bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating Climate Adaptation into a Forest Management Plan: A Case Study on the Research and Teaching Forest of Michigan Technological University
Authors: Rice Alex C , Froese Robert E 
Published: March 2024

Abstract
We incorporated climate adaptation into a forest management plan for Michigan Technological University’s Ford Forest, a 2,000-ha property in Michigan’s Upper Peninsula used for education, research, and timber revenues. Our process was an opportunity to test the existing climate adaptation literature, pulling from multiple sources to meet the diverse needs of the institution at the time the plan was created. We present outcomes as well as lessons learned summarized in a series of broad takeaway messages. (1) Climate adaptation is a means to an end. The end must be defined and is made up of critical values and an adapted state. (2) Given the instability inherent in climate change, achieving adaptation means adjusting forest attributes in response to change but also preparing for unforeseen outcomes via adaptive management. (3) Decisions surrounding goals affect the entire process. Considering climate change–driven constraints when setting goals will improve outcomes. (4) Flawed decision-making is a risk associated with certain organizational contexts and affects the identification of goals, vulnerabilities, and adaptation options. (5) Climate adaptation actions cannot be evaluated in the short term for efficacy because climate change is ongoing. However, the appropriateness of a plan in responding to anticipated change can be evaluated.
Study Implications: This work informs strategic planning for climate change adaptation in forests. We created a climate-informed forest management plan using adaptation frameworks for a university-owned forest in Upper Michigan at the confluence of the northern hardwoods and boreal forest ecotypes. We offer assessment of our plan outcomes and insights into how our decision-making context affected them. This case study expands on the ongoing scientific conversation, incorporating concepts from management science, on how best to adapt natural systems to climate change to protect human values derived from ecosystem services.
A genome sequence for the threatened whitebark pine
Authors: Neale David B , Zimin Aleksey V , Meltzer Amy , Bhattarai Akriti , Amee Maurice , Figueroa Corona Laura , Allen Brian J , Puiu Daniela , Wright Jessica , De La Torre Amanda R , McGuire Patrick E , Timp Winston , Salzberg Steven L , Wegrzyn Jill L 
Published: March 2024

Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
Invigorating human MSCs for transplantation therapy via Nrf2/DKK1 co-stimulation in an acute-on-chronic liver failure mouse model
Authors: Chen Feng , Che Zhaodi , Liu Yingxia , Luo Pingping , Xiao Lu , Song Yali , Wang Cunchuan , Dong Zhiyong , Li Mianhuan , Tipoe George L , Yang Min , Lv Yi , Zhang Hong , Wang Fei , Xiao Jia 
Published: March 2024

Abstract

Background
Since boosting stem cell resilience in stressful environments is critical for the therapeutic efficacy of stem cell-based transplantations in liver disease, this study aimed to establish the efficacy of a transient plasmid-based preconditioning strategy for boosting the capability of mesenchymal stromal cells (MSCs) for anti-inflammation/antioxidant defenses and paracrine actions in recipient hepatocytes.

Methods
Human adipose mesenchymal stem cells (hADMSCs) were subjected to transfer, either with or without the nuclear factor erythroid 2-related factor 2 (Nrf2)/Dickkopf1 (DKK1) genes, followed by exposure to TNF-α/H2O2. Mouse models were subjected to acute chronic liver failure (ACLF) and subsequently injected with either transfected or untransfected MSCs. These hADMSCs and ACLF mouse models were used to investigate the interaction between Nrf2/DKK1 and the hepatocyte receptor cytoskeleton-associated protein 4 (CKAP4).

Results
Activation of Nrf2 and DKK1 enhanced the anti-stress capacity of MSCs in vitro. In a murine model of ACLF, transient co-overexpression of Nrf2 and DKK1 via plasmid transfection improved MSC resilience against inflammatory and oxidative assaults, boosted MSC transplantation efficacy, and promoted recipient liver regeneration due to a shift from the activation of the anti-regenerative IFN-γ/STAT1 pathway to the pro-regenerative IL-6/STAT3 pathway in the liver. Importantly, the therapeutic benefits of MSC transplantation were nullified when the receptor CKAP4, which interacts with DKK1, was specifically removed from recipient hepatocytes. However, the removal of the another receptor low-density lipoprotein receptor-related protein 6 (LRP6) had no impact on the effectiveness of MSC transplantation. Moreover, in long-term observations, no tumorigenicity was detected in mice following transplantation of transiently preconditioned MSCs.

