Ecological Scale of Bird Community Response to Pinon-Juniper Removal

Pinon (Pinus spp.) and juniper (Juniperus spp.) removal is a common management approach to restore sagebrush (Artemisia spp.) vegetation in areas experiencing woodland expansion. Because many management treatments are conducted to benefit sagebrush-obligate birds, we surveyed bird communities to assess treatment effectiveness in establishing sagebrush bird communities at study sites in Utah, Nevada, Idaho, and Oregon. Our analyses included data from 1 or 2 yr prior to prescribed fire or mechanical treatment and 3 to 5 yr posttreatment. We used detrended correspondence analysis to 1) identify primary patterns of bird communities surveyed from 2006 to 2011 at point transects, 2) estimate ecological scale of change needed to achieve treatment objectives from the relative dissimilarity of survey points to the ordination region delineating sagebrush bird communities, and 3) measure changes in pre- and posttreatment bird communities. Birds associated with sagebrush, woodlands, and ecotones were detected on our surveys; increased dissimilarity of survey points to the sagebrush bird community was characterized by a gradient of increased juniper and decreased sagebrush cover. Prescribed fires burned between 30% and 97% of our bird survey points. However, from 6% to 24% cover of pit-ion-juniper still remained posttreatment on the four treatment plots. We measured only slight changes in bird communities, which responded primarily to current vegetation rather than relative amount of change from pretreatment vegetation structure. Bird communities at survey points located at greater ecological scales from the sagebrush bird community changed least and will require more significant impact to achieve changes. Sagebrush bird communities were established at only two survey points, which were adjacent to a larger sagebrush landscape and following almost complete juniper removal by mechanical treatment. Our results indicate that management treatments that leave residual woodland cover and are not adjacent to extensive sagebrush stands are unlikely to establish sagebrush birds

Exploring QSAR Models for Activity-Cliff Prediction

Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that quantitative structure-activity relationship (QSAR) models struggle to predict ACs and that ACs thus form a major source of prediction error. However, a study to explore the AC-prediction power of modern QSAR methods and its relationship to general QSAR-prediction performance is lacking. We systematically construct nine distinct QSAR models by combining three molecular representation methods (extended-connectivity fingerprints, physicochemical-descriptor vectors and graph isomorphism networks) with three regression techniques (random forests, k-nearest neighbours and multilayer perceptrons); we then use each resulting model to classify pairs of similar compounds as ACs or non-ACs and to predict the activities of individual molecules in three case studies: dopamine receptor D2, factor Xa, and SARS-CoV-2 main protease. We observe low AC-sensitivity amongst the tested models when the activities of both compounds are unknown, but a substantial increase in AC-sensitivity when the actual activity of one of the compounds is given. Graph isomorphism features are found to be competitive with or superior to classical molecular representations for AC-classification and can thus be employed as baseline AC-prediction models or simple compound-optimisation tools. For general QSAR-prediction, however, extended-connectivity fingerprints still consistently deliver the best performance. Our results provide strong support for the hypothesis that indeed QSAR methods frequently fail to predict ACs. We propose twin-network training for deep learning models as a potential future pathway to increase AC-sensitivity and thus overall QSAR performance.Comment: Submitted to Journal of Cheminformatic

Hybrid Software Development Approaches in Practice: A European Perspective

Agile and traditional development approaches are used in combination in todays software development. To improve the understanding and to provide better guidance for selecting appropriate development approaches, it is important to analyze such combinations in practice. Results obtained from an online survey strongly confirm that hybrid development approaches are widely used in industry. Our results show that hybrid development approaches: (i) have become reality for nearly all companies; (ii) are applied to specific projects even in the presence of company-wide policies for process usage; (iii) are neither planned nor designed but emerge from the evolution of different work practices; and, (iv) are consistently used regardless of company size or industry secto

Music and lyric characteristics of popular Dutch funeral songs

This study compared the characteristics of 150 songs (Dutch lyrics, N = 47, English lyrics, N = 103), popular at Dutch funerals, to an equal number of non-funeral songs. The variables explored included those linked with the music (valence, energy, danceability, acousticness, key, and tempo); and lyrics, namely: linguistics-related (first-person singular/plural, second-person pronouns; past, present, future tense; expressed emotion (positive, negative words, and the discrete emotional categories anger, anxiety, sadness); and category words (those relating to family, friends, death, religion). Funeral music was lower in valence, energy, and danceability and higher in acousticness than non-funeral music. Furthermore, English funeral music lyrics contained more second-person pronouns and were more future-focused than comparison songs. Funeral lyrics were not particularly negative, but English texts contained more words relating to sadness. In conclusion, funeral music differs in severable notable respects from general popular songs that may reflect the special purpose of this music

A Comparison of Music Characteristics of Funeral Music from Croatia, the Netherlands, and the United Kingdom

