bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economics of Dutch Elm Disease Control: A Model and Case Study
Authors: Baughman Melvin J. 
Published: April 2024

Abstract
A discounted cash-flow model is used to compare the economic efficiency of sanitation controls for Dutch elm disease. A case study in Minneapolis, Minnesota, considers intensive sanitation, winter sanitation, and minimum control. Costs and benefits are projected for each alternative over a period of ten years. Benefits are defined as savings from either intensive or winter sanitation over minimum control costs. Intensive sanitation produces the highest net present worth and saves the most trees at the lowest cost ($31.19 less per-tree saved than winter sanitation). Sensitivity analysis shows that reasonable changes in tree-loss rates, tree-removal costs, or the discount rate do not change the economic preference for intensive sanitation.
The Role of Indigenous Burning in Land Management
Authors: Kimmerer R.W. , Lake F.K. 
Published: April 2024

Abstract
This article highlights the findings of the literature on aboriginal fire from the human- and the land-centered disciplines, and suggests that the traditional knowledge of indigenous peoples be incorporated into plans for reintroducing fire to the nation's forests. Traditional knowledge represents the outcome of long experimentation with application of fire by indigenous people, which can inform contemporary policy discussions.
Genetic Engineering: FSC Says Risks Are Still Too Great
Authors: Cauley H. 
Published: April 2024

Abstract
The arguments of Strauss et al. (this issue) have reinforced my belief that the Forest Stewardship Council's embrace of genetic modification (GM) technology would be ill advised. More research is needed to identify the direct and indirect social, economic, and ecological implications at all scales of the introduction of GM technology. GM research must be carried out under high levels of security, and we must gain more insights, through the research process, of who may benefit when, to what degree, and at what costs to others.
Extension in Pennsylvania: Diverse Partners Working Together
Authors: Finley J.C. , Jacobson M.G. 
Published: April 2024

Abstract
At the turn of the 20th century, timber harvesting and other factors resulted in the high-value hardwood forests we see in Pennsylvania. One-half million private forest landowners own three-quarters of this forested area. Providing resource management information of these forest landowners demands that agencies and organizations cooperate to use limited human and fiscal resources effectively. This article describes a statewide commitment of diverse partners working together to support private forest landowners and sustain the state's hardwood forests.
Carbon Sequestration in Forests: Addressing the Scale Question
Authors: Harmon M.E. 
Published: April 2024

Abstract
Forests may have an important role to play in removing carbon dioxide from the atmosphere. However, the extent of their role depends not only on the area available but also the management system that is applied and whether it is based on sound scientific principles, including those of basic ecosystem science. One aspect of ecosystem science that generally has been overlooked in forestry-related carbon projects is that of scale. By paying closer attention to scale, seemingly contradictory statements concerning forest management and carbon sequestration can be resolved, which can lead to the development of a viable carbon sequestration policy.
Forest Parcelization in the United States: A Study of Contributing Factors
Authors: Mehmood S.R. , Zhang D. 
Published: April 2024

Abstract
Over the past few decades, the number of nonindustrial private forest landowners in the United States has been increasing while the average size of parcels has been decreasing. This trend is often referred to as forest parcelization. This article reviews the causes of parcelization suggested in the existing literature and attempts to provide some empirical evidence concerning their validity. Death, urbanization, income, regulatory uncertainty, and financial assistance for landowners are found to have significant impacts on the change in average parcel size in the United States.
Oak Wilt: A Potential Threat to Southern and Western Oak Forests
Authors: Wilson A.D. 
Published: April 2024

Abstract
Oak wilt is recognized as one of the most destructive diseases to afflict oak species in the United States. The distribution and development of oak wilt in our eastern and midwestern oak forests has been closely linked to changes in forest stand composition, forest management practices, and pathogen dissemination facilitated by human and vector activity. The potential for oak wilt to spread into southern and western states and its possible impacts are discussed. The Texas experience with an oak wilt epidemic provides useful perspectives and suppression alternatives for other states not yet touched by this malady.
Book Review: Aldo Leopold—For the Health of the Land: Previously Unpublished Essays and Other Writings
Authors: Miller C. 
Published: April 2024

Abstract
Aldo Leopold—For the Health of the Land: Previously Unpublished Essays and Other Writings edited by J. Baird Callicott and Eric T. Freyfogle, is the latest testament to Leopold's creative powers, a collection of essays about the midwestern landscape that once were little read because they were obscurely published.
Forests and Forestry in Ukraine: Standing on the Brink of a Market Economy
Authors: Strochinskii A.A. , Pozyvailo Y.M. , Jungst S.E. 
Published: April 2024