Conclusions
Co-stimulation with Nrf2/DKK1 safely improved the efficacy of human MSC-based therapies in murine models of ACLF through CKAP4-dependent paracrine mechanisms.
Plasma Ribonuclease Activity in Antiretroviral Treatment–Naive People With Human Immunodeficiency Virus and Tuberculosis Disease
Authors: Olsson Oskar , Søkilde Rolf , Tesfaye Fregenet , Karlson Sara , Skogmar Sten , Jansson Marianne , Björkman Per 
Published: March 2024

Abstract

Background
The role of ribonucleases in tuberculosis among people with human immunodeficiency virus (HIV; PWH) is unknown. We explored ribonuclease activity in plasma from PWH with and without tuberculosis.

Methods
Participants were identified from a cohort of treatment-naive PWH in Ethiopia who had been classified for tuberculosis disease (HIV positive [HIV+]/tuberculosis positive [tuberculosis+] or HIV+/tuberculosis negative [tuberculosis−]). Ribonuclease activity in plasma was investigated by quantification of synthetic spike-in RNAs using sequencing and quantitative polymerase chain reaction and by a specific ribonuclease activity assay. Quantification of ribonuclease 1, 2, 3, 6, 7, and T2 proteins was performed by enzyme-linked immunosorbent assay. Ribonuclease activity and protein concentrations were correlated with markers of tuberculosis and HIV disease severity and with concentrations of inflammatory mediators.

Results
Ribonuclease activity was significantly higher in plasma of HIV+/tuberculosis+ (n = 51) compared with HIV+/tuberculosis− (n = 78), causing reduced stability of synthetic spike-in RNAs. Concentrations of ribonucleases 2, 3, and T2 were also significantly increased in HIV+/tuberculosis+ compared with HIV+/tuberculosis−. Ribonuclease activity was correlated with HIV viral load, and inversely correlated with CD4 cell count, mid–upper arm circumference, and body mass index. Moreover, ribonuclease activity was correlated with concentrations of interleukin 27, procalcitonin and the kynurenine-tryptophan ratio.

Conclusions
PWH with tuberculosis disease have elevated plasma ribonuclease activity, which is also associated with HIV disease severity and systemic inflammation.
Development and Validation of Multiplex Assays for Mouse and Human IgG and IgA to Neisseria gonorrhoeae Antigens
Authors: Stover Erica L , Little Marguerite B , Connolly Kristie L , Li Lixin , Nicholas Robert A , Sikora Aleksandra E , Jerse Ann E , Hobbs Marcia M , Duncan J Alex , Macintyre Andrew N 
Published: March 2024

Abstract
There is an urgent need for vaccines against Neisseria gonorrhoeae, the causative agent of gonorrhea. Vaccination with an outer membrane vesicle–based Neisseria meningitidis vaccine provides some protection from N. gonorrhoeae; however, the mechanisms underlying this cross-protection are unknown. To address this need, we developed multiplexed bead-based assays for the relative quantification of human and mouse IgG and IgA against N gonorrhoeae antigens. The assays were evaluated for analyte independence, dilutional linearity, specificity, sensitivity, intra- and interassay variability, and robustness to sample storage conditions. The assay was then used to test samples from mice and humans immunized with an N meningitidis outer membrane vesicle vaccine.
Synergistic effects of ceftazidime/avibactam combined with meropenem in a murine model of infection with KPC-producing Klebsiella pneumoniae
Authors: Zheng Mei , Li Fu-Hao , Liu Juan , Li Wen-Jie , Yin Ruo-Xi , Cai Da-Tong , Andrey Diego O , Zheng Si-Lin , Gales Ana C , Zhang Wan-Jiang , Sun Jian , Liao Xiao-Ping , Yu Yang 
Published: March 2024

Abstract

Objectives
The emergence and expansion of carbapenem-resistant Klebsiella pneumoniae infections is a concern due to the lack of ‘first-line’ antibiotic treatment options. The ceftazidime/avibactam is an important clinical treatment for carbapenem-resistant K. pneumoniae infections but there is an increasing number of cases of treatment failure and drug resistance. Therefore, a potential solution is combination therapies that result in synergistic activity against K. pneumoniae carbapenemase: producing K. pneumoniae (KPC-Kp) isolates and preventing the emergence of KPC mutants resistant to ceftazidime/avibactam are needed in lieu of novel antibiotics.

