bluuebunny/crossref_metadata_2025_split huggingface dataset:
153 Meat Quality of Barbados Blackbelly and St. Croix Hair Sheep Lambs Rendered Short Scrotum or Castrated at Weaning
Authors: Beal Daisha , Lee Jung H , Wildeus Stephan , O’Brien Dahlia , Singh Anil , Kouakou Brou 
Published: May 2023

Abstract
This study evaluated meat quality parameters of short scrotum and castrated Barbados Blackbelly (BB; n = 16) and St. Croix (STX; n = 15) hair sheep ram lambs. Ram lambs born in April (n = 21) and December (n = 10) were rendered short scrotum (SS; n = 17) or castrated (CA; n = 14) using elastrator bands at weaning (63 days of age). Following a transition period of 2 months in a dry lot, ram lambs co-grazed with ewe lambs in a rotational pasture system and were provided soy hull at 3% BW daily. At target weights of app. 40 kg lambs were slaughtered and loin cuts from individual carcasses were collected for meat quality analysis. Data from the two lambing groups were pooled and analyzed as a completely randomized design with a 2 x 2 factorial treatment arrangement for breed (BB or STX) and sex class (SS or CA). The CIE L* (lightness), a* (redness), and b* (yellowness) values of loin cuts were not significantly influenced by breed or sex class. The longissimus muscle (LM) in loin cuts from CA lambs had a greater (P &lt; 0.0001) fat content (3.73 vs 2.55 ± 0.155%) and tended (P = 0.06) to have a decreased moisture content (69.63 vs 70.75 ± 0.413%) than that from SS lambs. Neither breed nor sex class significantly affected the myoglobin content, percent metmyoglobin and thiobarbituric acid reactive substances (TBARS) values of LM from lamb cuts. Cuts from SS lambs had greater (P &lt; 0.0001) shear force values (3.22 vs 2.64 ± 0.093 kg) than those from CA lambs. However, the cooking loss of loin cuts was not significantly influenced by breed or sex class. The fatty acid profiles of LM from experimental lambs were significantly influenced by breed and sex class. Compared with BB, STX had greater (P &lt; 0.05) concentrations of myristic (C14:0;.38 vs.23%), palmitic (C16:0; 20.15 vs8.98%) and oleic (C18:1n9; 45.01 vs 42.81%), but less than (P &lt; 0.05) concentrations of stearic (C18:0;7.29 vs9.33%) and linoleic (C18:2n6; 6.14 vs 7.47%) acids in LM. Furthermore, the LM from SS lambs had greater (P &lt; 0.05) concentrations of C18:2n6 (8.09 vs 5.51%) and arachidonic (C20:4n6, 2.04 vs.40%), but lless than (P &lt; 0.05) concentrations of C16:0 (19.07 vs 20.06%) and C18:1n9 (41.57 vs 46.24%) acids than that from CA lambs. Data suggest that meat quality parameters were more greatly influenced by sex class than breed when landrace hair sheep lambs were slaughtered at a target weight. Loin cuts from SS lambs were leaner, but less tender than those of CA lambs, and also differed in their fatty acid profiles. Hence meat quality will be impacted by the choice of rendering male lambs sterile.
In vitro gametogenesis from embryonic stem cells in livestock species: recent advances, opportunities, and challenges to overcome
Authors: Botigelli Ramon Cesar , Guiltinan Carly , Arcanjo Rachel Braz , Denicol Anna Carolina 
Published: May 2023

