bluuebunny/crossref_metadata_2025_split huggingface dataset:
Updating forest road networks using single photon LiDAR in northern Forest environments
Authors: Morley Ilythia D , Coops Nicholas C , Roussel Jean-Romain , Achim Alexis , Dech Jeff , Meecham Dawson , McCartney Grant , Reid Douglas E B , McPherson Scott , Quist Lauren , McDonell Chris 
Published: April 2023

Abstract
Knowledge about the condition and location of forest roads is important for forest management. Coupling accurate forest road information with planning and conservation strategies supports forest resource management. In Canada, spatial data of forestry road networks are available provincially; however, they lack spatial accuracy, and up-to-date information on key attributes such as road width is missing. In this study, we apply a novel approach to update forest road networks and characterize road conditions in Ontario’s Boreal and Great Lakes—St. Lawrence (GLSL) Forest regions. We use airborne laser scanning (ALS), to facilitate the identification of forest roads across densely forested landscapes. We categorized roads into four classes based on driveable width, edge vegetation, as well as surface and edge degradation as derived from high-density Single Photon LiDAR (SPL) data. Using a novel road extraction method, we produced a road probability raster and map road centerlines. We validated road location and attribute information using Global Navigation Satellite System (GNSS) ground truth data in two Ontario forest management units, in the boreal forest and the GLSL. Road segments in some regions have been altered to account for land cover changes, such as flooding or fallen trees. In other situations, the road path may deviate from the planned layout of the road, which is not always followed in the field. Our results highlight inaccuracies in the existing road networks, with 30 per cent of ‘Full access’ roads and 29 per cent of ‘Partial access’ roads being undriveable by standard vehicles and 45 per cent of ‘Status unknown’ roads, which make up 48 per cent of the pre-existing network, being driveable by standard vehicles. Results show that the average positional accuracy of updated road centerlines is 0.4 m, and the average road width error is 2 m. The production of spatially accurate forest road networks and road attribute information is important for characterizing large road networks for which often minimal information is available.
A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae
Authors: Ngo Katrina , Gittens Tristen H , Gonzalez David I , Hatmaker E Anne , Plotkin Simcha , Engle Mason , Friedman Geofrey A , Goldin Melissa , Hoerr Remington E , Eichman Brandt F , Rokas Antonis , Benton Mary Lauren , Friedman Katherine L 
Published: April 2023

Abstract
Telomere healing occurs when telomerase, normally restricted to chromosome ends, acts upon a double-strand break to create a new, functional telomere. De novo telomere addition (dnTA) on the centromere-proximal side of a break truncates the chromosome but, by blocking resection, may allow the cell to survive an otherwise lethal event. We previously identified several sequences in the baker's yeast, Saccharomyces cerevisiae, that act as hotspots of dnTA [termed Sites of Repair-associated Telomere Addition (SiRTAs)], but the distribution and functional relevance of SiRTAs is unclear. Here, we describe a high-throughput sequencing method to measure the frequency and location of telomere addition within sequences of interest. Combining this methodology with a computational algorithm that identifies SiRTA sequence motifs, we generate the first comprehensive map of telomere-addition hotspots in yeast. Putative SiRTAs are strongly enriched in subtelomeric regions where they may facilitate formation of a new telomere following catastrophic telomere loss. In contrast, outside of subtelomeres, the distribution and orientation of SiRTAs appears random. Since truncating the chromosome at most SiRTAs would be lethal, this observation argues against selection for these sequences as sites of telomere addition per se. We find, however, that sequences predicted to function as SiRTAs are significantly more prevalent across the genome than expected by chance. Sequences identified by the algorithm bind the telomeric protein Cdc13, raising the possibility that association of Cdc13 with single-stranded regions generated during the response to DNA damage may facilitate DNA repair more generally.
Tissue-specific chromatin-binding patterns of Caenorhabditis elegans heterochromatin proteins HPL-1 and HPL-2 reveal differential roles in the regulation of gene expression
Authors: de la Cruz-Ruiz Patricia , Rodríguez-Palero María Jesús , Askjaer Peter , Artal-Sanz Marta 
Published: April 2023

