bluuebunny/crossref_metadata_2025_split huggingface dataset:
The YAP1/TAZ-TEAD transcriptional network regulates gene expression at neuromuscular junctions in skeletal muscle fibers
Authors: Gessler Lea , Huraskin Danyil , Jian Yongzhi , Eiber Nane , Hu Zhaoyong , Prószyński Tomasz J , Hashemolhosseini Said 
Published: December 2023

Abstract
We examined YAP1/TAZ-TEAD signaling pathway activity at neuromuscular junctions (NMJs) of skeletal muscle fibers in adult mice. Our investigations revealed that muscle-specific knockouts of Yap1 or Taz, or both, demonstrate that these transcriptional coactivators regulate synaptic gene expression, the number and morphology of NMJs, and synaptic nuclei. Yap1 or Taz single knockout mice display reduced grip strength, fragmentation of NMJs, and accumulation of synaptic nuclei. Yap1/Taz muscle-specific double knockout mice do not survive beyond birth and possess almost no NMJs, the few detectable show severely impaired morphology and are organized in widened endplate bands; and with motor nerve endings being mostly absent. Myogenic gene expression is significantly impaired in the denervated muscles of knockout mice. We found that Tead1 and Tead4 transcription rates were increased upon incubation of control primary myotubes with AGRN-conditioned medium. Reduced AGRN-dependent acetylcholine receptor clustering and synaptic gene transcription were observed in differentiated primary Tead1 and Tead4 knockout myotubes. In silico analysis of previously reported genomic occupancy sites of TEAD1/4 revealed evolutionary conserved regions of potential TEAD binding motifs in key synaptic genes, the relevance of which was functionally confirmed by reporter assays. Collectively, our data suggest a role for YAP1/TAZ-TEAD1/TEAD4 signaling, particularly through TAZ-TEAD4, in regulating synaptic gene expression and acetylcholine receptor clustering at NMJs.
HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins
Authors: Zhang Jian , Basu Sushmita , Kurgan Lukasz 
Published: December 2023

AbstractCurrent predictors of DNA-binding residues (DBRs) from protein sequences belong to two distinct groups, those trained on binding annotations extracted from structured protein-DNA complexes (structure-trained) vs. intrinsically disordered proteins (disorder-trained). We complete the first empirical analysis of predictive performance across the structure- and disorder-annotated proteins for a representative collection of ten predictors. Majority of the structure-trained tools perform well on the structure-annotated proteins while doing relatively poorly on the disorder-annotated proteins, and vice versa. Several methods make accurate predictions for the structure-annotated proteins or the disorder-annotated proteins, but none performs highly accurately for both annotation types. Moreover, most predictors make excessive cross-predictions for the disorder-annotated proteins, where residues that interact with non-DNA ligand types are predicted as DBRs. Motivated by these results, we design, validate and deploy an innovative meta-model, hybridDBRpred, that uses deep transformer network to combine predictions generated by three best current predictors. HybridDBRpred provides accurate predictions and low levels of cross-predictions across the two annotation types, and is statistically more accurate than each of the ten tools and baseline meta-predictors that rely on averaging and logistic regression. We deploy hybridDBRpred as a convenient web server at http://biomine.cs.vcu.edu/servers/hybridDBRpred/ and provide the corresponding source code at https://github.com/jianzhang-xynu/hybridDBRpred.
Dalbergia odoriferaundergoes massive molecular shifts in response to waterlogging combined with salinity
Authors: Cisse El-Hadji Malick , Jiang Bai-Hui , Yin Li-Yan , Miao Ling-Feng , Zhou Jing-Jing , Mekontso Francine Ngaffo , Li Da-Dong , Xiang Li-Shan , Yang Fan 
Published: December 2023