Abstract
The breakup of the former Soviet Union has provided increased opportunities for exchanges between foresters in the United States and those in the former Soviet Union. Foresters in Ukraine manage state forestlands for many of the same goods and services as do foresters in the United States, but under a significantly different system. All forests in Ukraine are state-owned, and harvest activities, where permitted, are strictly regulated. Transition to a market economy in the forestry sector is considered by the State Committee on Forestry to be a matter of great importance, but strong state involvement in regulations relating to environmental protection will certainly be a part of that transition.
Efficacy of anifrolumab in long-term intractable alopecia due to discoid lupus erythematosus
Authors: Azuma Naoto , Natsuaki Masaru , Hashimoto Naoaki , Abe Takeo , Ueda Suzu , Ohno Yuko , Jinnin Masatoshi , Matsui Kiyoshi 
Published: April 2024

ABSTRACT
Alopecia associated with lupus erythematosus is broadly classified into reversible nonscarring alopecia seen in the acute phase, such as worsening of systemic lupus erythematosus (SLE) and cicatricial alopecia seen in chronic cutaneous lupus erythematosus represented by discoid lupus erythematosus (DLE). In DLE-induced alopecia, early therapeutic intervention before developing scarring alopecia is important, but the condition is often resistant to conventional treatment. Anifrolumab (ANI), a novel therapeutic agent for SLE that inhibits Type I interferon activity, has been shown to be effective against acute skin lesions, including alopecia, in patients with SLE. However, there are very few reports on the effect of ANI on alopecia due to DLE. We report on a 27-year-old Japanese woman with SLE whose alopecia due to chronic DLE was refractory to topical therapy and systemic therapy with oral glucocorticoid, multiple immunosuppressants, and belimumab for ∼8 years after onset and whose alopecia improved with ANI. ANI can be considered to be an effective treatment option in lupus patients presenting with alopecia due to DLE, even in the chronic refractory stage.
NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders
Authors: Ruiz-Arenas Carlos , Marín-Goñi Irene , Wang Liewei , Ochoa Idoia , Pérez-Jurado Luis A , Hernaez Mikel 
Published: April 2024

Abstract
Grouping gene expression into gene set activity scores (GSAS) provides better biological insights than studying individual genes. However, existing gene set projection methods cannot return representative, robust, and interpretable GSAS. We developed NetActivity, a machine learning framework that generates GSAS based on a sparsely-connected autoencoder, where each neuron in the inner layer represents a gene set. We proposed a three-tier training that yielded representative, robust, and interpretable GSAS. NetActivity model was trained with 1518 GO biological processes terms and KEGG pathways and all GTEx samples. NetActivity generates GSAS robust to the initialization parameters and representative of the original transcriptome, and assigned higher importance to more biologically relevant genes. Moreover, NetActivity returns GSAS with a more consistent definition and higher interpretability than GSVA and hipathia, state-of-the-art gene set projection methods. Finally, NetActivity enables combining bulk RNA-seq and microarray datasets in a meta-analysis of prostate cancer progression, highlighting gene sets related to cell division, key for disease progression. When applied to metastatic prostate cancer, gene sets associated with cancer progression were also altered due to drug resistance, while a classical enrichment analysis identified gene sets irrelevant to the phenotype. NetActivity is publicly available in Bioconductor and GitHub.
Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model
Authors: Lipps Georg 
Published: April 2024

Abstract
Protein binding microarrays (PBM), SELEX, RNAcompete and chromatin-immunoprecipitation have been intensively used to determine the specificity of nucleic acid binding proteins. While the specificity of proteins with pronounced sequence specificity is straightforward, the determination of the sequence specificity of proteins of modest sequence specificity is more difficult. In this work, an explorative data analysis workflow for nucleic acid binding data was developed that can be used by scientists that want to analyse their binding data. The workflow is based on a regressor realized in scikit-learn, the major machine learning module for the scripting language Python. The regressor is built on a thermodynamic model of nucleic acid binding and describes the sequence specificity with base- and position-specific energies. The regressor was used to determine the binding specificity of the T7 primase. For this, we reanalysed the binding data of the T7 primase obtained with a custom PBM. The binding specificity of the T7 primase agrees with the priming specificity (5′-GTC) and the template (5′-GGGTC) for the preferentially synthesized tetraribonucleotide primer (5′-pppACCC) but is more relaxed. The dominant contribution of two positions in the motif can be explained by the involvement of the initiating and elongating nucleotides for template binding.
HELLS regulates transcription in T-cell lymphomas by reducing unscheduled R-loops and by facilitating RNAPII progression
Authors: Tameni Annalisa , Mallia Selene , Manicardi Veronica , Donati Benedetta , Torricelli Federica , Vitale Emanuele , Salviato Elisa , Gambarelli Giulia , Muccioli Silvia , Zanelli Magda , Ascani Stefano , Martino Giovanni , Sanguedolce Francesca , Sauta Elisabetta , Tamagnini Ione , Puccio Noemi , Neri Antonino , Ciarrocchi Alessia , Fragliasso Valentina 
Published: April 2024

