bluuebunny/crossref_metadata_2025_split huggingface dataset:
Russian Invasion: Rapid Assessment of Impact on Ukraine’s Forests
Authors: Lloyd C. Irland , Iavorivska Lidiia , Zibtsev Sergiy , Myroniuk Viktor , Brian Roth , Bilous Andrii 
Published: April 2024

The War has had serious effects on Ukraine’s forests, in the form of direct damage and fires caused by various munitions. Important damage, though, includes extensive minefields, dud ordnance, and booby traps which are causing forests to be closed to all activities. A study using remotely sensed data reveals that in 2022, more than 70,000 ha of the forests suffered severe destruction and damage due to shelling, fires, and illegal logging by occupying forces. Substantial efforts and innovative strategies are needed to address reforestation and restoration in the face of future climate change. In much of the steppe region and adjacent areas, forests and shelterbelts have been under stress already. The loss of shelterbelts in these regions can compromise future harvests due to rising droughts, sandstorms, soil erosion, and other environmental challenges Important damage, though, is not visible in drone images: extensive minefields, dud ordnance, and booby traps are causing forests to be closed to all activities. Simply completing damage assessments and developing plans for addressing these issues will be an enormous task, involving all agencies, private groups, and local governments concerned with forests, and with international support. Difficult decisions on priorities will be required. Planning is underway on an international basis for programs of demining, bolstering fire management systems, and initiating restoration programs. An overstressed forest fire control system will need to be redesigned to handle future challenges. Shelterbelts will in many instances recover naturally on their own as it will be too hazardous for active restoration measures until demining is done, a task that will take decades. Full restoration of normal, safe activity in the rural areas and forests will only be achieved generations in the future. This paper presents a rapid assessment of the immediate issues and important longterm concerns.
IMPROVING AN EXISTING OR ERECTING A NEW OR ADDITIONAL STRUCTURE BY ESTA OCCUPIERS: AN ANALYSIS OF Daniels v Scribante 2017 (4) SA 341 (CC), Erasmus v Mtenje [2018] ZALCC 12, and De Jager v Mazibuko [2020] ZALCC 7
Authors: Lerato Rudolph Ngwenyama  
Published: April 2024

The conduct of occupiers (i.e., occupiers in terms of the Extension of Security of Tenure Act 62 of 1997 (ESTA)) was central in three court judgments in recent years. The first judgment in the matter of Daniels v Scribante (2017 (4) SA 341 (CC)) is widely regarded as a progressive and transformative judgment, and as having opened the door for ESTA occupiers to improve their dwellings. In Daniels v Scribante, the Constitutional Court considered whether an ESTA occupier has a right to make improvements to a dwelling to make it habitable. The court found that ESTA affords an occupier the right to make improvements to their dwelling without the consent of the owner. However, the court pointed out that meaningful engagement between an owner or person in charge and an ESTA occupier was still necessary, because the exercise of an occupier’s right to make improvements could potentially encroach on an owner’s right to property. Since the judgment in Daniels was delivered, some ESTA occupiers, without prior consent or engaging meaningfully with the owner or person in charge, have improved or erected new structures – both inside and outside the demarcated parcel of land where they reside.Despite the ESTA occupiers’ need to improve or erect new structures, Daniels is context-sensitive and is therefore not blanket authority to engage in building operations anywhere on private farmland without prior, meaningful engagement with the owner or person in charge. Furthermore, reliance on Daniels v Scribante must be clearly justified. It is in this context that the case note emphasises that, where the current dwellings of ESTA occupiers are not suitable for human habitation and it is necessary to improve them or erect new buildings, the improvement must be done after proper meaningful engagement between the ESTA occupier and the owner or person in charge in accordance with the general guidelines set out in Daniels v Scribante. This is because the principles established in Daniels v Scribante set the scene for the much-needed balancing of rights between ESTA occupiers and owners, by alluding to the fact that ESTA occupiers are obliged to engage meaningfully with owners or persons in charge prior to embarking on improving or building new structures.The first part of this case note sets out and analyses case law that has dealt with improving or building new structures. The next part explores the competing rights and interests of ESTA occupiers and owners in relation to improving or erecting new structures. The third and final part of the contribution highlights and emphasises the importance of meaningful engagement before an ESTA occupier improves or erects a new dwelling on property belonging to another.
Assessing cell lines with inducible depletion of cohesin and condensins components through analysis of metaphase chromosome morphology
Authors: Yunusova A. M. , Smirnov A. V. , Pristyazhnuk I. E. , Shnaider T. A. , Maltseva E. K. , Afonnikova S. D. , Gusev O. A. , Battulin N.  R. 
Published: April 2024