AbstractField and greenhouse studies attempting to describe the molecular responses of plant species under waterlogging (WL) combined with salinity (ST) are almost nonexistent. We integrated transcriptional, metabolic, and physiological responses involving several crucial transcripts and common differentially expressed genes and metabolites in fragrant rosewood (Dalbergia odorifera) leaflets to dissect plant-specific molecular responses and patterns under WL combined with ST (SWL). We discovered that the synergistic pattern of the transcriptional response of fragrant rosewood under SWL was exclusively characterized by the number of regulated transcripts. The response patterns under SWL based on transcriptome and metabolome regulation statuses revealed different patterns (additive, dominant, neutral, minor, unilateral, and antagonistic) of transcripts or metabolites that were commonly regulated or expressed uniquely under SWL. Under SWL, the synergistic transcriptional response of several functional gene subsets was positively associated with several metabolomic and physiological responses related to the shutdown of the photosynthetic apparatus and the extensive degradation of starch into saccharides through α-amylase, β-amylase, and α-glucosidase or plastoglobuli accumulation. The dissimilarity between the regulation status and number of transcripts in plants under combined stresses led to nonsynergistic responses in several physiological and phytohormonal traits. As inferred from the impressive synergistic transcriptional response to morpho-physiological changes, combined stresses exhibited a gradually decreasing effect on the changes observed at the molecular level compared to those in the morphological one. Here, by characterizing the molecular responses and patterns of plant species under SWL, our study considerably improves our understanding of the molecular mechanisms underlying combined stress.
The Impact of Moral Distress on Staff and Novice Nurses
Authors: Becker Richard Philip 
Published: December 2023

ABSTRACT:
Moral distress is an interior affliction associated with exterior conflicts between one's values, obligations, and actions. This article builds understanding of moral distress among nurses and the importance of reducing its harmful impact, particularly to novice nurses. Moral distress is defined along with ethical issues and concepts related to moral distress, its current impact, coping with moral distress and building moral reserve, and the significance of acting according to one's conscience.
Developing Faith Community Emergency Response Teams Through Simulation
Authors: Sweeney Amy , Papp Lisa 
Published: December 2023

ABSTRACT:
The development of a volunteer emergency response team is an effective method to mitigate the negative impacts and improve outcomes of health emergencies in faith communities and is supported by faith community nursing scope and standards of professional practice. Conducting simulated emergency drills with a core team of volunteers within one parish supported the confidence and comfort levels of the multidisciplinary group of volunteers, led by a nurse. Simulation and debriefing increased team members' preparedness for physical and mental health emergencies.
Mentoring New Graduate Nurses to Decrease Turnover
Authors: Palermo Kathryn 
Published: December 2023

ABSTRACT:
Nurse turnover may negatively impact patient outcomes, the nurse shortage, and hospital finances. This evidence-based practice project examined the effect of a formal mentorship program on new graduate nurses' (NGNs) intent to leave a healthcare position. The outcomes suggest that the mentoring intervention used has the potential to impact new graduate nurse retention rate. Small sample size limits evaluating the project, which needs to be replicated with a much larger number of NGN mentees and more experienced nurse mentors.
Defeating Nurse Workplace Bullying Through Political Activism
Authors: Madden Melissa A. 
Published: December 2023

ABSTRACT:
Workplace bullying is a social injustice with a detrimental impact on nurse retention, job satisfaction, self-esteem, and patient care. Nurses can engage in individual-, unit-, and policy-level activities aimed at promoting a healthier work environment. In the public sphere, political activism by nurses to promote the anti-bullying Healthy Workplace Bill can help improve the safety of healthcare work settings. Christian nurses' political advocacy enhances social justice as reflected in the Bible and can be seen as another avenue for godly service.
A Systematic Review of Interventions for Obesity Among Adults With Food Insecurity
Authors: Bach Randy , Hui Anna , Chao Ariana M. 
Published: December 2023

Objective
Food insecurity is associated with reduced dietary quality and excess weight gain. However, interventions that are effective for obesity among individuals with food insecurity are unclear. The purpose of this systematic review was to synthesize studies in which authors examined interventions for obesity among adults with food insecurity.

Methods
PubMed, PsycINFO, CINAHL, and EMBASE were searched from inception to October 2022. Studies were included if their authors reported on nonpharmacological and nonsurgical interventions that focused on adults with food insecurity and overweight/obesity and reported weight loss.

Results
A total of 1360 titles were reviewed during the electronic search, and only 5 studies met inclusion criteria. There were 2 primary types of interventions that have been tested: first, behavioral weight loss counseling with or without tailoring for individuals with food insecurity and, second, subsidies for food. Findings of the benefits of one type of intervention over another are mixed.

