bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determination of carbonyl groups in oxidized proteins
Authors: Shacter Emily , Williams Joy A , Stadtman Earl R , Levine Rodney L 
Published: November 2023

Abstract
There is now a bewildering array of biological processes in which free radicals have been implicated (2), and we assume that enzymes and structural proteins may be attacked whenever free radicals are generated. As a con sequence, oxidative modification of proteins may occur in a variety of physiological and pathological processes. Although the distinction is. some times arbitrary, these modifications may be primary or secondary. Primary modifications occur in metal-catalysed oxidation, radiation-mediated oxidation, and in oxidation by ozone or oxides of nitrogen. Secondary modifications occur when proteins are modified by molecules generated by oxidation of other molecules. One important example is the covalent modification of proteins by hydroxynonenal produced by oxidation of lipids (3).
In vivo selection of specific RNA binding polypeptides using a transcription anti-termination reporter assay
Authors: Harada Kazuo , Frankel Alan D 
Published: November 2023

Abstract
The recognition of specific RNA structures by proteins plays an important role in gene regulation. both at the transcriptional and post-transcriptional levels. but our understanding of the basic principles of recognition is still at an early stage. To help further our understanding. it will he useful to have in hand a set of methods by which to screen molecular libraries for specific RNA binding molecules. In this chapter we describe a method for selecting RNA binding polypeptides from combinatorial libraries.
Determination Of Protease Mechanism
Authors: Dunn Ben M 
Published: November 2023

Abstract
The opening chapter of this volume has outlined the four mechanistic classes: serine and cysteine proteases (those that form covalent enzyme complexes) and aspartic and metalloproteases (those that do not form covalent enzyme complexes). This distinction into two major mechanistic groups is of profound con sequence since the strategy for inhibition is totally different for these two classes. Those enzymes of the first general class have strongly nucleophilic amino acids at their catalytic site. These are usually aligned with hydrogen bond acceptors to promote the dissociation of the nucleophile in the approach to the transition state and, thus, increase the fraction in the hyperreactive state, Design and synthesis of inhibitors of this broad class will therefore be concentrated on introduction of electrophilic groups (-C=C-, -C-C(=O)-Cl, etc,) that will chemically modify the nucleophile or general base. This will render the catalytic apparatus inactive and prevent the action of that protease. The second category of proteolytic enzymes includes two classes that catalyse the hydrolysis of peptide bonds without nucleophilic attack by a functional group of the enzyme. These enzymes rely more upon general acid/general base catalysis of the attack of a water molecule and therefore the catalytic residues lack the aggressive nucleophilicity of the serine or cysteine proteases. Inhibitor design for this second broad group relies on more subtle means of complexation, including a greater necessity for secondary binding interactions along the active-site cleft and transition state analogues. The metalloproteinases offer an additional handle for inhibitors, since functional groups such as -SH can be introduced at precise points to lead to nearly irreversible metal ion chelation.
Inhibition Of Proteolytic Enzymes
Authors: Salvesen Guy S , Nagase Hideaki 
Published: November 2023

Abstract
The two most frequent questions asked by those not working on proteases every day are: ‘ How do I prevent proteolysis in my particular system?’ and ‘ How do I find out which protease is cutting my protein?’ There are no ‘ bullet-proof’ recipes to help with these questions, possibly because of the many varied or even overlapping specificities and catalytic strategies adopted by proteases. Nevertheless, there are a number of general issues and specific techniques that we and others use to address these and other related questions. This usually involves employing natural and synthetic protease inhibitors in complex bio logical environments such as tissue fluids or cells in culture. Many of the methods rely on the theoretical backgrounds illustrated in Chapter 6.
Analysis of transcription factor modifications
Authors: Thomas N Shaun B 
Published: November 2023