Abstract
Chromatin modifiers are emerging as major determinants of many types of cancers, including Anaplastic Large Cell Lymphomas (ALCL), a family of highly heterogeneous T-cell lymphomas for which therapeutic options are still limited. HELLS is a multifunctional chromatin remodeling protein that affects genomic instability by participating in the DNA damage response. Although the transcriptional function of HELLS has been suggested, no clues on how HELLS controls transcription are currently available. In this study, by integrating different multi-omics and functional approaches, we characterized the transcriptional landscape of HELLS in ALCL. We explored the clinical impact of its transcriptional program in a large cohort of 44 patients with ALCL. We demonstrated that HELLS, loaded at the level of intronic regions of target promoters, facilitates RNA Polymerase II (RNAPII) progression along the gene bodies by reducing the persistence of co-transcriptional R-loops and promoting DNA damage resolution. Importantly, selective knockdown of HELLS sensitizes ALCL cells to different chemotherapeutic agents, showing a synergistic effect. Collectively, our work unveils the role of HELLS in acting as a gatekeeper of ALCL genome stability providing a rationale for drug design.
JASMINE: Near-infrared astrometry and time-series photometry science
Authors: Kawata Daisuke , Kawahara Hajime , Gouda Naoteru , Secrest Nathan J , Kano Ryouhei , Kataza Hirokazu , Isobe Naoki , Ohsawa Ryou , Usui Fumihiko , Yamada Yoshiyuki , Graham Alister W , Pettitt Alex R , Asada Hideki , Baba Junichi , Bekki Kenji , Dorland Bryan N , Fujii Michiko , Fukui Akihiko , Hattori Kohei , Hirano Teruyuki , Kamizuka Takafumi , Kashima Shingo , Kawanaka Norita , Kawashima Yui , Klioner Sergei A , Kodama Takanori , Koshimoto Naoki , Kotani Takayuki , Kuzuhara Masayuki , Levine Stephen E , Majewski Steven R , Masuda Kento , Matsunaga Noriyuki , Miyakawa Kohei , Miyoshi Makoko , Morihana Kumiko , Nishi Ryoichi , Notsu Yuta , Omiya Masashi , Sanders Jason , Tanikawa Ataru , Tsujimoto Masahiro , Yano Taihei , Aizawa Masataka , Arimatsu Ko , Biermann Michael , Boehm Celine , Chiba Masashi , Debattista Victor P , Gerhard Ortwin , Hirabayashi Masayuki , Hobbs David , Ikenoue Bungo , Izumiura Hideyuki , Jordi Carme , Kohara Naoki , Löffler Wolfgang , Luri Xavier , Mase Ichiro , Miglio Andrea , Mitsuda Kazuhisa , Newswander Trent , Nishiyama Shogo , Obuchi Yoshiyuki , Ootsubo Takafumi , Ouchi Masami , Ozaki Masanobu , Perryman Michael , Prusti Timo , Ramos Pau , Read Justin I , Rich R Michael , Schönrich Ralph , Shikauchi Minori , Shimizu Risa , Suematsu Yoshinori , Tada Shotaro , Takahashi Aoi , Tatekawa Takayuki , Tatsumi Daisuke , Tsujimoto Takuji , Tsuzuki Toshihiro , Urakawa Seitaro , Uraguchi Fumihiro , Utsunomiya Shin , Van Eylen Vincent , van Leeuwen Floor , Wada Takehiko , Walton Nicholas A 
Published: April 2024