Abstract
Heterochromatin is characterized by an enrichment of repetitive elements and low gene density and is often maintained in a repressed state across cell division and differentiation. The silencing is mainly regulated by repressive histone marks such as H3K9 and H3K27 methylated forms and the heterochromatin protein 1 (HP1) family. Here, we analyzed in a tissue-specific manner the binding profile of the two HP1 homologs in Caenorhabditis elegans, HPL-1 and HPL-2, at the L4 developmental stage. We identified the genome-wide binding profile of intestinal and hypodermal HPL-2 and intestinal HPL-1 and compared them with heterochromatin marks and other features. HPL-2 associated preferentially to the distal arms of autosomes and correlated positively with the methylated forms of H3K9 and H3K27. HPL-1 was also enriched in regions containing H3K9me3 and H3K27me3 but exhibited a more even distribution between autosome arms and centers. HPL-2 showed a differential tissue-specific enrichment for repetitive elements conversely with HPL-1, which exhibited a poor association. Finally, we found a significant intersection of genomic regions bound by the BLMP-1/PRDM1 transcription factor and intestinal HPL-1, suggesting a corepressive role during cell differentiation. Our study uncovers both shared and singular properties of conserved HP1 proteins, providing information about genomic binding preferences in relation to their role as heterochromatic markers.
Cell state-dependent chromatin targeting in NUT carcinoma
Authors: Alekseyenko Artyom A , Zee Barry M , Dhoondia Zuzer , Kang Hyuckjoon , Makofske Jessica L , Kuroda Mitzi I 
Published: April 2023

Abstract
Aberrant transcriptional programming and chromatin dysregulation are common to most cancers. Whether by deranged cell signaling or environmental insult, the resulting oncogenic phenotype is typically manifested in transcriptional changes characteristic of undifferentiated cell growth. Here we analyze targeting of an oncogenic fusion protein, BRD4-NUT, composed of 2 normally independent chromatin regulators. The fusion causes the formation of large hyperacetylated genomic regions or megadomains, mis-regulation of c-MYC, and an aggressive carcinoma of squamous cell origin. Our previous work revealed largely distinct megadomain locations in different NUT carcinoma patient cell lines. To assess whether this was due to variations in individual genome sequences or epigenetic cell state, we expressed BRD4-NUT in a human stem cell model and found that megadomains formed in dissimilar patterns when comparing cells in the pluripotent state with the same cell line following induction along a mesodermal lineage. Thus, our work implicates initial cell state as the critical factor in the locations of BRD4-NUT megadomains. These results, together with our analysis of c-MYC protein-protein interactions in a patient cell line, are consistent with a cascade of chromatin misregulation underlying NUT carcinoma.
Tsunami initial profile and maximum runup through earthquake source parameters
Authors: Sharghivand Naeimeh , Kânoğlu Utku 
Published: April 2023

SUMMARY
The 1992 September 1 Nicaragua tsunami manifested itself with an initial shoreline recession, resulting in a fundamental change in approach to define the initial waveform of tsunamis from a solitary wave to an N-wave. Here, we first fit N-wave profile to seafloor deformation for a large set of earthquake scenarios, assuming that the seafloor deformation resulting from an earthquake instantaneously transfers to the sea surface. Then, relating the N-wave parameters to the earthquake source parameters, we express the initial tsunami profile in terms of the earthquake source parameters. Further, we calculate the maximum tsunami runup through earthquake source parameters and test our results against field runup measurements for several events, observing good agreement.
ART and the forgotten siblings: a call for research
Authors: Somigliana Edgardo , Parazzini Fabio , Goisis Alice , Esposito Giovanna , Li Piani Letizia , Filippi Francesca , Vigano’ Paola 
Published: April 2023

Abstract
A broader definition of infertility is the incapacity to have the intended number of children. However, most literature on ART exclusively focuses on live birth as an outcome, rather than on the capacity to fully realize the reproductive wishes of the couples. This issue has probably received scant attention because the total fertility rate is below replacement levels in affluent countries, and one may simplistically assume that only a minority of couples may be interested in more than one child. This assumption, however, is unproven and presumably erroneous. Unfortunately, evidence on the rate of return in couples who conceived their first child with ART is scant and information on the intended number of children in infertile couples is lacking. In general, we plea for more research on this subject. The documentation of an intended number of children above two and a high return rate in infertile couples may lead to changes in clinical practice, such as the storage of oocytes or embryos prior to initiating embryo transfers. This could improve the chance of conceiving the second child when the couple comes back some years later. In addition, the identification of the determinants for non-return as well as those explaining the gap between the intended and the realized number of children may reveal specific barriers and possibly how to tackle them. However, at present, available evidence is insufficient to advocate any intervention. Thorough research is warranted.
Human organoid systems in modeling reproductive tissue development, function, and disease
Authors: Haider Sandra , Beristain Alexander G 
Published: April 2023