Conclusions
This systematic review highlights that the current evidence for interventions that address food insecurity and obesity is mixed and limited in scope. There is a need for rigorous controlled trials to examine the effectiveness and cost-effectiveness of interventions for weight management among individuals with food insecurity and obesity while considering sustainability.
Visual change as the presenting symptom of a suspected metastatic brain lesion in esophageal cancer: A case report
Authors: Hsieh Yun-Chen , Wu Jian-Sheng 
Published: December 2023

Introduction:
Esophageal cancer is the seventh most common malignancy worldwide and the sixth leading cause of cancer mortality with an overall survival rate of <20%. Esophageal cancer frequently metastasizes to distant lymph nodes, lungs, liver, and bones. Cerebral metastases originating from esophageal cancer are rare and often carry a poor prognosis as do most all metastatic lesions in esophageal cancer.

Case presentation:
In this report, we describe a 55-year-old patient with past history of esophageal carcinoma who presented with blurred vision after taking ethambutol for tuberculosis. Ethambutol-induced optic neuropathy was the lead diagnosis. Initial vision testing was normal so additional testing with visual field examination was warranted. The visual field examination revealed homonymous hemianopsia. Subsequent magnetic resonance imaging of his brain, demonstrated a focal lesion, consistent with but not diagnostic of a brain metastasis likely from his primary esophageal malignancy.

Conclusion:
We conclude that a careful review of the medical history and comprehensive assessment are essential in establishing an obscure clinical diagnosis especially in the event that an uncommon metastatic lesion is encountered.
False Positive in [99mTc]Tc-DPD Scintigraphy for Cardiac Amyloidosis Due to Intravenous Iron Administration
Authors: Rudolphi Solero Teodoro , Feriche Aragón Manuel , Amrani Raissouni Tomader , Delgado-García Alberto , Cañada-Rodríguez Maria José , Sanz Viedma Salomé 
Published: December 2023

Abstract
[99mTc]Tc-DPD (3,3-diphosphono-1,2-propanodicarboxylic acid) scintigraphy is an essential tool for diagnosing transthyretin amyloid cardiac amyloidosis. An 86-year-old woman suffering from heart failure with preserved ejection fraction underwent [99mTc]Tc-DPD scintigraphy and a SPECT/CT for suspected transthyretin amyloid cardiac amyloidosis. The scan showed intracardiac and liver uptake. As the patient had taken intravenous iron on the morning of the scan, we decided to repeat the scan, but this time, it showed no uptake in the heart or the liver. Accordingly, we concluded the first result was a false positive due to drug interaction.
Axillary Nodal Response to Neoadjuvant T-DM1 Combined with Pertuzumab in a Prospective Phase II Multi-Institution Clinical Trial
Authors: Weiss Anna , Jin Qingchun , Waks Adrienne G , Yardley Denise , Spring Laura M , Wrabel Eileen , Tayob Nabihah , Viale Giuseppe , Krop Ian E , King Tari A , Metzger-Filho Otto 
Published: December 2023

BACKGROUND:
Patients with ERBB2 (HER2)-positive breast cancer experience high pathologic complete response (pCR) rates after standard neoadjuvant anti-HER2 systemic therapy. We examined axillary pathologic nodal response to neoadjuvant dual HER2-targeted therapy alone, based on breast pathologic response, in a multi-institution clinical trial.

STUDY DESIGN:
Patients with HER2-positive breast cancer were enrolled to a phase II single-arm trial, which administered 6 cycles of neoadjuvant trastuzumab emtansine (T-DM1) plus pertuzumab. Rates of pathologic nodal disease (ypN) in patients who were clinically node-negative (cN0) and node-positive (cN1) were analyzed, by residual breast disease (pCR and residual cancer burden [RCB] I to III).

RESULTS:
One hundred fifty-eight patients completed preoperative treatment and proceeded to surgery. Of 92 patients who were cN0, 48 (52.2%) and 10 (10.9%) experienced breast pCR and RCB I, respectively. Of these, 100% were ypN0. Of 34 with RCB II to III, 26 (76.5%) were ypN0. Of 30 patients who were cN1 with breast pCR, 100% were ypN0; of the 12 patients who were cN1 with RCB I, 66.7% were ypN0; and of the 24 patients who were cN1 with RCB II to III, 25% were ypN0. ypN0 rates were significantly different between patients who did and did not experience a pCR, in both cN0 (p = 0.002) and cN1 (p < 0.001) subgroups.