AbstractPluripotent stem cells (PSC) can be stabilized in vitro from pre-implantation stage embryos (embryonic stem cells, ESC) or by reprogramming adult somatic cells (induced pluripotent stem cells, iPSC). The last decade has seen significant advances in the livestock PSC field, particularly the development of robust methods for long-term culture of PSC from several livestock species. Along with this, considerable progress has been made in understanding the states of cellular pluripotency and what they mean for cell differentiation capacity, and significant efforts are ongoing to dissect the critical signaling pathways required for the maintenance of PSC in different species and distinct states of pluripotency. Among the cell types that can be generated from PSC, the germline holds special importance as they are the genetic link between generations; and devising methods to enable in vitro gametogenesis (IVG) and produce viable gametes could revolutionize animal agriculture, wildlife conservation, and human assisted reproduction alike. Within the last decade, many pivotal studies about IVG were published using rodent models, filling some critical knowledge gaps in the field. Most importantly, the entire female reproductive cycle was reproduced in vitro from mouse ESC. Although complete male gametogenesis in vitro has not yet been reported, significant advances were made showing the capacity of germline stem cell-like cells to generate healthy offspring. In this review, we provide an overview of PSC and advances in the establishment of livestock PSC; we present the breakthroughs made in rodents regarding IVG and the current progress towards livestock IVG, including the importance of a detailed understanding of fetal germline development. Finally, we discuss some key advances that will be critical to enable this technology at scale. Given the potential impact of IVG for animal agriculture, major efforts will likely continue to be employed by research institutions and industry towards the development of methods to achieve efficient generation of gametes in vitro.
Increased dietary Trp, Thr, and Met supplementation improves growth performance and protein deposition of salmonella-challenged growing pigs under poor housing conditions
Authors: Alves da Cunha Valini Graziela , Righetti Arnaut Pedro , França Ismael , Trevisan Ortiz Manoela , Karpeggiane de Oliveira Marllon José , Brandão Melo Antonio Diego , Alves Marçal Danilo , Reis Furtado Campos Paulo Henrique , Khun Htoo John , Gastmann Brand Henrique , Hauschild Luciano 
Published: May 2023

AbstractHighly intensified rearing conditions and precarious sanitary management predispose pigs to immune system activation, altered amino acid (AA) metabolism, and decreased growth performance. Thus, the main objective of this study was to evaluate the effects of increased dietary tryptophan (Trp), threonine (Thr), and methionine + cysteine (Met + Cys) supplementation on performance, body composition, metabolism, and immune responses of group-housed growing pigs under challenging sanitary conditions. A hundred and twenty pigs (25.4 ± 3.7 kg) were randomly assigned to a 2 × 2 factorial arrangement, consisting of two sanitary conditions (SC, good [GOOD] or salmonella-challenge and poor housing condition [Salmonella Typhimurium (ST) + POOR]) and two diets, control (CN) or supplemented with AA (Trp, Thr, and Met + Cys:Lys ratios 20% higher than those of the CN diet [AA&gt;+]). Pigs were followed during the growing phase (25–50 kg) and the trial lasted 28 d. The ST + POOR SC pigs were challenged with Salmonella Typhimurium and raised in a poor housing condition. The ST + POOR SC increased rectal temperature, fecal score, serum haptoglobin, and urea concentration (P &lt; 0.05) and decreased serum albumin concentration (P &lt; 0.05) compared with GOOD SC. Body weight, average daily feed intake, average daily gain (ADG), feed efficiency (G:F), and protein deposition (PD) were greater in GOOD SC than in ST + POOR SC (P &lt; 0.01). However, pigs housed in ST + POOR SC fed with AA+ diet had lower body temperature (P &lt; 0.05), increased ADG (P &lt; 0.05) and nitrogen efficiency (P &lt; 0.05), and a tendency for improved PD and G:F (P &lt; 0.10) compared with CN diet fed pigs. Regardless of the SC, pigs fed AA+ diet had lower serum albumin (P &lt; 0.05) and tended to decrease serum urea levels (P &lt; 0.10) compared with CN diet. The results of this study suggest that the ratio of Trp, Thr, and Met + Cys to Lys for pigs are modified by sanitary conditions. Furthermore, supplementation of diets with a blend of Trp, Thr, and Met + Cys improves performance, especially under salmonella-challenge and poor housing conditions. Dietary tryptophan, threonine, and methionine supplementation can modulate immune status and influence resilience to sanitary challenges.
Who Gets Burned in Brazil?
Authors: Graner Mariana , Gutierre Marcela , Salgado Lucas S , Mishaly Asher , Baptista João , Calheiros Gregory , Buda Alexandra M , Bowder Alexis N , Corlew D Scott , Botelho Fabio , de Souza Gomez David , Alonso Nivaldo , Pompermaier Laura 
Published: May 2023