AbstractResearch focused on human reproductive biology has primarily relied upon clinical samples affording mainly descriptive studies with limited implementation of functional or mechanistic understanding. More importantly, restricted access to human embryonic material has necessitated the use of animals, primarily rats and mice, and short-term primary cell cultures derived from human patient material. While reproductive developmental processes are generally conserved across mammals, specific features unique to human reproduction have resulted in the development of human-based in vitro systems designed to retain or recapitulate key molecular and cellular processes important in humans. Of note, major advances in 3D epithelial stem cell-based systems modeling human reproductive organ development have been made. These cultures, broadly referred to as organoids, enable research aimed at understanding cellular hierarchies and processes controlling cellular differentiation and function. Moreover, organoids allow the pre-clinical testing of pharmacological substances, both from safety and efficacy standpoints, and hold large potential in driving aspects of personalized medicine that were previously not possible with traditional models. In this mini-review, we focus on summarizing the current state of regenerative organoid culture systems of the female and male reproductive tracts that model organ development, maintenance, and function. Specifically, we will introduce stem cell-based organoid models of the ovary/fallopian tube, endometrium, cervix, prostate gland, and testes. We will also describe organoid systems of the pre-implanting blastocyst and trophoblast, as the blastocyst and its extraembryonic trophectoderm are central to fetal, maternal, and overall pregnancy health. We describe the foundational studies leading to their development and outline the utility as well as specific limitations that are unique and common to many of these in vitro platforms.
Biogeographic provinces and genomically delineated stocks are congruent in snapper (Chrysophrys auratus) from southeastern Australia
Authors: Bertram A , Bell J , Brauer C J , Fowler A , Hamer P , Sandoval-Castillo J , Stewart J , Wellenreuther M , Beheregaray L B 
Published: April 2023

AbstractMarine species often exhibit genetic discontinuities concordant with biogeographic boundaries, frequently occurring due to changes in ocean circulation, bathymetry, coastline topography, and temperature. Here, we used 10 916 single nucleotide polymorphisms (SNPs) to assess the concordance between population genomic differentiation and coastal biogeography in the fishery-important snapper (Chrysophrys auratus) across southeastern Australia. Additionally, we investigated whether spatial scales of assessment and management of snapper align with evidence from population genomics. We detected genomic structure concordant with the region's three biogeographic provinces across snapper from 11 localities (n = 488) between the west coast of South Australia and the south coast of New South Wales. We also detected fine-scale genetic structuring relating to spatial variation in spawning and recruitment dynamics, as well as temporal stability in the genomic signal associated with two important spawning areas. The current management boundaries in the region coincided with either the genetic breaks at bioregional boundaries or with local-scale variation. Our study highlights the value of population genomic surveys in species with high dispersal potential for uncovering stock boundaries and demographic variation related to spawning and recruitment. It also illustrates the importance of marine biogeography in shaping population structure in commercial species with high dispersal potential.
Effect of SCD probiotics supplemented with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota composition
Authors: Ceylani Taha 
Published: April 2023

Abstract

Aims
In this study, the effects of SCD Probiotics with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota (GM) composition were investigated.

Methods and results
Twenty-four-month-old Sprague–Dawley rats were given 300 mg/kg of TUDCA along with 3 mL (1 × 108 CFU) of SCD probiotics for 7 days. The bacterial profile was determined by the metagenome applied to the cecum content. TUDCA, SCD probiotics, and TUDCA with SCD probiotics designed GM differently. TUDCA and SCD probiotics have the most different dominant species profiles.