Methods
To evaluate their synergistic activity, antibiotic combinations were tested against 26 KPC-Kp strains. Antibiotic resistance profiles, molecular characteristics and virulence genes were investigated by susceptibility testing and whole-genome sequencing. Antibiotic synergy was evaluated by in vitro chequerboard experiments, time-killing curves and dose–response assays. The mouse thigh model was used to confirm antibiotic combination activities in vivo. Additionally, antibiotic combinations were evaluated for their ability to prevent the emergence of ceftazidime/avibactam resistant mutations of blaKPC.

Results
The combination of ceftazidime/avibactam plus meropenem showed remarkable synergistic activity against 26 strains and restored susceptibility to both the partnering antibiotics. The significant therapeutic effect of ceftazidime/avibactam combined with meropenem was also confirmed in the mouse model and bacterial loads in the thigh muscle of the combination groups were significantly reduced. Furthermore, ceftazidime/avibactam plus meropenem showed significant activity in preventing the occurrence of resistance mutations.

Conclusions
Our results indicated that the combination of ceftazidime/avibactam plus meropenem offers viable therapeutic alternatives in treating serious infections due to KPC-Kp.
Injunctions and damages for patent infringement under the UPCA in light of the principle of proportionality—Part I: injunctions
Authors: Hofmann Franz , Raue Benjamin 
Published: March 2024

Abstract
This article examines the availability of injunctions and the award of damages for patent infringement under the Agreement on a Unified Patent Court, in light of the principle of proportionality. Part I focuses on the injunctive relief and analyses the application of the principle of proportionality to injunctions, outlining key factors and scenarios. Part II, which will be published in the next issue, discusses the principles and methods applicable to the calculation of damages, assessing their suitability in light of the principle of proportionality, as defined in European Union law and in the case law of select contracting states.
What does rally length tell us about player characteristics in tennis?
Authors: Epasinghege Dona Nirodha , Gill Paramjit S , Swartz Tim B 
Published: March 2024

Abstract
This article proposes increasingly complex models based on publicly available data involving rally length. The models provide insights regarding player characteristics involving the ability to extend rallies and relates these characteristics to performance measures. The analysis highlights some important features that make a difference between winning and losing, and therefore provides feedback on how players may improve.
Follicular fluid-derived exosomes rejuvenate ovarian aging through miR-320a-3p-mediated FOXQ1 inhibition
Authors: Liu Yu , Mu Hongbei , Chen Yu , Li Kexin , Mei Qiaojuan , Wang Lingjuan , Tang Tianyu , Shen Qiuzi , Li Huaibiao , Zhang Ling , Li Jing , Xiang Wenpei 
Published: March 2024

Abstract
Ovarian aging is mainly characterized by a progressive decline in oocyte quantity and quality, which ultimately leads to female infertility. Various therapies have been established to cope with ovarian aging, among which exosome-based therapy is considered a promising strategy that can benefit ovarian functions via multiple pathways. Here, we isolated and characterized exosomes derived from ovarian follicular fluid and profiled the differential expression patterns of noncoding exosomal RNAs in young and aged women. Treatment with young mouse-derived exosomes efficiently rescued ovarian function in aged mice. The follicular fluid exosomes from young mice and miR-320-3p can also promote the proliferation of ovarian granulosa cells and improve mitochondrial function from old mice in vitro. The mechanism may be involve that exosomes transfer miR-320-3p to granulosa cells, and inhibit the expression of FOXQ1. Exosomes also can increase the number of primordial and growing follicles, and improve the developmental ability of oocytes in the old mice in vivo. And hnRNPA2B1 controls miR-320-3p entry into exosomes. This work provides insights into the antiaging potential of follicular fluid-derived exosomes and the underlying molecular mechanisms, which may facilitate prevention of ovarian aging and an improvement in female fertility.
Comparison of Indicators of Dependence for Vaping and Smoking: Trends Between 2017 and 2022 Among Youth in Canada, England, and the United States
Authors: Gomes Makenna N , Reid Jessica L , Rynard Vicki L , East Katherine A , Goniewicz Maciej L , Piper Megan E , Hammond David 
Published: March 2024

Abstract

Introduction
The current study sought to examine trends in indicators of dependence for youth vaping and smoking during a period of rapid evolution in the e-cigarette market.