Abstract
The Japan Astrometry Satellite Mission for INfrared Exploration (JASMINE) is a planned M-class science space mission by the Institute of Space and Astronautical Science, the Japan Aerospace Exploration Agency. JASMINE has two main science goals. One is Galactic archaeology with a Galactic Center survey, which aims to reveal the Milky Way’s central core structure and formation history from Gaia-level (∼25 ${\mu} $as) astrometry in the near-infrared (NIR) Hw band (1.0–1.6 ${\mu} $m). The other is an exoplanet survey, which aims to discover transiting Earth-like exoplanets in the habitable zone from NIR time-series photometry of M dwarfs when the Galactic Center is not accessible. We introduce the mission, review many science objectives, and present the instrument concept. JASMINE will be the first dedicated NIR astrometry space mission and provide precise astrometric information on the stars in the Galactic Center, taking advantage of the significantly lower extinction in the NIR. The precise astrometry is obtained by taking many short-exposure images. Hence, the JASMINE Galactic Center survey data will be valuable for studies of exoplanet transits, asteroseismology, variable stars, and microlensing studies, including discovery of (intermediate-mass) black holes. We highlight a swath of such potential science, and also describe synergies with other missions.
Regulation of the transcription factor CdnL promotes adaptation to nutrient stress in Caulobacter
Authors: Smith Erika L , Panis Gaël , Woldemeskel Selamawit Abi , Viollier Patrick H , Chien Peter , Goley Erin D 
Published: April 2024

Abstract
In response to nutrient deprivation, bacteria activate a conserved stress response pathway called the stringent response (SR). During SR activation in Caulobacter crescentus, SpoT synthesizes the secondary messengers guanosine 5′-diphosphate 3′-diphosphate and guanosine 5′-triphosphate 3′-diphosphate (collectively known as (p)ppGpp), which affect transcription by binding RNA polymerase (RNAP) to down-regulate anabolic genes. (p)ppGpp also impacts the expression of anabolic genes by controlling the levels and activities of their transcriptional regulators. In Caulobacter, a major regulator of anabolic genes is the transcription factor CdnL. If and how CdnL is controlled during the SR and why that might be functionally important are unclear. In this study, we show that CdnL is down-regulated posttranslationally during starvation in a manner dependent on SpoT and the ClpXP protease. Artificial stabilization of CdnL during starvation causes misregulation of ribosomal and metabolic genes. Functionally, we demonstrate that the combined action of SR transcriptional regulators and CdnL clearance allows for rapid adaptation to nutrient repletion. Moreover, cells that are unable to clear CdnL during starvation are outcompeted by wild-type cells when subjected to nutrient fluctuations. We hypothesize that clearance of CdnL during the SR, in conjunction with direct binding of (p)ppGpp and DksA to RNAP, is critical for altering the transcriptome in order to permit cell survival during nutrient stress.
Deep learning enables automatic detection of joint damage progression in rheumatoid arthritis—model development and external validation
Authors: Venäläinen Mikko S , Biehl Alexander , Holstila Milja , Kuusalo Laura , Elo Laura L 
Published: April 2024

Abstract

Objectives
Although deep learning has demonstrated substantial potential in automatic quantification of joint damage in RA, evidence for detecting longitudinal changes at an individual patient level is lacking. Here, we introduce and externally validate our automated RA scoring algorithm (AuRA), and demonstrate its utility for monitoring radiographic progression in a real-world setting.

Methods
The algorithm, originally developed during the Rheumatoid Arthritis 2–Dialogue for Reverse Engineering Assessment and Methods (RA2-DREAM) challenge, was trained to predict expert-curated Sharp–van der Heijde total scores in hand and foot radiographs from two previous clinical studies (n = 367). We externally validated AuRA against data (n = 205) from Turku University Hospital and compared the performance against two top-performing RA2-DREAM solutions. Finally, for 54 patients, we extracted additional radiograph sets from another control visit to the clinic (average time interval of 4.6 years).

Results
In the external validation cohort, with a root mean square error (RMSE) of 23.6, AuRA outperformed both top-performing RA2-DREAM algorithms (RMSEs 35.0 and 35.6). The improved performance was explained mostly by lower errors at higher expert-assessed scores. The longitudinal changes predicted by our algorithm were significantly correlated with changes in expert-assessed scores (Pearson’s R = 0.74, P &lt; 0.001).

