bluuebunny/crossref_metadata_2025_split huggingface dataset:
The nutritional quality of a fresh orange pulp-wheat straw mixture ensiled with either sugar beet pulp, wheat bran, or urea compared to corn silage (Zea mays) in sheep
Authors: Dadashi Ali , Rouzbehan Yousef , Fazaeli Hassan , Rezaei Javad 
Published: February 2023

Abstract
This study compares corn silage (CS) with an orange pulp-wheat straw mixture (OW) ensiled with either sugar beet pulp (SBP), wheat bran (WB), or urea in terms of intake, chemical composition, phenolic compounds, silage fermentation characteristics, digestibility, in vivo rumen variables and biochemical blood variables in 48 Shall male sheep, and in vitro methane (CH4) production. In addition to CS, five other silages: OW (i.e., 87.5% fresh orange pulp + 12.5% wheat straw); OWU (OW + 1% urea); OWS (87.5% fresh orange pulp + 8.6% wheat straw + 3.9% SBP); OWSU (87.5% fresh orange pulp + 8.6% wheat straw + 1% urea + 3.9% SBP); and OWB (87.5% fresh orange pulp + 8.6% wheat straw + 3.9% SBP) were ensiled for 90 days. All diets, which contained a mineral-vitamin premix (10 g/kg of dry matter [DM]), were each randomly assigned to five sheep (live weight 40 ± 2.5 kg) using a completely randomized design, and the SAS software MIXED method was used for data analysis. Among all silages, OWU and OWSU had the highest (P &lt; 0.01) ammonia-N concentration, but there were no differences in other fermentation characteristics. Animals fed on the CS diet had higher DM intake (P = 0.01) and DM (P = 0.01), organic matter (P = 0.01), and neutral detergent fiber (P = 0.02) digestibilities compared with other diets. However, sheep receiving OWU and OWSU diets had higher (P &lt; 0.01) crude protein digestibility than those fed on other diets. The OWU and OWSU-fed sheep had the highest (P = 0.04) ruminal ammonia-N concentration. Sheep fed on CS had higher (P = 0.03) ruminal total short-chain fatty acids, acetate concentration (P = 0.02), total protozoa (P &lt; 0.01), and cellulolytic bacteria numbers (P &lt; 0.01), but had a lower (P = 0.03) propionate concentration compared with the other sheep. In vitro CH4 production was higher (P = 0.01) with the CS diet compared to the orange pulp diets. Estimated microbial protein supply was lower (P = 0.05) with CS compared to all orange silages. In conclusion, the variation in the nutritive quality among the OWS, OWSU, and OWB is relatively small, and the OWB, which is most comparable to CS, was judged to be nutritionally the best among the diets.
Structure and function of bark and wood chloroplasts in a drought-tolerant tree (Fraxinus ornusL.)
Authors: Natale Sara , La Rocca Nicoletta , Battistuzzi Mariano , Morosinotto Tomas , Nardini Andrea , Alboresi Alessandro 
Published: February 2023

AbstractLeaves are the most important photosynthetic organs in most woody plants, but chloroplasts are also found in organs optimized for other functions. However, the actual photosynthetic efficiency of these chloroplasts is still unclear. We analyzed bark and wood chloroplasts of Fraxinus ornus L. saplings. Optical and spectroscopic methods were applied to stem samples and compared with leaves. A sharp light gradient was detected along the stem radial direction, with blue light mainly absorbed by the outer bark, and far-red-enriched light reaching the underlying xylem and pith. Chlorophylls were evident in the xylem rays and the pith and showed an increasing concentration gradient toward the bark. The stem photosynthetic apparatus showed features typical of acclimation to a low-light environment, such as larger grana stacks, lower chlorophyll a/b and photosystem I/II ratios compared with leaves. Despite likely receiving very few photons, wood chloroplasts were photosynthetically active and fully capable of generating a light-dependent electron transport. Our data provide a comprehensive scenario of the functional features of bark and wood chloroplasts in a woody species and suggest that stem photosynthesis is coherently optimized to the prevailing micro-environmental conditions at the bark and wood level.
Phylogenetic relationships in Hybosoridae (Coleoptera: Scarabaeoidea)
Authors: Basílio Daniel Silva , Cherman Mariana Alejandra , Vaz-De-Mello Fernando Zagury , Almeida Lúcia Massutti 
Published: February 2023