Abstract
Transcription factors are regulated by being modified by phosphorylation and glycosylation. Each can cause changes in protein charge, shape, hydrophilicity, and mass, all of which can be exploited in differentiating the modified from the unmodified protein. This chapter will cover how these post-transcriptional modifications can be analysed, the methods most frequently used, and the problems and limitations associated with each. I will assume that the transcription factor has been cloned and sequenced and that you have basic reagents to detect your factor—in particular, antibodies that can be used for Western blotting and immunoprecipitation. Thereafter, the questions to be answered will necessarily dictate which methods are most appropriate. In this chapter I shall start by introducing simple techniques to determine whether a given protein is phosphorylated or glycosylated before covering more complex and costly procedures to determine which sites are modified and the physiological relevance of such modifications.
Measuring inositol 1,4,5-trisphosphate- evoked 45Ca2+ release from intracellular Ca2+ stores
Authors: Taylor Colin W , Marchant Jonathan S 
Published: November 2023

Abstract
The receptors for inositol 1,4,5-trisphosphate (Ins(l,4,5)P3) are intracellular Ca2+ channels which open in response to the concerted effects of cytosolic Ca2+ and Ins(l,4,5)P3, and thereby allow Ca2+ stored within the lumen of the endoplasmic reticulum to leak into the cytosol. The resulting increase in cytosolic [Ca2+] regulates many aspects of cellular behaviour. In the twentyfive years since Ins(l,4,5)P3 was shown to provide the link between receptors in the plasma membrane that stimulate polyphosphoinositide hydrolysis and the release of Ca2+ from intracellular stores (1), novel experimental approaches have often provided the impetus for the steps towards our current understanding. Simple methods to separate [3H]-inositol phosphates, and the use of u+ to block the final step in their degradation (2), allowed the effects of numerous stimuli on polyphosphoinositide hydrolysis to be established in many cells. Methods that allowed selective permeabilization of the plasma membrane, without destroying the integrity of intracellular organelles (3), were instrumental in allowing the effects of Ins(l,4,5)P3 on intracellular Ca2+ stores to be demonstrated (1).
Isothermal titration calorimetry of biomolecules
Authors: O’Brien Ronan , Ladbury John E 
Published: November 2023

Abstract
One of the primary goals of contemporary molecular biology is to gain an understanding of the molecular basis of specificity and recognition phenomena, between proteins and ligands. Proteins can specifically recognize, and reversibly bind to small molecular weight target molecules, other macromolecules (e.g. proteins, nucleic acids) and to macromolecular assemblies. Characterization of these interactions necessarily involves investigation of the inter-relationship between function, structure (including dynamics), kinetics, and energetics (i.e. thermodynamics) of a system under defined physico-chemical conditions. In this chapter we focus on the determination of the latter of these quantities. The measurement of thermodynamic parameters is important because all reversible biomolecular interactions involve a redistribution of non-covalent bonds. The most experimentally accessible of the thermodynamic quantities occurring on a protein going from the free (unbound) to the bound state is the heat (enthalpy) uptake or release.
Cell cycle checkpoints
Authors: Forbes Kristi Chrispell , Enoch Tamar 
Published: November 2023

Abstract
During each yeast cell cycle, chromosomes must be copied faithfully and segregated accurately between daughter cells. Surveillance systems termed ‘checkpoints’ ensure the fidelity of chromosome duplication by detecting abnormal structures and blocking cell cycle transitions while problems are corrected. Studies in Saccharomyces cerevisiae and Schizosaccharomyces pombe have identified a plethora of checkpoint genes and proteins. Remarkably, as was predicted in 1989 by Hartwell and Weinert (1), the same checkpoint proteins that maintain the yeast genomes play a crucial role in preventing cancer in mammals (2, 3). Thus studies in yeasts have helped to elucidate an important cause of genomic instability and cancer. Now that many checkpoint proteins have been identified, current investigations are aimed at understanding how these checkpoints work in molecular detail. As this review will detail, considerable progress has been made in this area in the last 10 years. Because many of the checkpoint proteins arc conserved in higher eukaryotes, yeasts will continue to prove their value as model systems for the study of mechanisms that maintain the genome.
The morphology of larval and adult zebrafish
Authors: Schilling Thomas F 
Published: November 2023

