , Yun BS , Seong SJ , Kwon S‐H 
Published: June 2016

ObjectiveThe aim of the study was to investigate whether opportunistic salpingectomy has any deleterious effects on ovarian reserve and increases surgical risk in patients undergoing laparoscopic hysterectomy.DesignA multicentre, randomised controlled trial.SettingThree university hospitals in Korea.PopulationSixty‐eight patients undergoing laparoscopic hysterectomy for the treatment of symptomatic benign uterine diseases.MethodsPatients were randomised to undergo either opportunistic salpingectomy (n = 34) or no salpingectomy (n = 34) during laparoscopic hysterectomy.Main outcome measurementsThe primary and secondary outcome measures were the change of ovarian reserve, determined by the rate of decline in anti‐Müllerian hormone (AMH) level from before surgery to 3 months post‐surgery and surgical outcomes, respectively.ResultsBaseline demographic and clinical characteristics were similar between the two groups. There was also no difference in operative outcomes such as operative time, operative bleeding, or complications between the two groups. In both groups, postoperative AMH levels were significantly lower than preoperative AMH levels (both, P < 0.01). The decline rate in AMH was 12.5% (interquartile range 0.8–60.9%) in the opportunistic salpingectomy group and 10.8% (interquartile range 6.9–27.4%) in the no salpingectomy group, with no significant difference between both groups (P = 0.898).ConclusionsOpportunistic salpingectomy at the time of laparoscopic hysterectomy did not have any negative effects on ovarian reserve or increased surgical risk.Tweetable abstractOpportunistic salpingectomy did not have any negative effects on ovarian reserve or increased surgical risk.
Transthoracic and transoesophageal echocardiography: a systematic review of feasibility and impact on diagnosis, management and outcome after cardiac surgery
Authors: Heiberg J. , El‐Ansary D. , Royse C. F. , Royse A. G. , Alsaddique A. A. , Canty D. J. 
Published: June 2016

SummaryTransthoracic and transoesophageal echocardiography are increasingly used as tools to improve clinical assessment following cardiac surgery. However, most physicians are not trained in echocardiography, and there is no widespread agreement on the feasibility, indications or effect on outcome of transthoracic or transoesophageal echocardiography for patients after cardiac surgery. We performed a systematic review of electronic databases for focused transthoracic and transoesophageal echocardiography after cardiac surgery which revealed 15 full‐text articles. They consistently reported that echocardiography is feasible, whether performed by a novice or expert, and frequently resulted in important changes in diagnosis of cardiac abnormalities and their management. However, most were observational studies and there were no well‐designed trials investigating the impact of echocardiography on outcome. We conclude that both transthoracic and transoesophageal echocardiography are useful following cardiac surgery.
The tumour microenvironment influences survival and time to transformation in follicular lymphoma in the rituximab era
Authors: Blaker Yngvild Nuvin , Spetalen Signe , Brodtkorb Marianne , Lingjærde Ole Christian , Beiske Klaus , Østenstad Bjørn , Sander Birgitta , Wahlin Björn Engelbrekt , Melen Christopher Michael , Myklebust June Helen , Holte Harald , Delabie Jan , Smeland Erlend Bremertun 
Published: June 2016

SummaryThe tumour microenvironment influences outcome in patients with follicular lymphoma (FL), but its impact on transformation is less studied. We investigated the prognostic significance of the tumour microenvironment on transformation and survival in FL patients treated in the rituximab era. We examined diagnostic and transformed biopsies from 52 FL patients using antibodies against CD3, CD4, CD8, CD21 (CR2), CD57 (B3GAT1), CD68, FOXP3, TIA1, PD‐1 (PDCD1), PD‐L1 (CD274) and PAX5. Results were compared with a second cohort of 40 FL patients without signs of transformation during a minimum of five years observation time. Cell numbers and localization were semi‐quantitatively assessed. Better developed CD21+ follicular dendritic cell (FDC) meshworks at diagnosis was a negative prognostic factor for overall survival (OS), progression‐free survival (PFS) and time to transformation (TTT) in patients with subsequently transformed FL. Remnants of FDC meshworks at transformation were associated with shorter OS and PFS from transformation. High degrees of intrafollicular CD68+ and PD‐L1+ macrophage infiltration, high total area scores and an extrafollicular/diffuse pattern of FOXP3+ T cells and high intrafollicular scores of CD4+ T cells at diagnosis were associated with shorter TTT. Scores of several T‐cell subset markers from the combined patient cohorts were predictive for transformation, especially CD4 and CD57.
Left ventricular reverse remodeling after aortic valve surgery for acute versus chronic aortic regurgitation
Authors: Regeer Madelien V. , Versteegh Michel I. M. , Ajmone Marsan Nina , Schalij Martin J. , Klautz Robert J. M. , Bax Jeroen J. , Delgado Victoria 
Published: June 2016

