bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of a Virtual Professional Development Coaching Program on the Professional Fulfillment and Well-Being of Women Surgery Residents
Authors: Palamara Kerri , McKinley Sophia K. , Chu Jacqueline T. , Merrill Andrea L. , Yu Liyang , Parangi Sareh , Makowski Maryam S. , Park Yoon Soo , Donelan Karen , Stein Sharon L. 
Published: June 2022

Objective:
Evaluate the effect of a virtual coaching program offered to women surgery residents in a surgical society.

Background:
Randomized controlled experiments evaluating the effect of coaching on trainee well-being and burnout is lacking.

Methods:
Women surgery residents in the Association of Women Surgeons were recruited to participate in a randomized controlled trial of the effects of a virtual coaching program on trainee well-being. Attending surgeons served as coaches after completing in-person training. Residents (n=237) were randomized to intervention (three 1:1 coaching sessions over 9 mo) or control (e-mailed wellness resources). Participants were surveyed at baseline and postintervention using validated measures of well-being, burnout, and resilience. Changes in outcome measures between presurvey and postsurvey were compared between study arms.

Results:
Survey response rates were 56.9% (n=66) in the control group and 69.4% (n=84) in the intervention group (P=0.05). The intervention group showed significant improvement in professional fulfillment (P=0.021), burnout (0.026), work exhaustion (0.017), self-valuation (0.003), and well-being (P=0.002); whereas the control group showed significant improvement in self-valuation (P=0.015) and significant decline in resilience (P=0.025). The intervention group had a significant improvement in well-being (P=0.015) and intolerance of uncertainty (P=0.015) compared to controls.

Conclusions:
Women surgery residents who participated in a remote coaching program offered by a surgical society demonstrated improvement in aspects of well-being relative to peers who did not receive coaching. Therefore, remote coaching offered by a professional society may be a useful component of initiatives directed at trainee well-being.
Maternal high-dense diet programs interferon type I signaling and microglia complexity in the nucleus accumbens shell of rats showing food addiction-like behavior
Authors: Montalvo-Martínez Larisa , Cruz-Carrillo Gabriela , Maldonado-Ruiz Roger , Cárdenas-Tueme Marcela , Bernal-Vega Sofia , Garza-Ocañas Lourdes , Ortiz-López Rocío , Reséndez-Pérez Diana , Camacho-Morales Alberto 
Published: June 2022

Objective
This study aimed to characterize the molecular immune networks and microglia reactivity in the nucleus accumbens (NAc) shell affected by fetal nutritional programming leading to addiction-like behavior in the offspring of Wistar rats. Fetal nutritional programming by energy-dense foods leads to addiction-like behavior in the offspring. Exposure to energy-dense foods also activates systemic and central inflammation in the offspring.

Methods
Females Wistar rats were exposed to cafeteria (CAF) diet or control diet for 9 weeks (prepregnancy, pregnancy and lactation), and male offspring at 2 months of age were diagnosed with food addiction-like behavior using operant conditioning. Global microarray analysis, RTqPCR, proinflammatory plasma profile and microglia immunostaining were performed in the NAc shell of male rats. SIM-A9 microglia cells were stimulated with IFN-α and palmitic acid, and microglia activation and phagocytosis were determined by RTqPCR and incubation of green-fluorescent latex beads, respectively.

Results
Microarray analysis in the NAc shell of the male offspring exposed to CAF during development and diagnosed with addiction-like behavior showed increasing in the type I interferon-inducible gene, Ift1, gene network. Genomic and cellular characterization also confirmed microglia hyperreactivity and upregulation of the Ifit1 in the NAc shell of animals with addiction-like behavior. In-vitro models demonstrated that microglia do respond to IFN-α promoting a time-dependent genomic expression of Ift1, IL-1β and IL-6 followed by increased phagocytosis.

Conclusion
Prenatal exposure to energy-dense foods primes the IFN type I signaling and microglia complexity in the NAc shell of rats diagnosed with food addiction-like behavior.
Bones of contention: Johann Heinrich Merck's palaeontological encounters with academic scholars and professional printmakers
Authors: Jurkowlaniec Grażyna 
Published: June 2022