Abstract
With its emergence as a popular model system in developmental genetic studies, the zebrafish, Dania rerio (Teleostei,Cyprinidae), needs accurate anatomical descriptions and guides to staging (1). Staging by morphology helps resolve the problem of asynchrony during development and provides better accuracy in developmental analyses. There is a staging series for the embryonic period in zebrafish (2), but not for larvae and adults. This chapter brings together information on larval and adult morphology, most of which has been published separately in experimental papers. Although not a detailed staging series or atlas, it is meant to serve as a brief guide to late stages of zebrafish development in the laboratory, and to summarize knowledge and publications on zebrafish anatomy.
Inference and applications of molecular phylogenies: An introductory guide
Authors: Strimmer* Korbinian , Robertsont David L 
Published: November 2023

Abstract
Molecular phylogenies have a wide range of practical applications in the analysis of DNA sequences and are now an essential tool in areas ranging from population genetics to genomics to virology. The use of modem computers has fostered the development of sophisticated methodologies, and subsequently a large number of programs have become available. In this chapter we give an introductory overview of the most important methods of inferring phylogenetic trees from nucleotide or amino acid sequence data, emphasizing concept rather than mathematical detail (Box 1). We discuss simple guidelines for choosing a method appropriate for a data set. Advanced issues in molecular phylogenetics are briefly introduced, along with suggestions for further reading. The versatility of molecular phylogenetics is also highlighted and we present a range of practical problems where evolutionary trees have formed a key component of the analysis. Finally, we provide an overview of phylogenetic software and corresponding Internet resources (Box 2).
Laboratory websites: How to disseminate information, make friends, and influence people
Authors: Lu Chao , Woodgett James R 
Published: November 2023

Abstract
The Internet and World Wide Web were born of the need for scientists to communicate and collaborate. In its early DARPAnet days, the network provided teams of physics and computer scientists with a way to efficiently exchange data and commentary. While the popularization, commercialization, and hype of recent years have exploded the use of this network of networks to virtually anyone with a web-enabled device, its relevance to scientists remains as strong as ever. Scientists and students are less willing to physically visit a library to search for information that can be done more easily and faster at home or in the laboratory. There were about 3 million Internet servers worldwide in 1999 hosting about 8 million pages of web content (1). Of those, about 6% focused on scientific and educational content, with the remainder largely being commercial/corporate. The number has increased three-fold per year since then and shows little sign of slowing.
GRP78 acts as a cAMP/PKA signaling modulator through the MC4R pathway in porcine embryonic development
Authors: Heo Geun , Lee Song‐Hee , Kim Ji‐Dam , Lee Gyu‐Hyun , Sim Jae‐Min , Zhou Dongjie , Guo Jing , Cui Xiang‐Shun 
Published: November 2023

AbstractGlucose‐regulated protein 78 (GRP78) binds to and stabilizes melanocortin 4 receptor (MC4R), which activates protein kinase A (PKA) by regulating G proteins. GRP78 is primarily used as a marker for endoplasmic reticulum stress; however, its other functions have not been well studied. Therefore, in this study, we aimed to investigate the function of GRP78 during porcine embryonic development. The developmental quality of porcine embryos, expression of cell cycle proteins, and function of mitochondria were evaluated by inhibiting the function of GRP78. Porcine oocytes were activated to undergo parthenogenesis, and blastocysts were obtained after 7 days of in vitro culture. GRP78 function was inhibited by adding 20 μM HA15 to the in vitro culture medium. The inhibition in GRP78 function led to a decrease in G proteins release, which subsequently downregulated the cyclic adenosine monophosphate (cAMP)/PKA pathway. Ultimately, inhibition of GRP78 function induced the inhibition of CDK1 and cyclin B expression and disruption of the cell cycle. In addition, inhibition of GRP78 function regulated DRP1 and SIRT1 expression, resulting in mitochondrial dysfunction. This study provides new insights into the role of GRP78 in porcine embryonic development, particularly its involvement in the regulation of the MC4R pathway and downstream cAMP/PKA signaling. The results suggest that the inhibition of GRP78 function in porcine embryos by HA15 treatment may have negative effects on embryo quality and development. This study also demonstrated that GRP78 plays a crucial role in the functioning of MC4R, which releases the G protein during porcine embryonic development.
Invasive Multimodality Neuromonitoring to Manage Cerebral Edema in Pediatric Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disease
Authors: Fainberg Nina A. , Silver Maya R. , Arena John D. , Landzberg Elizabeth I. , Banwell Brenda , Gambrah-Lyles Claudia , Kirschen Matthew P. , Madsen Peter J. , McLendon Loren , Narula Sona , Tucker Alexander M. , Huh Jimmy W. , Kienzle Martha F. 
Published: November 2023