Aims and Methods
Data are from repeat cross-sectional online surveys conducted between 2017 and 2022 among youth aged 16–19 in Canada, England, and the United States (US). Participants were 23 145 respondents who vaped and/or smoked in the past 30 days. Four dependence indicators were assessed for smoking and vaping (perceived addiction, frequent strong urges, time to first use after waking, days used in past month) and two for vaping only (use events per day, e-cigarette dependence scale). Regression models examined differences by survey wave and country, adjusting for sex, age, race, and exclusive/dual use.

Results
All six indicators of dependence increased between 2017 and 2022 among youth who vaped in the past 30 days (p &lt; .001 for all). For example, more youth reported strong urges to vape at least most days in 2022 than in 2017 (Canada: 26.5% to 53.4%; England: 25.5% to 45.4%; US: 31.6% to 50.3%). In 2017, indicators of vaping dependence were substantially lower than for smoking; however, by 2022, youth vaping was associated with a greater number of days used in the past month (Canada, US), shorter time to first use (all countries), and a higher likelihood of frequent strong urges (Canada, US) compared to youth smoking.

Conclusions
From 2017 to 2022, indicators of vaping dependence increased substantially. By 2022, vaping dependence indices were comparable to those of smoking.

Implications
Indicators of vaping dependence among youth have increased substantially since 2017 to levels that are comparable to cigarette dependence among youth who smoke. Future research should examine factors underlying the increase in dependence among youth who vape, including changes to the nicotine profile and design of e-cigarette products.
Microbiological Methods Used in the Enterics for Global Health Shigella Surveillance Study
Authors: Horne Bri’Anna , Badji Henry , Bhuiyan Md Taufiqur Rahman , Romaina Cachique Lucero , Cornick Jennifer , Hotwani Aneeta , Juma Jane , Ochieng John Benjamin , Abdou Mahamadou , Apondi Evans , Atlas Hannah E , Awuor Alex O , Baker Kate S , Ceesay Bubacarr E , Charles Mary , Cunliffe Nigel A , Feutz Erika , Galagan Sean R , Guindo Ibrehima , Hossain M Jahangir , Iqbal Junaid , Jallow Fatima , Keita Noumou Yakhouba , Khanam Farhana , Kotloff Karen L , Maiden Victor , Manzanares Villanueva Katia , Mito Oscar , Mosharraf Md Parvej , Nkeze Joseph , Ikumapayi Usman N , Paredes Olortegui Maribel , Pavlinac Patricia B , Pinedo Vasquez Tackeshy , Qadri Firdausi , Qamar Farah Naz , Qureshi Sonia , Rahman Nazia , Sangare Aminata , Sen Sunil , Peñataro Yori Pablo , Yousafzai Mohammad Tahir , Ahmed Dilruba , Jere Khuzwayo C , Kosek Margaret N , Omore Richard , Permala-Booth Jasnehta , Secka Ousman , Tennant Sharon M 
Published: March 2024

Abstract

Background
Shigella is a major cause of diarrhea in young children worldwide. Multiple vaccines targeting Shigella are in development, and phase 3 clinical trials are imminent to determine efficacy against shigellosis.

Methods
The Enterics for Global Health (EFGH) Shigella surveillance study is designed to determine the incidence of medically attended shigellosis in 6- to 35-month-old children in 7 resource-limited settings. Here, we describe the microbiological methods used to isolate and identify Shigella. We developed a standardized laboratory protocol for isolation and identification of Shigella by culture. This protocol was implemented across all 7 sites, ensuring consistency and comparability of results. Secondary objectives of the study are to determine the antibiotic resistance profiles of Shigella, compare isolation of Shigella from rectal swabs versus whole stool, and compare isolation of Shigella following transport of rectal swabs in Cary-Blair versus a modified buffered glycerol saline transport medium.