Printed images played a role in the strategies of savant amateurs of the Enlightenment in consolidating their scientific networks, traced here through the case study of Johann Heinrich Merck. Convinced of the importance of his palaeontological findings, Merck developed an impressive network from Johann Wolfgang Goethe and Samuel Thomas Sömmerring to Petrus Camper and Joseph Banks. Academic celebrities set an important horizon for Merck's aspirations, but his ambitions also depended on professional artists. Increasingly disappointed with printmakers' contribution to natural history, Merck eventually emancipated himself as an etcher in his own right.
This article's focus is on printed images regarded as both visual and material sources; both preserved—some neglected hitherto—and those only known via written sources, whose record allows for a detailed reconstruction of events and the intentions behind them. As images used to disseminate knowledge, they were expected to be reliable; as objects employed in the pursuit of scholarly recognition, they were supposed to reach their recipients post-haste. An inspection of Merck's utilization of printed images, with their concomitant demand for reliability and speed, reveals a pattern of misjudgements in his career and a craving for attention and primacy, which repeatedly exposed him to predicaments.
Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering
Authors: Ullmann Theresa , Peschel Stefanie , Finger Philipp , Müller Christian L. , Boulesteix Anne-Laure 
Published: June 2022

AbstractIn recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the “best” ones. However, if only the best results are selectively reported, this may cause over-optimism: the “best” method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes three unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, and differential microbial network analysis. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the “best” method combination to the validation dataset. The results are then compared between discovery and validation data. In all three research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.
Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the Neolithic in the Danube Gorges
Authors: Hofmanová Zuzana , Reyna-Blanco Carlos S. , de Becdelièvre Camille , Schulz Ilektra , Blöcher Jens , Jovanović Jelena , Winkelbach Laura , Figarska Sylwia M. , Schulz Anna , Porčić Marko , Květina Petr , Tsoupas Alexandros , Currat Mathias , Buzhilova Alexandra , Gerritsen Fokke , Karul Necmi , McGlynn George , Orschiedt Jörg , Özbal Rana , Peters Joris , Ridush Bogdan , Terberger Thomas , Teschler-Nicola Maria , Zariņa Gunita , Zeeb-Lanz Andrea , Stefanović Sofija , Burger Joachim , Wegmann Daniel 
Published: June 2022

SummaryWhile early Neolithic populations in Europe were largely descended from early Aegean farmers, there is also evidence of episodic gene flow from local Mesolithic hunter-gatherers into early Neolithic communities. Exactly how and where this occurred is still unknown. Here we report direct evidence for admixture between the two groups at the Danube Gorges in Serbia. Analysis of palaeogenomes recovered from skeletons revealed that second-generation mixed individuals were buried amidst individuals whose ancestry was either exclusively Aegean Neolithic or exclusively local Mesolithic. The mixed ancestry is also reflected in a corresponding mosaic of grave goods. With its deep sequence of occupation and its unique dwellings that suggest at least semi-sedentary occupation since the late Mesolithic, the area of the Danube Gorges has been at the center of the debate about the contribution of Mesolithic societies to the Neolithisation of Europe. As suggested by our data, which were processed exclusively with uncertainty-aware bioinformatic tools, it may have been precisely in such contexts that close interactions between these societies were established, and Mesolithic ancestry and cultural elements were assimilated.
A novel preparation of the entire isolated CNS unveils the modulatory influences of supra-pontine structures on brainstem and spinal networks
Authors: Mohammadshirazi Atiyeh , Apicella Rosamaria , Taccola Giuliano 
Published: June 2022

ABSTRACTSeveral spinal motor output and essential rhythmic behaviors are controlled by supraspinal structures. Although of great advantage in deciphering their functional organization, existing preparations of the isolated brainstem and spinal networks only focus on local circuitry. The goal of our study has been to better characterize the contribution of higher centers to the neuronal networks involved in respiration and locomotion. Thus, a novel in vitro preparation from the isolated CNS of neonatal rodents was introduced to simultaneously record a stable respiratory rhythm from both cervical and lumbar ventral roots (VRs).Selective electrical pulses supplied to the pons and medulla evoked distinct VR responses in rostrocaudal direction with a staggered onset, while stimulation of ventrolateral medulla resulted in higher events from homolateral VRs. Moreover, electrical stimulation of a lumbar dorsal root (DR) elicited responses even from cervical VRs, albeit small and delayed, confirming functional ascending pathways. Furthermore, prototypical fictive locomotion was induced by trains of pulses applied to either the ventrolateral medulla or a DR.By progressively removing higher centers, duration of respiratory burst was reduced after a precollicular decerebration, which also affected the area of lumbar DR and VR potentials elicited by DR stimulation while frequency of respiration increased after a following pontobulbar transection. Keeping legs attached to the CNS allows for expressing the respiratory rhythm during peripheral stimulation of limbs.The study demonstrates that supra-pontine centers regulate the spontaneous respiratory rhythm, as well as electrically-evoked reflexes and spinal network activity. Thus, the current approach contributes to clarifying the modulatory influence of the brain on the brainstem and spinal micro-circuits.
Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion
Authors: Piedra Felipe-Andrés 
Published: June 2022