One of the most productive strategies for finding the functions of proteins is to study the consequences of loss of protein function. For this purpose, cells or organisms with a knockout of the gene encoding the protein of interest are obtained. However, many proteins perform important functions and cells or organisms could suddenly lose fitness when the function of a protein is lost. For such proteins, the most productive strategy is to use in ducible protein degradation systems. A system of auxin-dependent protein degradation is often implemented. To use this system, it is sufficient to introduce a transgene encoding a plant-derived auxin-dependent ubiquitin ligase into mammalian cells and insert a sequence encoding a degron domain into the gene of interest. A crucial aspect of development of cell lines engineered for inducible protein depletion is the selection of cell clones with efficient auxin-dependent degradation of the protein of interest. To select clones induced by depletion of the architectural chromatin proteins RAD21 (a component of the cohesin complex) and SMC2 (a component of the condensin complex), we propose to use the morphology of metaphase chromosomes as a convenient functional test. In this work, we obtained a series of clones of human HAP1 cells carrying the necessary genetic constructs for inducible depletion of RAD21 and SMC2. The degradation efficiency of the protein of interest was assessed by flow cytometry, Western blotting and metaphase chromosome morphology test. Based on our tests, we showed that the clones we established with the SMC2 degron effectively and completely lose protein function when induced by auxin. However, none of the HAP1 clones we created with the RAD21 degron showed complete loss of RAD21 function upon induction of degradation by auxin. In addition, some clones showed evidence of loss of RAD21 function even in the absence of induction. The chromosome morphology test turned out to be a convenient and informative method for clone selection. The results of this test are in good agreement with flow cytometry analysis and Western blotting data.
Aberrant methylation of placental development genes in chorionic villi of spontaneous abortions with trisomy 16
Authors: Vasilyeva О. Yu. , Tolmacheva E. N. , Dmitriev A. E. , Darkova Ya. A. , Sazhenova E. A. , Nikitina T. V. , Lebedev I. N. , Vasilyev S. A. 
Published: April 2024

In humans, aneuploidy is incompatible with the birth of healthy children and mainly leads to the death of embryos in the early stages of development in the first trimester of pregnancy. Trisomy 16 is the most common aneup loidy among spontaneous abortions of the first trimester of pregnancy. However, the mechanisms leading to the death of embryos with trisomy 16 remain insufficiently investigated. One of these potential mechanisms is abnormal placental development, including aberrant remodeling of spiral arteries. Spiral artery remodeling involves the migration of trophoblast cells into the maternal spiral arteries, replacing their endothelium and remodeling to ensure a stable embryonic nutrition and oxygen supply. This is a complex process which depends on many factors from both the embryo and the mother. We analyzed the methylation level of seven genes (ADORA2B, NPR3, PRDM1, PSG2, PHTLH, SV2C, and TICAM2) involved in placental development in the chorionic villi of spontaneous abortions with trisomy 16 (n = 14), compared with spontaneous abortions with a normal karyotype (n = 31) and the control group of induced abortions (n = 10). To obtain sequencing libraries, targeted amplification of individual gene regions using designed oligonucleot ide primers for bisulfite-converted DNA was used. The analysis was carried out using targeted bisulfite massive parallel sequencing. In the group of spontaneous abortions with trisomy 16, the level of methylation of the PRDM1 and PSG2 genes was significantly increased compared to induced abortions (p = 0.0004 and p = 0.0015, respectively). In the group of spontaneous abortions, there was no increase in the level of methylation of the PRDM1 and PSG2 genes, but the level of methylation of the ADORA2B gene was significantly increased compared to the induced abortions (p = 0.032). The results obtained indicate the potential mechanisms of the pathogenetic effect of trisomy 16 on the placental development with the participation of the studied genes.
Impact of Different Sowing Dates on Growth and Pod Yield of Vegetable Pea under Sub-Himalayan Foothills Region of India
Authors: Kumar Udit , Behera Nishiprabha , Prasad K. , . Pramila , . Dharminder , Kishor Kaushal , Tiwari R.K. , Upadhaya Bharati , Kumar Sunil , Kumar Vivek 
Published: April 2024