AbstractHybosoridae comprise five extant subfamilies (Anaidinae, Ceratocanthinae, Hybosorinae, Liparochrinae and Pachyplectrinae). The phylogenetics of Anaidinae and Ceratocanthinae have been analysed previously. This is the first thorough analysis with greater representation of the entire family, especially regarding Hybosorinae. The present study tested the monophyly of Hybosoridae; the monophyly and relationships of its subfamilies and among the genera; and the ‘incertae sedis’ placement of the hybosorid genera Borrochrus and Daimothoracodes and of Orubesa, currently assigned to Scarabaeidae. The matrix consisted of 111 morphological characters and 76 taxa. The monophyly of Hybosoridae and three subfamilies (Anaidinae, Ceratocanthinae and Liparochrinae) was supported. Few changes were necessary to recover the monophyly of Hybosorinae and Pachyplectrinae: Brenskea is transferred from Pachyplectrinae to Hybosorinae, and Borrochrus and Daimothoracodes are allocated to Pachyplectrinae. Hybosorinae include two paraphyletic genera: Apalonychus and Hybosorus. To recover their monophyly, two monotypic genera were synonymized: Hapalonychoides is now a junior subjective synonym of Apalonychus (Apalonychus similis comb. nov.) and Hybosoroides a junior subjective synonym of Hybosorus (Hybosorus alluaudi comb. nov.). Orubesa is more closely related to Ochodaeidae than to Hybosoridae.
Quantitative Sensory Changes Following Posterior Spinal Fusion to Treat Adolescent Idiopathic Scoliosis
Authors: O’Neill Nora , Ghessese Semhal , Hedequist Daniel , Lins Laura , Birch Craig , Hresko M. Timothy , Emans John , Karlin Lawrence , Cornelissen Laura , Glotzbecker Michael 
Published: February 2023

Background:
Sensory changes surrounding the incision frequently develop after posterior spinal fusion (PSF) to treat adolescent idiopathic scoliosis (AIS). Anecdotally, patients may experience sensory changes on the chest wall. Such postsurgical sensory changes are not well described quantitatively. This study aims to evaluate the presence, intensity, and duration of mechanical sensory changes in AIS patients postoperatively.

Methods:
A prospective cohort of AIS patients, 10 to 21 years old, was followed. Quantitative sensory testing (QST) included touch detection threshold [mechanical detection threshold (MDT)] and pain detection threshold (MPT), using VonFrey monofilaments and pinprick stimulators. QST was performed at 3 sites at T6: the right and left chest at the nipple line and adjacent to the incision below the inferior angle of the scapula. QST at the thenar eminence was the control. QST was collected at baseline, 3 days, 1, and 6 months postoperative.

Results:
Thirty-four patients (21% males; mean age: 14.9 years old; median preoperative curve: 58 degrees) completed all testing. Mean deformity correction was 64% (SD: 10.4). Adjacent to the incision site, MDT was significantly higher compared with baseline at 3 days and 1 month (P < 0.001) but not at 6 months (P = 0.19), whereas MPT was significantly higher at 3 days, (P < 0.001), 1 month (P < 0.001), and 6 months (P = 0.001). For the chest wall in all patients, MPT was higher on the left chest at 3 days (P = 0.04) and on the right chest at 3 days (P = 0.022) and 1 month (P = 0.05). For patients with right-sided curves, MDT (P = 0.01) and MPT (P = 0.015) overall were significantly higher on the concave side (left) chest postoperatively.

Conclusions:
PSF is associated with sensory disturbances that are detectable within days, persist at 1 month, and improve at 6 months postoperatively adjacent to the incision and on the chest wall. We suspect that these sensory changes are transient. Describing postoperative sensory changes will help us better set postoperative expectations for patients undergoing PSF.

Level of Evidence:
Level I.
A Qualitative Study of the Pain Experience of Black Individuals With Cancer Taking Long-Acting Opioids
Authors: Yeager Katherine A. , Rosa William E. , Belcher Sarah M. , Lee Stephanie M. , Lee Haerim , Bruner Deborah Watkins , Meghani Salimah H. 
Published: February 2023

Background
Little is known about the experience of Black individuals with cancer taking long-acting opioids for cancer pain.

Objective
This study aimed to describe the day-to-day experience of living with pain and the experiences of taking opioids for pain management among Black individuals with cancer prescribed with long-acting opioids.

Methods
This qualitative descriptive study was part of a larger investigation focused on opioid adherence. Participants (N = 14) were interviewed using a semistructured interview guide. Analysis followed conventional content analysis and constant comparison approaches. Sociodemographics, clinical information, and the Brief Pain Inventory form were collected.