AbstractInfections by nonsegmented negative-strand RNA viruses (NNSV) are widely thought to entail gradient gene expression from the well-established existence of a single promoter at the 3’ end of the viral genome and the assumption of constant transcriptional attenuation between genes. But multiple recent studies show viral mRNA levels in infections by respiratory syncytial virus (RSV), a major human pathogen and member of NNSV, that are inconsistent with a simple gradient. Here we integrate known and newly predicted phenomena into a biophysically reasonable model of NNSV transcription. Our model succeeds in capturing published observations of RSV and vesicular stomatitis virus (VSV) mRNA levels. We therefore propose a novel understanding of NNSV transcription based on the possibility of ejective polymerase-polymerase collisions and, in the case of RSV, biased polymerase diffusion.
Toxicological study on methanol root bark extract ofAcacia sieberiana(Fabaceae) in Wistar rats
Authors: Watafua Miriam , Ejiofor Jane I. , Musa Aminu , Ahmad Mubarak Hussaini 
Published: June 2022

AbstractBackgroundThe plantAcacia sieberianabelongs to the family Fabaceae. It has been used in ethnomedical practice to manage bleeding, rheumatism, pain, pyrexia, kidney diseases, gastrointestinal problems, parasitic and infectious diseases, hepatitis, cough, epilepsy, mouth ulcer and many more. Phytochemical compounds such as ellagic acid, quercetin, isoferulic acid, gallic acid, kaempferol, luteolin, apigenin, glucoside dihydroacacipetalin, acacipetalin and many others were isolated from Acacia sieberiana. Previous pharmacological investigations have reported that the plant has anticancer, antimicrobial, antidiarrhoeal and antitrypanosomal effects. Despite the therapeutic properties of this plant, no safety information is available in the literature. Hence, this work intends to investigate the sub-acute toxicity effects ofAcacia sieberianaroot bark extract (ASE). The phytochemical and oral median lethal dose (LD50) evaluations on the ASE were done in line with the standard protocols. The sub-acute toxic effects of the ASE (250, 750, and 1,500 mg/kg) were investigated following administration of the ASE daily for 28-consecutive days based on the Organization of Economic Cooperation and Development (OECD) 407 protocols in rats. The weekly body weights were monitored and the rats were euthanized on the 29thday. The blood samples from the animals were obtained for biochemical and haematological determinations. The liver, kidney, lung and heart were removed for histological investigations.ResultsThe ASE revealed triterpenes, tannins, saponins, cardiac glycosides, flavonoids, and alkaloids. The oral LD50values was >5,000 mg/kg. The ASE remarkably (p<0.05) declined the body weight of the rats in consideration to the control categories. There was also a remarkable (p<0.05) elevation in ALP, urea and lymphocytes. The cardiac histology revealed no abnormalities. However, the liver produced dose-dependent hepatocellular necrosis and vacuolations. Besides, lymphocyte hyperplasia and glomerular necrosis were observed in the kidneys and alveolar congestion in the lungs.ConclusionsThe ASE is relatively non-toxic on acute administration. In contrast, it could pose slight hepatic and renal toxicity on sub-acute administration.
Cooperation genes are more pleiotropic than private genes in the bacterium Pseudomonas aeruginosa
Authors: Scott Trey J. 
Published: June 2022

AbstractPleiotropy may affect the evolution of cooperation by limiting cheater mutants if such mutants also lose other important traits. Because pleiotropy limits cheaters, selection may favor cooperation genes that are more pleiotropic. However, the same should not be true for private genes with functions unrelated to cooperation. Pleiotropy in cooperative genes has mostly been studied with single genes and has not been measured on a wide scale or compared to a suitable set of control genes with private functions. I remedy this gap by comparing genomic measures of pleiotropy in previously identified cooperative and private gene sets in Pseudomonas aeruginosa. I found that cooperative genes in P. aeruginosa tended to be more pleiotropic than private genes according to the number of protein-protein interactions, the number of gene ontology terms, and gene expression specificity. These results show that pleiotropy may be a general way to limit cheating and that cooperation may shape pleiotropy in the genome.
Neurocomputational mechanisms underlying fear-biased adaptation learning in changing environments
Authors: Wang Zhihao , Nan Tian , Goerlich Katharina S. , Li Yiman , Aleman André , Luo Yuejia , Xu Pengfei 
Published: June 2022