Background: The optimum sowing date is crucial among the different agronomic procedures for maximizing output. Optimizing a crop's planting time may be one of the most significant climate resilient tactics for increasing production and hence it becomes necessary to study the crop growth behaviors in changing climatic conditions. The proposed field investigations were undertaken to study the influence of different sowing dates on yield of vegetable pea. Methods: Field investigations were undertaken during Rabi seasons of 2020-21 and 2021-22 at the Vegetable Research Farm, Department of Horticulture, Dr. Rajendra Prasad Central Agricultural University, Pusa (85.67oE - 25.98oN.), which comes under sub-Himalayan foothills region of India. The research study was performed in Randomized Block Design with three replications consisting of eight different sowing dates of vegetable pea. cv. Azad Pea-3 at 10 days interval between each sowing dates. Observations were made on various growth and yield attributing parameters. Result: Results revealed that the parameters under study were substantially affected by various sowing dates. Second week of sowing in November in the years produced maximum plant height at 60 DAS (83.77cm), number of branches per plant (3.97), number of nodules per plant at flowering (26.13), number of green pods per plant (20.80), 10 pods weight (75.67g) and pod yield (52.06q/ha).
iTP-Seq: a scalable profiling method to study context-dependent translational events in vitro
Authors: Gillard Mélanie , Innis C. Axel 
Published: April 2024

Abstract
Uneven translation rates resulting from the mRNA context, nascent amino acid sequence, or a variety of extraneous factors are key to controlling the expression level, folding, and regulation of the proteome. Although ribosome profiling (Ribo-Seq) is the method of choice to provide genome-wide information on protein synthesis in vivo, tools to systematically study this process in vitro are also needed. To this end, we developed inverse toeprinting coupled to next-generation sequencing (iTP-seq), a scalable profiling method that generates ribosome-protected mRNA fragments without a priori knowledge of the translated sequences (Ref. 1: Seip et al. 2018, Life Science Alliance). Protected mRNA fragments obtained by iTP-Seq consist of the entire coding region upstream of stalled ribosomes, making it possible to work with random or focused transcript libraries rather than sequenced genomes onto which short mRNA footprints must be mapped. We have used iTP-seq to investigate the context dependence of ribosome-targeting antibiotics (Ref. 2: Beckert et al. 2021, Nature Communications; Ref 3: Leroy et al. 2023, Nature Chemical Biology). More generally, iTP-Seq could be used to study any ribosome-related process in which the mRNA sequence or context impact the rate of translation.
Here, we present a reproducible protocol for iTP-Seq, which substantially reduces the time and effort required to generate sequencing libraries. This protocol consists in 12 main steps: DNA library amplification, in vitro transcription, 5'end mRNA biotinylation, in vitro translation, RNase R digestion, retention on straptavidin-coated beads, linker ligation, reverse transcription, second-strand syntesis, restriction enzyme digestion, PCR amplification and NGS-adapters addition. The time required to complete a single round of iTP-seq is approximately 10 days (Figure 1: Method overview).
Evaluation of Interventions in Online Grocery Shopping for Sustainability and Health: An Adaptive Design Randomized Controlled Trial
Authors: Bentil Helena , Oyebode Oyinlola , Rens Thijs van 
Published: April 2024