Conclusions
SCD probiotics and TUDCA have their own unique effects on the species found in GM, and when they are evaluated together, the species found in GM are restructured differently.
Multiphasic mixed growth models for turkeys
Authors: van der Klein Sasha A S , Willems Owen W , Zuidhof Martin J 
Published: April 2023

Abstract
Growth models are important for optimization of feed formulation and breeding programs in turkeys. The objectives of this study were 1) to compare sex and line differences in turkeys in parameter estimates of mono- and di-phasic Gompertz growth models, and 2) to evaluate mono and diphasic mixed Gompertz growth models to determine the variation in parameter estimates in a group of female line turkey toms. A total of 1,056 manually recorded weekly average body weight (BW) observations from male and female turkeys of a male and female line from weeks 1 to 20 were used for objective 1. Daily median values of automatically collected individual BW of female line turkey toms were used for objective 2 and random components associated with individual subject animals related to mature weight and/or timing of maximum gain during each phase were introduced in the Gompertz model. Growth curve shapes were different between male line toms, male line hens, female line toms, and female line hens (P &lt; 0.001). However, inflection points were similar between male and female line toms and between male and female line hens (14.06 vs. 13.72 wk and 11.22 and 10.71 wk, respectively), while mature BW differed between lines by 6.49 and 3.81 kg for toms and hens, respectively. The normalized growth rate constant (growth rate constant corrected for mature weight) was around the same magnitude between male and female line toms (0.0031 vs. 0.0038, respectively), but slightly lower in male line hens compared to female line hens (0.0072 vs. 0.0091, respectively). Diphasic Gompertz models described growth better in all line × sex combinations compared to the monophasic models (P &lt; 0.001) and mixed diphasic Gompertz models showed improved fit over mixed monophasic Gompertz models. The correlation structure of the random components identified that individuals with a higher mature weight had a later inflection point and lower growth rate coefficients. These results provide tools for improved breeding practices and a structure to evaluate the effects of dietary or environmental factors on growth trajectories.
Standardized ileal digestibility of amino acids in cottonseed meal fed to pregnant and non-pregnant sows
Authors: Zhuo Yong , Zou Xiangyang , Wang Ya , Jiang Xuemei , Sun Mengmeng , Xu Shengyu , Lin Yan , Hua Lun , Li Jian , Feng Bin , Fang Zhengfeng , Che Lianqiang , Wu De 
Published: April 2023

Abstract
This study determined the apparent ileal digestibility (AID) and standard ileal digestibility (SID) of crude protein (CP) and amino acids (AA) of six cottonseed meal (CSM) samples in pregnant and non-pregnant sows. Two CSM samples were processed by expelling with a CP level of 40.67% (ECSM41) and 44.64% (ECSM45), and four samples were processed by solvent-extracted which contained graded CP levels of 45% (SECSM45), 51.16% (SECSM51), 56.44% (SECSM56), and 59.63% (SECSM60). Landrace ×Yorkshire third parity sows, 7 at gestation and 14 non-pregnant, were fitted with T-cannula in the distal ileum. Pregnant sows were allotted to a 7 × 6 Latin square design with a cornstarch-based nitrogen-free (NF) diet and the six CSM diets, and non-pregnant sows were allotted to a replicated 7 × 3 Latin square design with seven diets and three periods, respectively, resulting in a total of six replicates per treatment. All experimental sows were fed 3.0 kg/d of the experimental diets. The AID of CP in ECSM41 (75.58%) was lower than in SECSM51 (80.42%), SECSM56 (80.50%), and SECSM60 (82.44%) diets for pregnant sows (P &lt; 0.05). The AID of CP in ECSM41 (77.88%) was significantly lower than in SECSM60 (81.87%) diets for non-pregnant sows (P &lt; 0.05). The physiological phase did not affect the AID of CP (P &gt; 0.05). The SID of CP was affected by diets for both pregnant (P &lt; 0.01) and non-pregnant sows (P = 0.06). The physiological phase also affected the SID of CP (P &lt; 0.01). The AID of histidine, leucine, methionine, threonine, and tryptophan significantly differed between different CSM samples in both pregnant (P &lt; 0.05) and non-pregnant sows (P &lt; 0.05). The AID of dispensable AA aspartic acid, cysteine, glutamic acid, serine, and tyrosine differed between different CSM samples of both pregnant (P &lt; 0.05) and non-pregnant sows (P &lt; 0.05). For pregnant sows, the indispensable AA cysteine, glycine, proline, and tyrosine had significantly different SID between different groups (P &lt; 0.05). For non-pregnant sows, the SID of arginine, lysine, methionine, threonine, aspartic acid, cysteine, and serine had different values among different diets (P &lt; 0.05). In conclusion, the current study presented that the ileal AA digestibility of CSM fed to pregnant and non-pregnant sows increased with the decreased of fiber content, and the current findings can contribute to a precise formulation of diets for sows using CSM.
Nutritional value of high protein ingredients fed to growing pigs in comparison to commonly used protein sources in swine diets
Authors: Garavito-Duarte Yesid R , Levesque Crystal L , Herrick Kevin , Perez-Palencia Jorge Y 
Published: April 2023

