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1. Long‐term seedling and small sapling census data from the B arro C olorado I sland 50 ha F orest D ynamics P lot, P anama

   https://doi.org/10.1002/ecy.4140  

   Comita, Liza S.; Aguilar, Salomón; Hubbell, Stephen P.; Pérez, Rolando (July 2023, Ecology)

   Abstract Tropical forests are well known for their high woody plant diversity. Processes occurring at early life stages are thought to play a critical role in maintaining this high diversity and shaping the composition of tropical tree communities. To evaluate hypothesized mechanisms promoting tropical tree species coexistence and influencing composition, we initiated a census of woody seedlings and small saplings in the permanent 50 ha Forest Dynamics Plot (FDP) on Barro Colorado Island (BCI), Panama. Situated in old‐growth, lowland tropical moist forest, the BCI FDP was originally established in 1980 to monitor trees and shrubs ≥1 cm diameter at 1.3 m above ground (dbh) at ca. 5‐year intervals. However, critical data on the dynamics occurring at earlier life stages were initially lacking. Therefore, in 2001 we established a 1‐m²seedling plot in the center of every 5 × 5 m section of the BCI FDP. All freestanding woody individuals ≥20 cm tall and <1 cm dbh (hereafter referred to as seedlings) were tagged, mapped, measured, and identified to species in 19,313 1‐m²seedling plots. Because seedling dynamics are rapid, we censused these seedling plots every 1–2 years. Here, we present data from the 14 censuses of these seedling plots conducted between the initial census in 2001 to the most recent census, in 2018. This data set includes nearly 1 M observations of ~185,000 individuals of >400 tree, shrub, and liana species. These data will permit spatially‐explicit analyses of seedling distributions, recruitment, growth, and survival for hundreds of woody plant species. In addition, the data presented here can be linked to openly‐available, long‐term data on the dynamics of trees and shrubs ≥1 cm dbh in the BCI FDP, as well as existing data sets from the site on climate, canopy structure, phylogenetic relatedness, functional traits, soil nutrients, and topography. This data set can be freely used for non‐commercial purposes; we request that users of these data cite this data paper in all publications resulting from the use of this data set. 

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2. New additions to the C lus P ro server motivated by CAPRI

   https://doi.org/10.1002/prot.25219  

   Vajda, Sandor; Yueh, Christine; Beglov, Dmitri; Bohnuud, Tanggis; Mottarella, Scott E.; Xia, Bing; Hall, David R.; Kozakov, Dima (January 2017, Proteins: Structure, Function, and Bioinformatics)

   ABSTRACT The heavily used protein–protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X‐ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435–444. © 2016 Wiley Periodicals, Inc. 

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3. Recent developments in the P y SCF program package

   https://doi.org/10.1063/5.0006074  

   Sun, Qiming; Zhang, Xing; Banerjee, Samragni; Bao, Peng; Barbry, Marc; Blunt, Nick S.; Bogdanov, Nikolay A.; Booth, George H.; Chen, Jia; Cui, Zhi-Hao; et al (July 2020, The Journal of Chemical Physics)
4. Abrupt transitions in a southwest USA desert grassland related to the P acific D ecadal O scillation

   https://doi.org/10.1002/ecy.4065  

   Christensen, Erica M.; James, Darren K.; Randall, Robb M.; Bestelmeyer, Brandon T. (May 2023, Ecology)

   Abstract Prediction of abrupt ecosystem transitions resulting from climatic change will be an essential element of adaptation strategies in the coming decades. In the arid southwest USA, the collapse and recovery of long‐lived perennial grasses have important effects on ecosystem services, but the causes of these variations have been poorly understood. Here we use a quality‐controlled vegetation monitoring dataset initiated in 1915 to show that grass cover dynamics during the 20th century were closely correlated to the Pacific decadal oscillation (PDO) index. The relationship out‐performed models correlating grasses to yearly precipitation and drought indices, suggesting that ecosystem transitions attributed only to local disturbances were instead influenced by climate teleconnections. Shifts in PDO phase over time were associated with the persistent loss of core grass species and recovery of transient species, so recovery of grasses in aggregate concealed significant changes in species composition. However, the relationship between PDO and grass cover broke down after 1995; grass cover is consistently lower than PDO would predict. The decoupling of grass cover from the PDO suggests that a threshold had been crossed in which warming or land degradation overwhelmed the ability of any grass species to recover during favorable periods. 

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5. M icro P rof : Code-level Attribution of Unnecessary Data Transfer in Microservice Applications

   https://doi.org/10.1145/3622787  

   Tariq, Syed Salauddin; Menard, Lance; Su, Pengfei; Roy, Probir (September 2023, ACM Transactions on Architecture and Code Optimization)

   The microservice architecture style has gained popularity due to its ability to fault isolation, ease of scaling applications, and developer’s agility. However, writing applications in the microservice design style has its challenges. Due to the loosely coupled nature, services communicate with others through standard communication APIs. This incurs significant overhead in the application due to communication protocol and data transformation. An inefficient service communication at the microservice application logic can further overwhelm the application. We perform a grey literature review showing that unnecessary data transfer is a real challenge in the industry. To the best of our knowledge, no effective tool is currently available to accurately identify the origins of unnecessary microservice communications that lead to significant performance overhead and provide guidance for optimization. To bridge the knowledge gap, we propose MicroProf, a dynamic program analysis tool to detect unnecessary data transfer in Java-based microservice applications. At the implementation level, MicroProfproposes novel techniques such as remote object sampling and hardware debug registers to monitor remote object usage. MicroProfreports the unnecessary data transfer at the application source code level. Furthermore, MicroProfpinpoints the opportunities for communication API optimization. MicroProfis evaluated on four well-known applications involving two real-world applications and two benchmarks, identifying five inefficient remote invocations. Guided by MicroProf, API optimization achieves an 87.5% reduction in the number of fields within REST API responses. The empirical evaluation further reveals that the optimized services experience a speedup of up to 4.59 ×. 

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