Abstract
Effective interventions are needed to promote more sustainable and healthier food choices for both human and planetary health. This study will evaluate two interventions in two independent adaptive design randomised controlled trials (one 2-arm and one 3-arm trial) within the same study population (a factorial design is not powered). The interventions are (i) eco-labelling, which will provide participants with information on the environmental impact of their food purchases using a score ranging from A (most sustainable) to G (least sustainable); and (ii) price discounts on alternative products with a better sustainability profile (and equal or better nutritional profile) in place of specific products in their basket. To implement these interventions, we will use a browser extension on online shopping websites for one or multiple large UK supermarkets, accessed using the Google Chrome browser on a desktop or laptop computer. We will assess the effect of these interventions on the average eco-score of the basket (primary outcome) as well as its nutritional content (secondary outcome). Health outcomes of the intervention will be modelled using nutrition scores.
Diminished lactate utilization in LDHB-deficient neurons leads to impaired long-term memory retention
Authors: Park Chan Bae 
Published: April 2024

Abstract
The brain's substantial energy consumption primarily arises from the continuous activity of its neurons, which are involved in information processing, transmission, and storage. The astrocyte-neuron lactate shuttle (ANLS) suggests that neurons preferentially utilize lactate over glucose due to its higher efficiency. Astrocytes are proposed to supply neurons with lactate through LDHA expression, while neurons predominantly express LDHB to facilitate lactate oxidation. In this study, LDHB-deficient neurons demonstrated reduced capacity to utilize lactate, which correlated with impaired long-term memory retention in LDHB-deficient mice. However, these mice retained normal short-term memory and showed no macroscopic brain anomalies or neuronal cell death. In a high-glucose environment, the energy metabolism of LDHB-deficient neurons remained typical, suggesting that lactate is not the sole or primary substrate for neuronal energy metabolism, with glucose and other substrates sufficiently supporting the requirements. The observed expression of LDHA in neurons further corroborates the glucose-driven energy metabolism in these cells
Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield
Authors: Wang Min , Li Qiushuang , Ma Zhiyuan , Huo Jiabin , Zhang Xiu Min , Wang Rong , Zhang Shizhe , Jiao Jin Zhen , Dong Xiyang , Janssen Peter , Ungerfeld Emilio , Greening Chris , Tan Zhiliang 
Published: April 2024

Abstract
Ruminants are important for global food security but are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism, and how this varies between ruminants with different methane-emitting phenotypes. Here we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-yield Holstein and high-methane-yield Jersey dairy cattle. The microbiota of Holstein cattle disposed of reductant via propionate and amino acid production and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration. In contrast, Jersey microbiota primarily disposed of H2 through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. These findings were supported by two in vitro measurements of microbiota activities and metabolites, as well as public global rumen microbiome data from sheep and beef cattle. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for the synthesis of host-beneficial metabolites and the reduction of methane production in ruminants.
Increasing Drilling Efficiency: Rock Drillability Assessment with Improved Reliability Methods
Authors: Fattahi Hadi , Jiryaee Fateme 
Published: April 2024

Abstract
The assessment of a successful and cost-effective drilling operation hinges on the evaluation of the Drilling Rate Index (DRI). Moreover, the DRI's value, subject to fluctuations driven by various rock parameters, remains beyond control, introducing an element of unpredictability. Consequently, deterministic methods prove inadequate for the analysis of rock drillability. Nonetheless, the reliability analysis, which incorporates the uncertainty surrounding these parameters while addressing the problem, offers the advantage of providing assessments that better align with real-world conditions. In this study, rock drillability was appraised by employing various reliability methods, including the First Order Reliability Method (FORM), Monte Carlo Simulation (MCS), and the Second Order Reliability Method (SORM). Additionally, Genetic Algorithm (GA) was employed in the optimization processes associated with these methods. A critical aspect within reliability methods concerns the definition of the Limit State Function (LSF), which, in this context, is articulated using the Group Method of Data Handling (GMDH) neural network approach, yielding an explicit function. In this approach, the random variables include Brazilian Tensile Strength (BTS), Uniaxial Compressive Strength (UCS), axial point load strength index (Is(50)↓), diametral point load strength index (Is(50)→), and Shore Scleroscope Hardness (SSH), while the DRI serves as the output parameter. To evaluate the efficacy of the proposed reliability methods, field datasets from previously published literature were employed. Lastly in this paper, according to the US Army Corps of Engineers, the probability of failure (PF) calculated using the FORM, SORM, and MCS methods is low.
Shaking table tests of a one-quarter scale model of concrete hollow block masonry houses retrofitted with fiber-reinforced paint
Authors: Multazam Zamzam , Yamamoto Kenjiro , Timsina Kishor , Gadagamma Chaitanya Krishna , Meguro Kimiro 
Published: April 2024