Results
The majority of the subsample was female (64.3%), not married (78.6%), and with a median age of 52.5 years. Participants were taking either MS Contin (85.7%) or OxyContin (14.3%). The Brief Pain Inventory median “average” pain severity scores and pain interference scores were 5.1/10 (interquartile range [IQR] = 6.1) and 3.5/10 (IQR = 6.7), respectively. Three themes are reported from the analyses: desire for control, barriers to pain relief, and isolation versus connectedness.

Conclusion
Our findings highlight the persistent nature of moderate to severe cancer pain and how pain and its treatment interfere with patients’ lives. The findings describe ways that patients learn to manage and exert control over pain despite conflicting attitudes and dealing with opioid stigma.

Implication for Practice
Clinicians should partner with patients with cancer, especially people of color, who may experience intersecting stigmas related to their cancer pain and opioid use, to best provide an individualized and culturally sensitive pain treatment plan.
Barking up the wrong tree: the importance of morphology in plant molecular phylogenetic studies
Authors: de Almeida Rafael Felipe , Cheek Martin , Pellegrini Marco O.O. , de Morais Isa L. , Simão-Bianchini Rosangela , Rattanakrajang Pantamith , Simões Ana Rita G. 
Published: February 2023

AbstractBackground and aimsKerauneais a genus recently described in Convolvulaceae, though it has sat uncomfortably in this family. A recent molecular phylogenetic study suggests that its two morphologically almost identical species actually belong to different families, Malpighiaceae (Superrosids) and Ehretiaceae (Superasterids), although with little-to-no morphological evidence to support it.Material and methodsSequences ofmatK, rbcL, and ITS for all the 77 currently accepted genera of Malpighiaceae,K. brasiliensisand Elatinaceae (outgroup) were compiled from Genbank and analysed with Maximum Likelihood and Bayesian Inference criteria for nuclear, plastid and combined datasets. Additional database and herbarium studies were performed to locate and analyse all duplicates of the holotype ofK. brasiliensisto check for misidentified or contaminated materials.Key resultsOur examination of expanded DNA datasets and herbarium sheets of allK. brasiliensisisotypes revealed that an error in tissue sampling was, in fact, what led to this species being placed in Malpighiaceae. Kew’s isotype had a leaf of Malpighiaceae (likely fromMascagnia cordifolia) stored in the fragment capsule, which was unfortunately sampled and sequenced instead of the actual leaves ofK. brasiliensis.ConclusionsDNA sequences can be helpful in classifying taxa when morphology is conflicting or of a doubtful interpretation, with molecular phylogenetic placement becoming a popular tool that potentially accelerates the discovery of systematic relationships. However, good knowledge of plant morphology is essential for formulating the phylogenetic hypotheses to be tested and for a critical re-interpretation of the results in the context of biological information of the species or families. Thus, these techniques are, much like any others, prone to methodological errors. We highlight the crucial need to observe plant morphology alongside molecular phylogenetic results, particularly when the new hypotheses are in disagreement with the existing classification and at risk of incurring gross taxonomic mistakes.
The effects of adverse childhood experiences on depression and suicidal behaviors are partially mediated by neuroticism, a forme fruste of major depression
Authors: Jirakran Ketsupar , Vasupanrajit Asara , Tunvirachaisakul Chavit , Maes Michael 
Published: February 2023

AbstractNeuroticism, a personality trait, can predict major depressive disorder (MDD). The current study aims to determine whether a) neuroticism is a feature of the acute state of MDD, including suicidal behaviors (SB); and b) adverse childhood experiences (ACEs) are associated with neuroticism in MDD. This study included 133 participants, 67 normal controls and 66 MDD patients, and assessed the Big 5 Inventory (BFI), ACEs using the ACE Questionnaire, and the phenome of depression using the Hamilton Depression (HAMD) Rating Scale (HAMD), Beck Depression Inventory (BDI), The State-Trait Anxiety Inventory (STAI) and Columbia Suicide Severity Rating Scale (C-SSRS) scores to assess current SB. Neuroticism was significantly higher in MDD than controls, and it explained 64.9% of the variance in the depression phenome (a latent vector extracted from HAMD, BDI, STAI, and current SB scores). The other BFI domains had much less (extraversion, agreeableness) or no effect (openness, conscientiousness). One latent vector could be extracted from the phenome, lifetime dysthymia, lifetime anxiety disorders and neuroticism scores. Neglect (physical and emotional) and abuse (physical, neglect and sexual) account for approximately 30% of the variance in this latent vector. Partial Least Squares analysis showed that the effects of neglect on the phenome were partially mediated by neuroticism, whereas the effects of abuse were completely mediated by neuroticism. Neuroticism (trait) and the MDD phenome (state) are both manifestations of the same latent core, with neuroticism being a less severe manifestation of major depression, which in fact is a multiplicative manifestation of neuroticism.
Metabolic impact of trans 10, cis 12-conjugated linoleic acid on pai transgenic mice
Authors: Rao Yu , Li Shi-Li , Li Mei-Juan , Wang Bao-Zhu , Wang Yang-Yang , Liang Lu-Wen , Yu Shuai , Liu Zong-Ping , Cui Sheng , Gou Ke-Mian 
Published: February 2023