CONCLUSIONS:
Patients with HER2-positive breast cancer treated with dual HER2-targeted therapy who experienced a breast pCR or RCB I response were frequently ypN0. These findings support future trials considering omission of axillary surgical staging for patients with HER2-positive breast cancer in neoadjuvant trials of active HER2-targeted regimens, particularly if they experience breast pCR or RCB I.
Ablation of Mitochondrial RCC1-L Induces Nigral Dopaminergic Neurodegeneration and Parkinsonian-like Motor Symptoms
Authors: Ellioff Kaylin J. , Osting Susan M.K. , Lentine Alyssa , Welper Ashley D. , Burger Corinna , Greenspan Daniel S. 
Published: December 2023

ABSTRACTMitochondrial dysfunction has been linked to both idiopathic and familial forms of Parkinson’s disease (PD). We have previously identified RCC1-like (RCC1L) as a protein of the inner mitochondrial membrane important to mitochondrial fusion. Herein, to test whether deficits in RCC1L mitochondrial function might be involved in PD pathology, we have selectively ablated theRcc1lgene in the dopaminergic (DA) neurons of mice. A PD-like phenotype resulted that includes progressive movement abnormalities, paralleled by progressive degeneration of the nigrostriatal tract. Experimental and control groups were examined at 2, 3-4, and 5-6 months of age. Animals were tested in the open field task to quantify anxiety, exploratory drive, locomotion, and immobility; and in the cylinder test to quantify rearing behavior. Beginning at 3-4 months, both female and maleRcc1lknockout mice show rigid muscles and resting tremor, kyphosis and a growth deficit compared with heterozygous or wild type littermate controls.Rcc1lknockout mice begin showing locomotor impairments at 3-4 months, which progress until 5-6 months of age, at which age theRcc1lknockout mice die. The progressive motor impairments were associated with progressive and significantly reduced tyrosine hydroxylase immunoreactivity in the substantia nigra pars compacta (SNc), and dramatic loss of nigral DA projections in the striatum. Dystrophic spherical mitochondria are apparent in the soma of SNc neurons inRcc1lknockout mice as early as 1.5-2.5 months of age and become progressively more pronounced until 5-6 months. Together, the results reveal the RCC1L protein to be essential toin vivomitochondrial function in DA neurons. Further characterization of this mouse model will determine whether it represents a new model forin vivostudy of PD, and the putative role of the humanRCC1Lgene as a risk factor that might increase PD occurrence and severity in humans.
Network-level encoding of local neurotransmitters in cortical astrocytes
Authors: Cahill Michelle K. , Collard Max , Tse Vincent , Reitman Michael E. , Etchenique Roberto , Kirst Christoph , Poskanzer Kira E. 
Published: December 2023

Summary ParagraphAstrocytes—the most abundant non-neuronal cell type in the mammalian brain—are crucial circuit components that respond to and modulate neuronal activity via calcium (Ca2+) signaling1–8. Astrocyte Ca2+activity is highly heterogeneous and occurs across multiple spatiotemporal scales: from fast, subcellular activity3,4to slow, synchronized activity that travels across connected astrocyte networks9–11. Furthermore, astrocyte network activity has been shown to influence a wide range of processes5,8,12. While astrocyte network activity has important implications for neuronal circuit function, the inputs that drive astrocyte network dynamics remain unclear. Here we usedex vivoandin vivotwo-photon Ca2+imaging of astrocytes while mimicking neuronal neurotransmitter inputs at multiple spatiotemporal scales. We find that brief, subcellular inputs of GABA and glutamate lead to widespread, long-lasting astrocyte Ca2+responses beyond an individual stimulated cell. Further, we find that a key subset of Ca2+activity—propagative events—differentiates astrocyte network responses to these two major neurotransmitters, and gates responses to future inputs. Together, our results demonstrate that local, transient neurotransmitter inputs are encoded by broad cortical astrocyte networks over the course of minutes, contributing to accumulating evidence across multiple model organisms that significant astrocyte-neuron communication occurs across slow, network-level spatiotemporal scales13–15. We anticipate that this study will be a starting point for future studies investigating the link between specific astrocyte Ca2+activity and specific astrocyte functional outputs, which could build a consistent framework for astrocytic modulation of neuronal activity.
Substrate recognition and selectivity in SARS-CoV-2 main protease: Unveiling the role of subsite interactions through dynamical nonequilibrium molecular dynamics simulations
Authors: Chan H. T. Henry , Oliveira A. Sofia F. , Mulholland Adrian J. , Schofield Christopher J. , Duarte Fernanda 
Published: December 2023