Abstract
Two experiments were conducted to test the hypothesis that two high protein dried distillers with solubles and yeast mass added (GDDY) products fed to growing pigs had comparable amino acid (AA) digestibility and metabolizable energy (ME) to feeds commonly used in swine diets. In experiment 1, seven barrows with an initial body weight (BW) of 25 ± 0.8 kg were fitted with a simple T-cannula at the distal ileum to allow for digesta collection. Experimental diets were N-free diets and six cornstarch-based diets containing six ingredients as the sole source of AA: spray dried GDDY, ring dried GDDY, corn distillers dried grains with solubles (DDGS), soybean meal (SBM), enzymatically treated soybean meal (ESBM), and fish meal (FM) provided at 4% of BW. The experiment was conducted as a 7 × 7 Latin square design with seven collection periods of 7 d (5 d adaptation and 2 d ileal digesta collection). In experiment 2, a total of 28 barrows (28.8 ± 1.4 kg BW) were used in a two-period switch-back design with seven diets and four replicate pigs in each period (n = 8 reps per diet). Experimental diets were a corn-based basal diet and six corn-based diets containing spray dried GDDY, ring dried GDDY, DDGS, SBM, ESBM, and FM. Fecal and urine samples were collected using the marker-to-marker approach for 5 d after 7 d of adaptation to determine ME concentration. Overall, standardized ileal digestibility (SID) values were within the mean ± SD of NRC (2012) values for all ingredients evaluated. The SID of AA was greater (P &lt; 0.05) in ESBM than the other protein feedstuffs (90.09% vs. 78.71%–81.51%). There were no significant differences in SID of AA (P &gt; 0.05) in SBM, FM, spray dried GDDY, and ring dried GDDY (81.49%, 78.71%, 81.52%, and 79.20%). With respect to the most common first limiting AA for swine, the SID of Lys was greater (P &lt; 0.05) in spray dried GDDY than ring dried GDDY and DDGS (83.56% vs. 77.33% and 68.53%, respectively). There were no significant differences (P &gt; 0.05) for ME in corn (3,313 kcal/kg), ESBM (3,323 kcal/kg), and FM (3,454 kcal/kg) when compared with spray dried GDDY and ring dried GDDY (3,995 and 3,442 kcal/kg respectively). However, spray dried GDDY had greater DE and ME when compared to SBM. Collectively, this study demonstrates that GDDY products have an AA profile and digestibility comparable to SBM; ME in GDDY products is not different from corn. Therefore, GDDY has the potential as a feed ingredient for pigs, which could provide an alternative source of protein and energy in swine diets.
Reflections on a career as graduate mentor—from baby steps at Wisconsin to today
Authors: Hansen Peter J 
Published: April 2023

Abstract
Graduate education is an important aspect of the life of most academic scientists and a serious responsibility because it comes with the obligation to help students achieve their career and life goals. It can also be very fulfilling for the graduate mentor in terms of personal satisfaction and advancement of the research program. Learning to be a good major professor is an active process that depends on developing a formal framework of education and modifying that framework for each student based on past experiences and experimentation, advice from colleagues, and the individual personality of the student. Perhaps most important is for the graduate mentor to buy into the success and well-being of the student. Among the characteristics that a major professor could seek to instill in his or her students are critical and independent thinking, self-confidence, a thick skin, teamwork, laboratory skills and understanding, and the ability for hard work. Work to make science joyful by celebrating accomplishments, creating a fun environment in the lab, and stressing the societal value of science as compared to personal rewards or ambition.