ABSTRACT
Burns are preventable injuries that still represent a relevant public health issue. The identification of risk factors might contribute to the development of specific preventive strategies. Data of patients admitted at the Hospital due to acute burn injuries from May 2017 to December 2019, was extracted manually from medical records. The population was analyzed descriptively, and differences between groups were tested using the appropriate statistical test. The study population consisted of 370 patients with burns admitted to the Hospital burn unit during the study period. The majority of the patients were males (257/370, 70%), median age was 33 (IQR:18–43), median TBSA% was 13 (IQR 6.35–21.5 and range 0–87.5%), and 54% of patients had full-thickness burns (n = 179). Children younger than 13 years old represented 17% of the study population (n = 63), 60% of them were boys (n = 38), and scalds was the predominant mechanism of burn injury (n = 45). No children died, however 10% of adults did (n = 31). Self-inflicted burns were observed in 16 adults (5%), of whom 6 (38%) died during admission, however self-inflicted burns were not observed in children. Psychiatric disorders and substance misuse were frequent in this subgroup. White adults male from urban areas who had not completed primary school degree were the major risk group for burns. Smoking and alcohol misuse were the most frequent comorbidities. Accidental domestic flame burns were the predominant injuries in the adult population and scalds in the pediatric.
Muscle loss during cancer therapy is associated with poor outcomes in advanced ovarian cancer
Authors: Polen-De Clarissa , Giri Smith , Fadadu Priyal , Weaver Amy , Mcgree Michaela E , Moynagh Michael , Takahashi Naoki , Jatoi Aminah , Lebrasseur Nathan K , Cliby William , Williams Grant , Kumar Amanika 
Published: May 2023

Abstract
Data evaluating change in body composition during treatment of advanced cancer are limited. Here we evaluated computed tomography (CT)–based changes in muscle mass during treatment for advanced ovarian cancer (OC) and association with outcomes. We analyzed the preoperative and posttreatment skeletal muscle index (SMI), skeletal muscle area normalized for height of 109 patients with advanced OC who underwent primary surgery and platinum-based chemotherapy from 2006 to 2016. Based on an SMI less than 39 cm2/m2, 54.1% of patients were never sarcopenic, 24.8% were sarcopenic on both CT scans, and 21.1% were newly sarcopenic upon treatment completion. Patients who lost muscle during treatment had the worst survival of the 3 groups identified: median survival 2.6 years vs 4.6 years if sarcopenic on both CT scans and 4.8 years if never sarcopenic. Loss of muscle portends a poor prognosis among patients with OC. Additional research is needed to better understand and best mitigate these changes.
Borderland Porosities: Migratory Journeys and Migrant Politics in Lebanon and Turkey
Authors: Ilcan Suzan , Dağtaş Seçil , Balyk Lana Gonzalez 
Published: May 2023

AbstractThis article focuses on displaced peoples’ migratory journeys to the borderlands of Lebanon and Turkey. Building on a selection of ethnographic, interview, policy, and programme materials, it advances the argument that Syrian encounters with these borderlands encompass multidirectional movements and context-specific and fluid processes imbricated in relations of power that often stimulate migrant politics, processes that involve, what we term, borderland porosities. Contributing to critical migration and border studies, the analysis emphasizes how displaced people negotiate the permeabilities of borderlands, engage intermediaries to assist in their perilous journeys, and employ their pre- and post-war transnational networks during their movements. This perspective places borderland porosities front and centre. It illuminates how these dynamic and penetrable spaces shape peoples’ movements, foster a diverse web of actors and encounters in migratory journey and resettlement processes, and cultivate a migrant politics of presence and invisibility.
Resequencing the Hubble sequence and the quadratic (black hole mass)–(spheroid stellar mass) relation for elliptical galaxies
Authors: Graham Alister W 
Published: May 2023