Music forms an integral and essential part of funeral rituals worldwide, but has to date received little systematic research attention. Recent investigations into funeral music used in the Netherlands showed that it is lower in tempo and valence, less energetic, and more acoustic than popular music. Funeral music is also often in a major mode. The present study sought to replicate these findings for a Dutch (NL) funeral music sample and to expand upon previous knowledge by investigating the audio features provided by Spotify, namely: valence, energy, tempo, acousticness, instrumentalness, mode, and danceability for funeral music samples from Croatia (HR) and the United Kingdom (UK). First, values of music characteristics for funeral music used in HR, N = 388 pieces, NL, N = 500 pieces, and UK, N = 439 pieces, were compared to values of popular control music from each country separately. Previous findings were replicated: for HR, NL, and UK, funeral music displayed a similar pattern as described above. Second, the values of Spotify audio features for funeral music were compared between countries. Analyses revealed significant differences between NL/UK and HR, namely lower valence and energy and higher acousticness (only HR-UK) and instrumentalness for NL/UK compared to HR. Effect sizes were, however, small and are likely due to differences in music selections. These results suggest that, even though there is much diversity in music pieces and songs, funeral music within and across these European countries is more alike than different in terms of its audio characteristics

An Efficient Algorithm for Enumerating Chordless Cycles and Chordless Paths

A chordless cycle (induced cycle) $C$ of a graph is a cycle without any chord, meaning that there is no edge outside the cycle connecting two vertices of the cycle. A chordless path is defined similarly. In this paper, we consider the problems of enumerating chordless cycles/paths of a given graph $G=(V,E),$ and propose algorithms taking $O(|E|)$ time for each chordless cycle/path. In the existing studies, the problems had not been deeply studied in the theoretical computer science area, and no output polynomial time algorithm has been proposed. Our experiments showed that the computation time of our algorithms is constant per chordless cycle/path for non-dense random graphs and real-world graphs. They also show that the number of chordless cycles is much smaller than the number of cycles. We applied the algorithm to prediction of NMR (Nuclear Magnetic Resonance) spectra, and increased the accuracy of the prediction

Light trapping gratings for solar cells an analytical period optimization approach

Solar cells can harvest incident sunlight very efficiently by utilizing grating based light trapping. As the working principle of such gratings strongly depends on the number as well as the propagation directions of the diffraction orders, the grating period is a key parameter. We present an analytical model for optimizing the grating period, focusing on its impact on light path enhancement and outcoupling probability. Based on the presented model, we formulate guidelines to maximize light trapping in state of the art high end solar cells. The model increases the understanding of the grating performance in systems like the III V Si triple junction solar cell achieving record efficienc

Endothelial cell cytosolic free calcium regulates neutrophil migration across monolayers of endothelial cells

Polymorphonuclear leukocytes (PMN) traverse an endothelial cell (EC) barrier by crawling between neighboring EC. Whether EC regulate the integrity of their intercellular adhesive and junctional contacts in response to chemotaxing PMN is unresolved. EC respond to the binding of soluble mediators such as histamine by increasing their cytosolic free calcium concentration ([Ca++]i) (Rotrosen, D., and J.I. Gallin. 1986. J. Cell Biol. 103:2379-2387) and undergoing shape changes (Majno, G., S. M. Shea, and M. Leventhal. 1969. J. Cell Biol. 42:617-672). Substances such as leukotriene C4 (LTC4) and thrombin, which increased the permeability of EC monolayers to ions, as measured by the electrical resistance of the monolayers, transiently increased EC [Ca++]i. To determine whether chemotaxing PMN cause similar changes in EC [Ca++]i, human umbilical vein endothelial cells (HUVEC) maintained as monolayers were loaded with fura-2. [Ca++]i was measured in single EC during PMN adhesion to and migration across these monolayers. PMN-EC adhesion and transendothelial PMN migration in response to formyl-methionyl-leucyl-phenylalanine (fMLP) as well as to interleukin 1 (IL-1) treated EC induced a transient increase in EC [Ca++]i which temporally corresponded with the time course of PMN-EC interactions. When EC [Ca++]i was clamped at resting levels with a cell permeant calcium buffer, PMN migration across EC monolayers and PMN induced changes in EC monolayer permeability were inhibited. However, clamping of EC [Ca++]i did not inhibit PMN-EC adhesion. These studies provide evidence that EC respond to stimulated PMN by increasing their [Ca++]i and that this increase in [Ca++]i causes an increase in EC monolayer permeability. Such [Ca++]i increases are required for PMN transit across an EC barrier. We suggest EC [Ca++]i regulates transendothelial migration of PMN by participating in a signal cascade which stimulates EC to open their intercellular junctions to allow transendothelial passage of leukocytes

Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion.

The advent of cell culture-based methods for the establishment and expansion of human corneal endothelial cells (CEnC) has provided a source of transplantable corneal endothelium, with a significant potential to challenge the one donor-one recipient paradigm. However, concerns over cell identity remain, and a comprehensive characterization of the cultured CEnC across serial passages has not been performed. To this end, we compared two established CEnC culture methods by assessing the transcriptomic changes that occur during in vitro expansion. In confluent monolayers, low mitogenic culture conditions preserved corneal endothelial cell state identity better than culture in high mitogenic conditions. Expansion by continuous passaging induced replicative cell senescence. Transcriptomic analysis of the senescent phenotype identified a cell senescence signature distinct for CEnC. We identified activation of both classic and new cell signaling pathways that may be targeted to prevent senescence, a significant barrier to realizing the potential clinical utility of in vitro expansion