AbstractTrans10,cis12-conjugated linoleic acid (t10c12-CLA) from ruminant-derived foodstuffs can induce body fat loss in mammals after oral administration, while its mechanism on fat reduction has yet to be clarified fully until now. In the current study, a transgenic mouse that produced t10c12-CLA had been generated by inserting the Propionibacterium acnes isomerase (Pai) expression cassette into the Rosa26 locus, and its male offspring were used to decipher an irreversible long-term impact of t10c12-CLA on health and its mechanism of action. Compared to their wild-type C57BL/6J littermates, comprehensive phenotype profiling of biallelic pai/pai mice indicated that white fat was decreased while brown fat was increased reversely; meanwhile, more heat was released and the central activities were reduced. Besides decreased plasma triglycerides in both pai genotypes and increased serum FGF21 in pai/wt mice, RNA and protein analysis revealed that the fatty acid oxidation and thermogenesis capacity of brown adipose tissues were elevated via CPT1B and UCP1/2 over-expression. The results indicate that the t10c12-CLA-induced fat loss might be caused by the excess FGF21 and the increased mass and extra thermogenesis of brown adipose tissue in transgenic mice.
Deep-Learning Assisted, Single-molecule Imaging analysis (Deep-LASI) of multi-color DNA Origami structures
Authors: Wanninger Simon , Asadiatouei Pooyeh , Bohlen Johann , Salem Clemens-Bässem , Tinnefeld Philip , Ploetz Evelyn , Lamb Don C. 
Published: February 2023

ABSTRACTSingle-molecule experiments have changed the way we investigate the physical world but data analysis is typically time-consuming and prone to human bias. Here, we present Deep-LASI (Deep-Learning Assisted Single-molecule Imaging analysis), a software package consisting of an ensemble of deep neural networks to rapidly analyze single-, two- and three-color single-molecule data, in particular from single-molecule Förster Resonance Energy Transfer (FRET) experiments. Deep-LASI automatically sorts single molecule traces, determines FRET correction factors and classifies the state transitions of dynamic traces, all in ~20-100 ms per trajectory. We thoroughly benchmarked Deep-LASI using ground truth simulations as well as experimental data analyzed manually by an expert user and compared the results with a conventional Hidden Markov Model analysis. We illustrate the capabilities of the technique using a highly tunable L-shaped DNA origami structure and use Deep-LASI to perform titrations, analyze protein conformational dynamics and demonstrate its versatility for analyzing both total internal reflection fluorescence microscopy and confocal smFRET data.
A method for defining tissue injury criteria reveals ligament deformation thresholds are multimodal
Authors: Luetkemeyer Callan M. , Neu Corey P. , Calve Sarah 
Published: February 2023

AbstractSoft tissue injuries (such as ligament, tendon, and meniscus tears) are the result of extracellular matrix damage from excessive tissue stretching. Deformation thresholds for soft tissues, however, remain largely unknown due to a lack of methods that can measure and compare the spatially heterogeneous damage and deformation that occurs in these materials. Here, we propose a method for definingtissue injury criteria: multimodal strain limits for biological tissues analogous to yield criteria that exist for crystalline materials. Specifically, we developed a method for defining injury criteria for mechanically-driven fibrillar collagen denaturation in soft tissues, using regional multimodal deformation and damage data. We established this new method using the murine medial collateral ligament (MCL) as our model tissue. Our findings revealed that multiple modes of deformation contribute to collagen denaturation in the murine MCL, contrary to the common assumption that collagen damage is driven by strain in the fiber direction alone. Remarkably, our results indicated that hydrostatic strain, or volumetric expansion, may be the best predictor of mechanically-driven collagen denaturation in ligament tissue, suggesting crosslink-mediated stress transfer plays a role in molecular damage accumulation. This work demonstrates that collagen denaturation can be driven by multiple modes of deformation and provides a method for defining deformation thresholds, or injury criteria, from spatially heterogeneous data.
The Cancer Testes Antigen, HORMAD1, is a Tumor-Specific Replication Fork Protection Factor
Authors: Herrera Luis Reza , McGlynn Kathleen , Gibbs Zane A. , Davis Anthony J. , Whitehurst Angelique W. 
Published: February 2023