ABSTRACT
One of the most protracted problems in astronomy has been understanding the evolution of galaxy morphology. Much discussion has surrounded how lenticular galaxies may form a bridging population between elliptical and spiral galaxies. However, with recourse to a galaxy’s central black hole mass, accretion-built spiral galaxies have emerged as the bridging population between low-mass lenticular galaxies and the dusty merger-built lenticular galaxies contiguous with elliptical galaxies and ‘brightest cluster galaxies’ in the black hole/galaxy mass diagram. Spiral galaxies, including the Milky Way, appear built from gas accretion and minor mergers onto what were initially lenticular galaxies. These connections are expressed as a new morphology sequence, dubbed the ‘Triangal’, which subsumes elements of the Hubble sequence and the van den Bergh trident and reveals the bridging nature of the often overlooked ellicular galaxies. Furthermore, a quadratic black hole/galaxy mass relation is found to describe ordinary elliptical galaxies. The relation is roughly parallel to the quadratic-like relations observed for the central spheroidal component of spiral galaxies, dust-rich lenticular galaxies, and old dust-poor lenticular galaxies. The brightest cluster galaxies are offset according to expectations from an additional major merger. The findings have implications for feedback from active galactic nuclei, mapping morphology into simulations, and predicting gravitational wave signals from colliding supermassive black holes. A new galaxy speciation model is presented. It disfavours the ‘monolithic collapse’ scenario for spiral, dusty lenticular, and elliptical galaxies. It reveals substantial orbital angular momentum in the Universe’s first galaxies and unites dwarf and ordinary ‘early-type’ galaxies.
Evolutionary Trajectories of New Duplicated and Putative De Novo Genes
Authors: Montañés José Carlos , Huertas Marta , Messeguer Xavier , Albà M Mar 
Published: May 2023

Abstract
The formation of new genes during evolution is an important motor of functional innovation, but the rate at which new genes originate and the likelihood that they persist over longer evolutionary periods are still poorly understood questions. Two important mechanisms by which new genes arise are gene duplication and de novo formation from a previously noncoding sequence. Does the mechanism of formation influence the evolutionary trajectories of the genes? Proteins arisen by gene duplication retain the sequence and structural properties of the parental protein, and thus they may be relatively stable. Instead, de novo originated proteins are often species specific and thought to be more evolutionary labile. Despite these differences, here we show that both types of genes share a number of similarities, including low sequence constraints in their initial evolutionary phases, high turnover rates at the species level, and comparable persistence rates in deeper branchers, in both yeast and flies. In addition, we show that putative de novo proteins have an excess of substitutions between charged amino acids compared with the neutral expectation, which is reflected in the rapid loss of their initial highly basic character. The study supports high evolutionary dynamics of different kinds of new genes at the species level, in sharp contrast with the stability observed at later stages.
Phenotypic and Genotypic Adaptation of Escherichia coli to Thermal Stress is Contingent on Genetic Background
Authors: Batarseh Tiffany N , Batarseh Sarah N , Rodríguez-Verdugo Alejandra , Gaut Brandon S 
Published: May 2023

Abstract
Evolution can be contingent on history, but we do not yet have a clear understanding of the processes and dynamics that govern contingency. Here, we performed the second phase of a two-phase evolution experiment to investigate features of contingency. The first phase of the experiment was based on Escherichia coli clones that had evolved at the stressful temperature of 42.2 °C. The Phase 1 lines generally evolved through two adaptive pathways: mutations of rpoB, which encodes the beta subunit of RNA polymerase, or through rho, a transcriptional terminator. We hypothesized that epistatic interactions within the two pathways constrained their future adaptative potential, thus affecting patterns of historical contingency. Using ten different E. coli Founders representing both adaptive pathways, we performed a second phase of evolution at 19.0 °C to investigate how prior genetic divergence or adaptive pathway (rpoB vs. rho) affects evolutionary outcomes. We found that phenotype, as measured by relative fitness, was contingent on founder genotypes and pathways. This finding extended to genotypes, because E. coli from different Phase 1 histories evolved by adaptive mutations in distinct sets of genes. Our results suggest that evolution depends critically on genetic history, likely due to idiosyncratic epistatic interactions within and between evolutionary modules.
Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs
Authors: Huszár Krisztina , Welker Zsombor , Györgypál Zoltán , Tóth Eszter , Ligeti Zoltán , Kulcsár Péter István , Dancsó János , Tálas András , Krausz Sarah Laura , Varga Éva , Welker Ervin 
Published: May 2023