Conclusions
Data generated from EFGH using culture methods described herein can potentially be used for microbiological endpoints in future phase 3 clinical trials to evaluate vaccines against shigellosis and for other clinical and public health studies focused on these organisms.
The Enterics for Global Health (EFGH) Shigella Surveillance Study in Bangladesh
Authors: Khanam Farhana , Islam Md Taufiqul , Bhuiyan Taufiqur Rahman , Hossen Md Ismail , Rajib Md Nazmul Hasan , Haque Shahinur , Ireen Mahzabeen , Qudrat-E-Khuda Syed , Biswas Prasanta Kumar , Bhuiyan Md Amirul Islam , Islam Kamrul , Rahman Nazia , Alam Raz S M Azadul , Mosharraf Md Parvej , Shawon Bhuiyan Md Elias , Islam Sadia , Ahmed Dilruba , Ahmmed Faisal , Zaman Khalequ , Clemens John D , Qadri Firdausi 
Published: March 2024

Abstract

Background
Shigella is an important cause of diarrhea in Bangladeshi children &lt;5 years of age, with an incidence rate of 4.6 per 100 person-years. However, the report was more than a decade old, and data on Shigella consequences are similarly outdated and heterogeneously collected.

Methods
Facility-based disease surveillance is planned to be carried out under the Enterics for Global Health (EFGH) Shigella Surveillance Study consortium for 2 years with aims to optimize and standardize laboratory techniques and healthcare utilization and coverage survey, clinical and anthropometric data collection, safety monitoring and responsiveness, and other related activities. The EFGH is a cohesive network of multidisciplinary experts, capable of operating in concert to conduct the study to generate data that will pave the way for potential Shigella vaccine trials in settings with high disease burden. The study will be conducted within 7 country sites in Asia, Africa, and Latin America.

Conclusions
We outline the features of the Bangladesh site as part of this multisite surveillance network to determine an updated incidence rate and document the consequences of Shigella diarrhea in children aged 6–35 months, which will help inform policymakers and to implement the future vaccine trials.
Population Enumeration and Household Utilization Survey Methods in the Enterics for Global Health (EFGH): Shigella Surveillance Study
Authors: Dodd Ryan , Awuor Alex O , Garcia Bardales Paul F , Khanam Farhana , Mategula Donnie , Onwuchekwa Uma , Sarwar Golam , Yousafzai Mohammad Tahir , Ahmed Naveed , Atlas Hannah E , Amirul Islam Bhuiyan Md , Colston Josh M , Conteh Bakary , Diawara Manan , Dilruba Nasrin , Elwood Sarah , Fatima Irum , Feutz Erika , Galagan Sean R , Haque Shahinur , Taufiqul Islam Md , Karim Mehrab , Keita Belali , Kosek Margaret N , Kotloff Karen L , Lefu Clement , Mballow Mamadou , Ndalama Maureen , Ndeketa Latif , Ogwel Billy , Okonji Caleb , Paredes Olortegui Maribel , Pavlinac Patricia B , Pinedo Vasquez Tackeshy , Platts-Mills James A , Qadri Firdausi , Qureshi Sonia , Rogawski McQuade Elizabeth T , Sultana Shazia , Traore Moussa Oumar , Cunliffe Nigel A , Jahangir Hossain M , Omore Richard , Qamar Farah Naz , Tapia Milagritos D , Peñataro Yori Pablo , Zaman K , McGrath Christine J 
Published: March 2024

Abstract

Background
Accurate estimation of diarrhea incidence from facility-based surveillance requires estimating the population at risk and accounting for case patients who do not seek care. The Enterics for Global Health (EFGH) Shigella surveillance study will characterize population denominators and healthcare-seeking behavior proportions to calculate incidence rates of Shigella diarrhea in children aged 6–35 months across 7 sites in Africa, Asia, and Latin America.

Methods
The Enterics for Global Health (EFGH) Shigella surveillance study will use a hybrid surveillance design, supplementing facility-based surveillance with population-based surveys to estimate population size and the proportion of children with diarrhea brought for care at EFGH health facilities. Continuous data collection over a 24 month period captures seasonality and ensures representative sampling of the population at risk during the period of facility-based enrollments. Study catchment areas are broken into randomized clusters, each sized to be feasibly enumerated by individual field teams.

Conclusions
The methods presented herein aim to minimize the challenges associated with hybrid surveillance, such as poor parity between survey area coverage and facility coverage, population fluctuations, seasonal variability, and adjustments to care-seeking behavior.