SUMMARYTumors frequently activate the expression of genes that are only otherwise required for meiosis. HORMAD1, which is essential for meiotic recombination in multiple species, is expressed in over 50% of human lung adenocarcinoma cells (LUAD). We previously found that HORMAD1 promotes DNA double strand break (DSB) repair in LUAD. Here, we report that HORMAD1 takes on an additional role in protecting genomic integrity. Specifically, we find HORMAD1 is critical for protecting stalled DNA replication forks in LUAD. Loss of HORMAD1 leads to nascent DNA degradation, an event which is mediated by the MRE11-DNA2-BLM pathway. Moreover, following exogenous induction of DNA replication stress, HORMAD1 deleted cells accumulate single stranded DNA (ssDNA). We find that these phenotypes are the result of a lack of RAD51 and BRCA2 loading onto stalled replication forks. Ultimately, loss of HORMAD1 leads to increased DSBs and chromosomal aberrations in response to replication stress. Collectively, our data support a model where HORMAD1 expression is selected to mitigate DNA replication stress, which would otherwise induce deleterious genomic instability.
Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA polyubiquitination
Authors: Wang Yi-Chang , Kelso Andrew A. , Karamafrooz Adak , Chen Yi-Hsuan , Chen Wei-Kai , Cheng Chun-Ting , Qi Yue , Gu Long , Malkas Linda , Kung Hsing-Jien , Moldovan George-Lucian , Ciccia Alberto , Stark Jeremy M. , Ann David K 
Published: February 2023

SUMMARYThe unique arginine dependencies of cancer cell proliferation and survival creates metabolic vulnerability. Here, we investigate the impact of extracellular arginine availability on DNA replication and genotoxic resistance. Using DNA combing assays, we find that when extracellular arginine is limited, cancer cells are arrested at S-phase and DNA replication forks slow or stall instantly until arginine is re-supplied. The translation of new histone H4 is arginine-dependent and impacts DNA replication and the expression of newly synthesized histone H4 is reduced in the avascular nutrient-poor breast cancer xenograft tumor cores. Furthermore, we demonstrate that increased PCNA occupancy and HLTF-catalyzed PCNA K63-linked polyubiquitination protects arginine-starved cells from hydroxyurea-induced, DNA2-catalyzed nascent strand degradation. Finally, arginine-deprived cancer cells are tolerant to genotoxic insults in a PCNA K63-linked polyubiquitination-dependent manner. Together, these findings reveal that extracellular arginine is the “linchpin” for nutrient-regulated DNA replication. Such information could be leveraged to expand current modalities or design new drug targets against cancer.
Alpha-synuclein pre-formed fibrils injected into prefrontal cortex primarily spread to cortical and subcortical structures and lead to isolated behavioral symptoms
Authors: Weber Matthew A. , Kerr Gemma , Thangavel Ramasamy , Conlon Mackenzie M. , Abdelmotilib Hisham A. , Halhouli Oday , Zhang Qiang , Geerling Joel C. , Narayanan Nandakumar S. , Aldridge Georgina M. 
Published: February 2023

AbstractParkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) are characterized by diffuse spread of alpha-synuclein (α-syn) throughout the brain. Patients with PDD and DLB have a neuropsychological pattern of deficits that include executive dysfunction, such as abnormalities in planning, timing, working memory, and behavioral flexibility. The prefrontal cortex (PFC) plays a major role in normal executive function and often develops α-syn aggregates in DLB and PDD. To investigate the consequences of α-syn pathology in the cortex, we injected human α-syn pre-formed fibrils into the PFC of wildtype mice. We report that PFC PFFs: 1) induced α-syn aggregation in multiple cortical and subcortical regions with sparse aggregation in midbrain and brainstem nuclei; 2) did not affect interval timing or spatial learning acquisition but did mildly alter behavioral flexibility as measured by intraday reversal learning; 3) increased open field exploration; and 4) did not affect susceptibility to an inflammatory challenge. This model of cortical-dominant pathology aids in our understanding of how local α-syn aggregation might impact some symptoms in PDD and DLB.