Abstract
Unreinforced Masonry (URM) buildings are prone to significant damage when subjected to ground motion. Some strengthening methods have been proposed to increase the seismic capacity. However, the widespread adoption of these methods faces various challenges, including economic constraints experienced by common people in developing countries, the complexity of implementation, efficiency, and seismic safety of each technique. This paper introduces a new retrofitting method of fiber-reinforced paint using fiberglass as the primary reinforcing material. The advantage of this technique lies in its simplicity and ease of application, with the added benefit of using the paint to improve the appearance of the house. Two 1:4 scale Concrete Hollow Block (CHB) masonry houses were constructed to represent unreinforced masonry and retrofitted masonry structures using Fiber-Reinforced Paint (FR-Paint). The shake table test results indicate that the retrofitted house model showed improvements of up to 18 times in deformation capacity and up to 13 times in energy dissipation compared to the non-retrofitted model. FR-Paint has a robust performance even in high input motion at a seismic intensity JMA of 7 (Japan Meteorological Agency). This confirms that this retrofitting method has a high earthquake-resistant performance.
GPT-4 Performance on Querying Scientific Publications: Reproducibility, Accuracy, and Impact of an Instruction Sheet
Authors: Tao Kaiming , Osman Zachary A. , Tzou Philip L. , Rhee Soo-Yon , Ahluwalia Vineet , Shafer Robert W. 
Published: April 2024

Abstract
Background: Large language models (LLMs) that could efficiently screen and identify studies fulfilling specific criteria, as well as those capable of data extraction from publications, would streamline literature reviews and enhance knowledge discovery by lessening the burden on human reviewers.
Methods: We created an automated pipeline utilizing OpenAI GPT-4 32K API version “2023-05-15” to evaluate the accuracy of the LLM GPT-4 when responding to queries about published papers on HIV drug resistance (HIVDR) with and without an instruction sheet. The instruction sheet contained specialized knowledge designed to assist a person trying to answer questions about an HIVDR paper. We designed 60 questions pertaining to HIVDR and created markdown versions of 60 published HIVDR papers in PubMed. We presented the 60 papers to GPT-4 in four configurations: (1) all 60 questions simultaneously; (2) all 60 questions simultaneously with the instruction sheet; (3) each of the 60 questions individually; and (4) each of the 60 questions individually with the instruction sheet.
Results: GPT-4 achieved a mean accuracy of 86.9% – 24.0% higher than when the answers to papers were permuted. The overall recall and precision were 72.5% and 87.4%, respectively. The standard deviation of three replicates for the 60 questions ranged from 0 to 5.3% with a median of 1.2%. The instruction sheet did not significantly increase GPT-4’s accuracy, recall, or precision. GPT-4 was more likely to provide false positive answers when the 60 questions were submitted individually compared to when they were submitted together.
Conclusions: GPT-4 reproducibly answered 3600 questions about 60 papers on HIVDR with moderately high accuracy, recall, and precision. The inability of the instruction sheet to increase these metrics suggests that more sophisticated prompt engineering approaches or the finetuning of an open source model are required to further improve the ability of an LLM to answer questions about highly specialized HIV drug resistance papers.