AimsExtent of left ventricular (LV) reverse remodeling after aortic valve repair or replacement (AVR) may differ between patients operated for acute aortic regurgitation (AR) and chronic AR. The aim of this study was to compare changes in LV volumes and function between patients with acute and chronic AR who underwent AVR.Methods and ResultsA total of 98 patients (54±15 years, 61% men) with acute (n=21) or chronic AR (n=77) were included in the present retrospective evaluation. LV volumes, LV ejection fraction, and global longitudinal strain indexed for LV end‐diastolic volume (GLSi) were assessed preoperatively and after a median follow‐up of 28 months (interquartile range: 17–66 months). Patients with acute AR tended to have smaller preoperative LV end‐diastolic volume compared with chronic AR (156±15 vs 183±6 mL; P=.070). Both in patients with acute and chronic AR, significant LV reverse remodeling with sustained reduction in LV volumes occurred during follow‐up with a significant smaller LV end‐diastolic volume in acute AR compared with chronic AR (106±8 vs 128±5 mL; P=.032). Preoperative and postoperative LV ejection fractions were not significantly different between groups. In contrast, GLSi was better in patients with acute AR compared with chronic AR before AVR (−1.34±0.20 vs −0.96±0.07%/10 mL; P=.042) and during follow‐up (−1.65±0.16 vs −1.29±0.07%/10 mL; P=.017).ConclusionsAfter AVR, LV reverse remodeling occurs both in patients with acute and chronic AR. However, LV end‐diastolic volume was more reduced and GLSi was more preserved during follow‐up in acute AR than in chronic AR.
Do River Otters Conform to Habitat Suitability Assessments?
Authors: Holland Angela , van der Merwe Jorista 
Published: June 2016

AbstractRiver otters (Lontra canadensis) were reintroduced from 1994–1996 into parts of Illinois where the species was extirpated due to over harvest and habitat loss. At the time of reintroduction, managing for the persistence of the population through habitat was very important and research was conducted to determine which watersheds had quality habitat and which needed increased management and protection. In a study conducted in the mid‐1990s, biologists used pattern recognition (PATREC) modeling to identify high and low quality habitat for river otters at the subunit level (i.e., divided watershed), based on specific habitat attributes including wooded area, sinuosity, and wetland edge. We compared the habitat quality ratings of subunits with river otter use at 112 bridge sites from 2012–2014 to determine if river otters have distributed themselves according to previously determined habitat quality. We found that the PATREC model was a poor predictor of river otter use when sites were located close to the otter reintroduction points. The PATREC model was most likely a poor predictor of river otter use due to an over‐emphasis on the importance of woody vegetation to habitat suitability for river otter in the model. We recommend that future work on the assessment of habitat suitability for river otter use, and accuracy of this assessment, be conducted at a local spatial scale and over a shorter temporal scale. We also recommend that watershed policies and habitat assessments consider changes to land‐cover and follow an adaptive management approach to assess habitat suitability for reintroduced species.
Species range expansion constrains the ecological niches of resident butterflies
Authors: Audusseau Hélène , Le Vaillant Maryline , Janz Niklas , Nylin Sören , Karlsson Bengt , Schmucki Reto 
Published: June 2016

AbstractAimChanges in community composition resulting from environmental changes modify biotic interactions and affect the distribution and density of local populations. Such changes are currently occurring in nettle‐feeding butterflies in Sweden where Araschnia levana has recently expanded its range northward and is now likely to interact with resident species (Aglais urticae and Aglais io). Butterfly occurrence data collected over years and across regions enabled us to investigate how a recent range expansion of A. levana may have affected the environmental niche of resident species.LocationWe focused on two regions of Sweden (Skåne and Norrström) where A. levana has and has not established and two time periods (2001–2006 and 2009–2012) during its establishment in Skåne.MethodsWe performed two distinct analyses in each region using the PCA‐env and the framework described in Broennimann et al. (2012). First, we described the main sources of variation in the environment. Second, in each time period and region, we characterized the realized niches of our focal species across topographic and land use gradients. Third, we quantified overlaps and differences in realized niches between and within species over time.ResultsIn Skåne, A. levana has stabilized its distribution over time, while the distribution of the native species has shifted. These shifts depicted a consistent pattern of avoiding overlap between the native species and the environmental space occupied by A. levana, and it was stronger for A. urticae than for A. io. In both regions, we also found evidence of niche partitioning between native species.Main conclusionsInterspecific interactions are likely to affect local species distributions. It appears that the ongoing establishment of A. levana has modified local biotic interactions and induced shifts in resident species distributions. Among the mechanisms that can explain such patterns of niche partitioning, parasitoid‐driven apparent competition may play an important role in this community.
The internal structure of situational judgement tests reflects candidate main effects: Not dimensions or situations
Authors: Jackson Duncan J. R. , LoPilato Alexander C. , Hughes Dan , Guenole Nigel , Shalfrooshan Ali 
Published: June 2016

Despite their popularity and capacity to predict performance, there is no clear consensus on the internal measurement characteristics of situational judgement tests (SJTs). Contemporary propositions in the literature focus on treating SJTs as methods, as measures of dimensions, or as measures of situational responses. However, empirical evidence relating to the internal structure of SJT scores is lacking. Using generalizability theory, we decomposed multiple sources of variance for three different SJTs used with different samples of job candidates (N1 = 2,320; N2 = 989; N3 = 7,934). Results consistently indicated that (1) the vast majority of reliable observed score variance reflected SJT‐specific candidate main effects, analogous to a general judgement factor, and that (2) the contribution of dimensions and situations to reliable SJT variance was, in relative terms, negligible. These findings do not align neatly with any of the proposals in the contemporary literature; however, they do suggest an internal structure for SJTs.Practitioner points

To help optimize reliable variance, overall‐level aggregation should be used when scoring SJTs.

The majority of reliable variance in SJTs reflects a general performance factor, relative to variance pertaining to specific dimensions or situations.

SJT‐based developmental feedback should be delivered in terms of general SJT performance rather than on performance relating to specific dimensions or situations.

Generalizability theory, although underutilized in organizational multifaceted measurement, offers an approach to informing on the psychometric properties of SJTs that is well suited to the complexities of SJT measurement designs.