AbstractStreptococcus pyogenes Cas9 (SpCas9) nuclease exhibits considerable position-dependent sequence preferences. The reason behind these preferences is not well understood and is difficult to rationalise, since the protein establishes interactions with the target-spacer duplex in a sequence-independent manner. We revealed here that intramolecular interactions within the single guide RNA (sgRNA), between the spacer and the scaffold, cause most of these preferences. By using in cellulo and in vitro SpCas9 activity assays with systematically designed spacer and scaffold sequences and by analysing activity data from a large SpCas9 sequence library, we show that some long (&gt;8 nucleotides) spacer motifs, that are complementary to the RAR unit of the scaffold, interfere with sgRNA loading, and that some motifs of more than 4 nucleotides, that are complementary to the SL1 unit, inhibit DNA binding and cleavage. Furthermore, we show that intramolecular interactions are present in the majority of the inactive sgRNA sequences of the library, suggesting that they are the most important intrinsic determinants of the activity of the SpCas9 ribonucleoprotein complex. We also found that in pegRNAs, sequences at the 3′ extension of the sgRNA that are complementary to the SL2 unit are also inhibitory to prime editing, but not to the nuclease activity of SpCas9.
PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks
Authors: Elfmann Christoph , Stülke Jörg 
Published: May 2023

Abstract
The development of AlphaFold for protein structure prediction has opened a new era in structural biology. This is even more the case for AlphaFold-Multimer for the prediction of protein complexes. The interpretation of these predictions has become more important than ever, but it is difficult for the non-specialist. While an evaluation of the prediction quality is provided for monomeric protein predictions by the AlphaFold Protein Structure Database, such a tool is missing for predicted complex structures. Here, we present the PAE Viewer webserver (http://www.subtiwiki.uni-goettingen.de/v4/paeViewerDemo), an online tool for the integrated visualization of predicted protein complexes using a 3D structure display combined with an interactive representation of the Predicted Aligned Error (PAE). This metric allows an estimation of the quality of the prediction. Importantly, our webserver also allows the integration of experimental cross-linking data which helps to interpret the reliability of the structure predictions. With the PAE Viewer, the user obtains a unique online tool which for the first time allows the intuitive evaluation of the PAE for protein complex structure predictions with integrated crosslinks.
HER2 chimeric antigen receptor T cell immunotherapy is an effective treatment for diffuse intrinsic pontine glioma
Authors: Wang Stacie S , Davenport Alexander J , Iliopoulos Melinda , Hughes-Parry Hannah E , Watson Katherine A , Arcucci Valeria , Mulazzani Matthias , Eisenstat David D , Hansford Jordan R , Cross Ryan S , Jenkins Misty R 
Published: May 2023

Abstract

Background
Diffuse intrinsic pontine glioma (DIPG) and other diffuse midline gliomas (DMG) of the thalamus and spinal cord are rare but devastating high-grade glial tumors of childhood with no curative treatment. Despite aggressive treatment attempts the prognosis has remained poor. Chimeric antigen receptor (CAR) T cell therapy has been identified as a promising new approach in the treatment of DMG tumors; however, additional targets are urgently required given known tumor heterogeneity and the prospect of antigen escape of this cancer.

Methods
Using cell surface mass spectrometry, we detected high HER2 cell surface protein across a panel of patient-derived DIPG cells, thereby identifying an existing CAR T cell therapy for use in DIPG. Primary human T cells were transduced to express a second-generation HER2 CAR and interrogated for efficacy against patient-derived DIPG cells.

Results
HER2 CAR T cells demonstrated potent and antigen-specific cytotoxicity and cytokine secretion when co-cultured with patient-derived DIPG cells. Furthermore, HER2 CAR T cells provided a significant regression in intracranial DIPG xenograft tumors.

Conclusions
HER2 CAR T cells are already in clinic development and are well tolerated in pediatric patients. Here we provide strong preclinical evidence for the inclusion of DIPG patients in future pediatric CNS tumor HER2 CAR T cell clinical trials.