AbstractThe main protease (Mpro) of the SARS-CoV-2 coronavirus employs a cysteine-histidine dyad in its active site to catalyse hydrolysis of the viral polyproteins. It is well established that binding of the substrate P1-Gln in the S1 subsite of Mproactive site is crucial for catalysis and this interaction has been employed to inform inhibitor design; however, how Mprodynamically recognises and responds to substrate binding remains difficult to probe by experimental methods. We thus employed the dynamical nonequilibrium molecular dynamics (D-NEMD) approach to probe the response of Mproto systematic substrate variations. The results emphasise the importance of P1-Gln for initiating a productive enzymatic reaction. Specifically, substituting P1-Gln with alanine disrupts the conformations of the Cys145 and His41 dyad, causing Cys145 to transition from the productivegaucheconformation to the non-productivetransconformation. Importantly, our findings indicate that Mproexhibits dynamic responses to substrate binding and likely to substrate-mimicking inhibitors within each of the S4-S2′ subsites. The results inform on the substrate selectivity requirements and shed light on the observed variations in hydrolytic efficiencies of Mprotowards different substrates. Some interactions between substrate residues and enzyme subsites involve more induced fit than others, implying that differences in functional group flexibility may optimise the binding of a substrate or inhibitor in a particular subsite.
Inducing representational change in the hippocampus through real-time neurofeedback
Authors: Peng Kailong , Wammes Jeffrey D. , Nguyen Alex , Iordan Marius Cătălin , Norman Kenneth A. , Turk-Browne Nicholas B. 
Published: December 2023

AbstractWhen you perceive or remember one thing, other related things come to mind. This competition has consequences for how these items are later perceived, attended, or remembered. Such behavioral consequences result from changes in how much the neural representations of the items overlap, especially in the hippocampus. These changes can reflect increased (integration) or decreased (differentiation) overlap; previous studies have posited that the amount of coactivation between competing representations in cortex determines which will occur: high coactivation leads to hippocampal integration, medium coactivation leads to differentiation, and low coactivation is inert. However, those studies used indirect proxies for coactivation, by manipulating stimulus similarity or task demands. Here we induce coactivation of competing memories in visual cortex more directly using closed-loop neurofeedback from real-time fMRI. While viewing one object, participants were rewarded for implicitly activating the representation of another object as strongly as possible. Across multiple real-time fMRI training sessions, they succeeded in using the neurofeedback to induce coactivation. Compared with untrained objects, this coactivation led to behavioral and neural integration: The trained objects became harder for participants to discriminate in a categorical perception task and harder to decode from patterns of fMRI activity in the hippocampus.
A dynamic attractor network model of memory formation, reinforcement and forgetting
Authors: Boscaglia Marta , Gastaldi Chiara , Gerstner Wulfram , Quiroga Rodrigo Quian 
Published: December 2023

AbstractEmpirical evidence shows that memories that are frequently revisited are easy to recall, and that familiar items involve larger hippocampal representations than less familiar ones. In line with these observations, here we develop a modelling approach to provide a mechanistic hypothesis of how hippocampal neural assemblies evolve differently, depending on the frequency of presentation of the stimuli. For this, we added an online Hebbian learning rule, background firing activity, neural adaptation and heterosynaptic plasticity to a rate attractor network model, thus creating dynamic memory representations that can persist, increase or fade according to the frequency of presentation of the corresponding memory patterns. Specifically, we show that a dynamic interplay between Hebbian learning and background firing activity can explain the relationship between the memory assembly sizes and their frequency of stimulation. Frequently stimulated assemblies increase their size independently from each other (i.e. creating orthogonal representations that do not share neurons, thus avoiding interference). Importantly, connections between neurons of assemblies that are not further stimulated become labile so that these neurons can be recruited by other assemblies, providing a neuronal mechanism of forgetting.