Background:
Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is an inflammatory disorder of the CNS with a variety of clinical manifestations, including cerebral edema.

Case Summary:
A 7-year-old boy presented with headaches, nausea, and somnolence. He was found to have cerebral edema that progressed to brainstem herniation. Invasive multimodality neuromonitoring was initiated to guide management of intracranial hypertension and cerebral hypoxia while he received empiric therapies for neuroinflammation. Workup revealed serum myelin oligodendrocyte glycoprotein antibodies. He survived with a favorable neurologic outcome.

Conclusion:
We describe a child who presented with cerebral edema and was ultimately diagnosed with MOGAD. Much of his management was guided using data from invasive multimodality neuromonitoring. Invasive multimodality neuromonitoring may have utility in managing life-threatening cerebral edema due to neuroinflammation.
Central Sleep Apnea in Patients With Coronary Heart Disease Taking P2Y12 Inhibitors
Authors: Tzeng William S. , Klein Christian F. , Roth Robert H. , Cho Yeilim , Munagala Rohit , Bonner Heather , Mazimba Sula , Khayat Rami , Healy William , Lobo Jennifer M. , Kapur Vishesh K. , Kwon Younghoon 
Published: November 2023

Abstract:
Central sleep apnea (CSA) is common in patients with heart failure. Recent studies link ticagrelor use with CSA. We aimed to evaluate CSA prevalence in patients with coronary heart disease (CHD) and whether ticagrelor use is associated with CSA. We reviewed consecutive patients with CHD who underwent a polysomnography (PSG) test over a 5-year period from 3 sleep centers. We sampled patients who were on ticagrelor or clopidogrel during a PSG test at a 1:4 ticagrelor:clopidogrel ratio. Patients with an active opioid prescription during PSG test were excluded. Age, left ventricle (LV) dysfunction, and P2Y12 inhibitor use were included in a multivariate logistic regression. A total of 135 patients were included with 26 on ticagrelor and 109 on clopidogrel (age 64.1 ± 11.4, 32% male). High CSA burden (12%) and strict CSA (4.4%) were more common in patients on ticagrelor than in those on clopidogrel (27% vs. 8.3% and 10.0% vs. 1.8%). Ticagrelor use (vs. clopidogrel) was associated with high CSA burden (OR 3.53, 95% CI 1.04–12.9, P = 0.039) and trended toward significance for strict CSA (OR 6.32, 95% CI 1.03–51.4, P = 0.052) when adjusting for age and LV dysfunction. In an additional analysis also adjusting for history of atrial fibrillation, ticagrelor use and strict CSA became significantly associated (OR 10.0, 95% CI 1.32–117, P = 0.035). CSA was uncommon in patients with CHD undergoing sleep studies. Ticagrelor use (vs. clopidogrel) was associated with high CSA burden and trended toward significance for strict CSA.
Phosphorylated-S6 Expression in Sturge-Weber Syndrome Brain Tissue
Authors: McCann Meghan , Cho Andrew , Pardo Carlos A. , Phung Thuy , Hammill Adrienne , Comi Anne M. 
Published: November 2023

Background:
Sturge-Weber Syndrome (SWS) is a rare neurovascular disorder associated with port-wine birthmarks, glaucoma, and abnormal leptomeningeal blood vessels. It is most commonly caused by a R183Q somatic mutation in GNAQ predicted to result in impaired deactivation of the protein Gαq, and downstream pathways such as the Ras-Raf-MEK-ERK and mTOR pathways. The GNAQ mutation is reportedly enriched in endothelial cells.