Conclusion
AuRA had the best external validation performance and demonstrated potential for detecting longitudinal changes in joint damage. Available from https://hub.docker.com/r/elolab/aura, our algorithm can easily be applied for automatic detection of radiographic progression in the future, reducing the need for laborious manual scoring.
A Calcium-Dependent Protein Kinase Regulates the Defense Response in Citrus sinensis
Authors: Zhang Jinghan , Sun Lifan , Wang Yu , Li Baiyang , Li Xiangguo , Ye Ziqin , Zhang Jie 
Published: April 2024

Citrus Huanglongbing (HLB), which is caused by ‘ Candidatus Liberibacter asiaticus’ (CLas), is one of the most destructive citrus diseases worldwide, and defense-related Citrus sinensis gene resources remain largely unexplored. Calcium signaling plays an important role in diverse biological processes. In plants, a few calcium-dependent protein kinases (CDPKs/CPKs) have been shown to contribute to defense against pathogenic microbes. The genome of C. sinensis encodes dozens of CPKs. In this study, the role of C. sinensis calcium-dependent protein kinases (CsCPKs) in C. sinensis defense was investigated. Silencing of CsCPK6 compromised the induction of defense-related genes in C. sinensis. Expression of a constitutively active form of CsCPK6 (CsCPK6CA) triggered the activation of defense-related genes in C. sinensis. Complementation of CsCPK6 rescued the defense-related gene induction in an Arabidopsis thaliana cpk4/11 mutant, indicating that CsCPK6 carries CPK activity and is capable of functioning as a CPK in Arabidopsis. Moreover, an effector derived from CLas inhibits defense induced by the expression of CsCPK6CA and autophosphorylation of CsCPK6, which suggests the involvement of CsCPK6 and calcium signaling in defense. These results support a positive role for CsCPK6 in C. sinensis defense against CLas, and the autoinhibitory regulation of CsCPK6 provides a potential genome-editing target for improving C. sinensis defense. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Highest Achievable Outcomes for Adult Spinal Deformity Corrective Surgery
Authors: Passias Peter G. , Onafowokan Oluwatobi O. , Tretiakov Peter , Williamson Tyler , Kummer Nicholas , Mir Jamshaid , Das Ankita , Krol Oscar , Passfall Lara , Joujon-Roche Rachel , Imbo Bailey , Yee Timothy , Sciubba Daniel , Paulino Carl B. , Schoenfeld Andrew J. , Smith Justin S. , Lafage Renaud , Lafage Virginie 
Published: April 2024

Study Design.
Retrospective single-center study.

Objective.
To assess the influence of frailty on optimal outcome following ASD corrective surgery.

Summary of Background Data.
Frailty is a determining factor in outcomes after ASD surgery and may exert a ceiling effect on the best possible outcome.

Methods.
ASD patients with frailty measures, baseline, and 2-year ODI included. Frailty was classified as Not Frail (NF), Frail (F) and Severely Frail (SF) based on the modified Frailty Index, then stratified into quartiles based on two-year ODI improvement (most improved designated “Highest”). Logistic regression analyzed relationships between frailty and ODI score and improvement, maintenance, or deterioration. A Kaplan-Meier survival curve was used to analyze differences in time to complication or reoperation.

Results.
A total of 393 ASD patients were isolated (55.2% NF, 31.0% F, and 13.7% SF), then classified as 12.5% NF-Highest, 17.8% F-Highest, and 3.1% SF-Highest. The SF group had the highest rate of deterioration (16.7%, P=0.025) in the second postoperative year, but the groups were similar in improvement (NF: 10.1%, F: 11.5%, SF: 9.3%, P=0.886). Improvement of SF patients was greatest at six months (ΔODI of −22.6±18.0, P<0.001), but NF and F patients reached maximal ODI at 2 years (ΔODI of −15.7±17.9 and −20.5±18.4, respectively). SF patients initially showed the greatest improvement in ODI (NF: −4.8±19.0, F: −12.4±19.3, SF: −22.6±18.0 at six months, P<0.001). A Kaplan-Meier survival curve showed a trend of less time to major complication or reoperation by 2 years with increasing frailty (NF: 7.5±0.381 yr, F: 6.7±0.511 yr, SF: 5.8±0.757 yr; P=0.113).

Conclusions.
Increasing frailty had a negative effect on maximal improvement, where severely frail patients exhibited a parabolic effect with greater initial improvement due to higher baseline disability, but reached a ceiling effect with less overall maximal improvement. Severe frailty may exert a ceiling effect on improvement and impair maintenance of improvement following surgery.

Level of Evidence.
Level III.