AbstractHumans are able to adapt to the fast-changing world by estimating statistical regularities of the environment. Although fear can profoundly impact adaptive behaviors, the neural mechanisms underlying this phenomenon remain elusive. Here, we conducted a behavioral experiment (n = 21) and a functional magnetic resonance imaging experiment (n = 37) with a novel cue-biased adaptation learning task, during which we simultaneously manipulated emotional valence (fearful/neutral expressions of the cue) and environmental volatility (frequent/infrequent reversals of reward probabilities). Across two experiments, computational modelling consistently revealed a higher learning rate for the environment with frequent versus infrequent reversals following neutral cues. In contrast, this flexible adjustment was absent in the environment with fearful cues, suggesting a suppressive role of fear in adaptation to environmental volatility. This suppressive effect was underpinned by activity of the posterior parietal cortex, ventral striatum, hippocampus and dorsal anterior cingulate cortex (dACC) as well as increased functional connectivity between the dACC and temporal-parietal junction (TPJ) for fear with environmental volatility. Dynamic causal modelling identified that the driving effect was located in the TPJ and was associated with dACC activation, suggesting that the suppression of fear on adaptive behaviors occurs at the early stage of bottom-up processing. These findings provide a neuro-computational account of how fear interferes with adaptation to volatility during dynamic environments.
Ageing leads to nonspecific antimicrobial peptide responses in Drosophila melanogaster
Authors: Shit Biswajit , Prakash Arun , Sarkar Saubhik , Vale Pedro F. , Khan Imroze 
Published: June 2022

ABSTRACTEvolutionary theory predicts a late-life decline in the force of natural selection, possibly leading to late-life deregulations of the immune system. A potential outcome of such immune-deregulation is the inability to produce specific immunity against target pathogens. We tested this possibility by infecting multiple Drosophila melanogaster lines (with bacterial pathogens) across age-groups, where either individual or different combinations of Imd- and Toll-inducible antimicrobial peptides (AMPs) were deleted using CRISPR gene editing. We show a high degree of non-redundancy and pathogen-specificity of AMPs in young flies: in some cases, even a single AMP could confer complete resistance. In contrast, ageing led to a complete loss of such specificity, warranting the action of multiple AMPs across Imd- and Toll-pathways during infections. Moreover, use of diverse AMPs either had no survival benefits, or even accompanied survival costs post-infection. These features were also sexually dimorphic: females expressed a larger repertoire of AMPs than males, but extracted equivalent survival benefits. Finally, age-specific expansion of the AMP-pool was associated with downregulation of negative-regulators of the Imd-pathway and a potential damage to renal function, as features of poorly-regulated immunity, Overall, we could establish ageing as an important driver of nonspecific AMP responses, across sexes and bacterial infections.
First De novo whole genome sequencing and assembly of mutant Dendrobium hybrid cultivar ‘Emma White’
Authors: Sherpa Rubina , Devadas Ramgopal , Suprasanna P , Bolbhat Sadashiv Narayan , Nikam Tukaram Dayaram 
Published: June 2022

ABSTRACTDendrobium hybrid cultivar ‘Emma White’ is an ornamental orchid with high commercial demand. We have used gamma-ray induced ‘early flowering mutant’ to generate draft genome sequences with total length (bp) with 678,650,699 and contigs at 447,500 with N50 at 1,423 using the Illumina HiSeqX10 sequencing platform. Here, we report first de novo whole genome sequencing and assembly of an early flowering gamma mutant of Emma White hybrid for developing a genomics resource for further studies. The GC content of genome was 33.48%, and predicted 95,529 genes from contig assembly. The predicted genes from the MaSuRCA (version 4.0.3) assembled contigs, when compared with uniprot database using BLASTX program with e-valuecutoff of 10−3 resulted 60,741 potential genes governing different pathways in terms for molecular functions, biological process and cellular components. We also identified 216,232 SSRs and 138,856 microsatellite markers. Chromosome level genome assembly of Dendrobium huoshanense species was used to RagTag scaffold the available contigs of mutant, where it contained total length of 687,254,899 bp with N50 value 2,096. Largest contiguous length was found with 18,000,059 bp from 30,571 bp. The genome completeness for Emma White RagTag scaffold assembly was assessed to be 93.6% complete using BUSCO v5.2.1 against the Viridiplantae odb10 orthologous dataset. De novo whole genome sequencing of gamma mutant Dendrobium hybrid cultivar Emma White (10Gy) isolate was deposited to National Centre for Biotechnology Information (NCBI) with SRA accession SRR16008784, Genebank assembly accession GCA_021234465.1(https://www.ncbi.nlm.nih.gov/assembly/GCA_021234465.1#/st) and Transcriptional Shot Gun assembly accession GJVE00000000 under BioProject ID PRJNA763052. This study could provide valuable information for investigating the potential mechanisms of mutation, and guidance for developing Dendrobium hybrid cultivars using mutation breeding.