Methods:
Using a phosphorylated-S6 (p-S6) antibody, a marker for mTOR pathway activity, we analyzed p-S6 protein expression in human brain tissue samples from SWS subjects and epilepsy controls.

Results:
SWS brain tissue was more likely to have leptomeningeal endothelial p-S6 antibody staining, compared with epilepsy controls, while the percentage of samples with p-S6 staining in perivascular cells and cortex were not significantly different.

Conclusions:
Leptomeningeal endothelial mTOR activity may contribute to abnormal endothelial cell morphology and function. This finding implicates mTOR as a potential treatment target for Sturge-Weber Syndrome.
High-Frequency Gain and Maximum Output Effects on Speech Recognition in Bone-Conduction Hearing Devices: Blinded Study
Authors: Sassi Tyuana Sandim da Silveira , Bucuvic Erika Cristina , Castiquini Eliane Aparecida Techi , Chaves Juliana Nogueira , Kimura Marcia , Buzo Byanka Cagnacci , Lourençone Luiz Fernando Manzoni 
Published: November 2023

Introduction
Bone-conduction hearing device (BCHD) uses natural sound transmission through bone and soft tissue, directly to the cochlea, via an external processor that captures and processes sound, which is converted into mechanical vibrations. Key parameters, as maximum power output (MPO) and broader frequency range (FR), must be considered when indicating a BCHD because they can be decisive for speech recognition, especially under listening challenge conditions.

Objectives
Compare hearing performance and speech recognition in noise of two sound processors (SPs), with different features of MPO and FR, among BCHD users.

Materials and Methods
This single-blinded, comparative, observational study evaluated 21 individuals Baha 4 system users with conductive or mixed hearing impairment. The free-field audiometry and speech recognition results were blindly collected under the following conditions: unaided, with Baha 5, and with Baha 6 Max SP.

Results
In free-field audiometry, significant differences were observed between the SP at 0.25, 3, 4, 6, and 8 kHz, with Baha 6 Max outperforming Baha 5. The Baha 6 Max provided significantly better speech recognition than Baha 5 under all the speech in noise conditions evaluated. Separating the transcutaneous from the percutaneous users, Baha 6 Max Attract SP provided the best results and significantly lowered the free-field thresholds than Baha 5 Attract. The Baha 6 Max also significantly improved speech recognition in noise, among both Attract and Connect users.

Conclusion
The present study revealed that the greater MPO and broader FR of the Baha 6 Max device helped increase high-frequency gain and improved speech recognition in BCHD-experimented users.
Negative Beliefs About Suicide Disclosure
Authors: Bell Kerri-Anne , O'Loughlin Caitlin M. , Piccirillo Marilyn L. , Ammerman Brooke A. 
Published: November 2023

Abstract
This study examined the differences in negative beliefs about disclosing suicidal thoughts and behaviors (STBs) between US Veterans and non-Veterans, and between Veterans who are and are not enrolled in Veterans Health Administration (VHA) care. Participants included 495 adults with a history of suicide ideation who completed an online self-report questionnaire inquiring about history of STBs, STB disclosure, and beliefs about STB disclosures. Group differences in STB disclosure beliefs were analyzed. Results showed that Veterans (vs. non-Veterans) more strongly believed that STB disclosure would result in firearm confiscation. VHA-enrolled (vs. non-VHA enrolled) Veterans reported stronger beliefs that STB disclosures result in involuntary hospitalization. Among VHA-enrolled Veterans, stronger beliefs regarding providers' interest regarding true STB experiences and others' comfort with STB disclosures were associated with lower STB disclosure likelihood. Findings highlight that educating Veterans on the benefits of STB disclosure and limiting misinformation regarding its consequences is paramount, specifically through improved suicide-related communication within the VHA and stigma reduction campaigns.
Systematic Review and Meta-Analysis of Effects of Nurse-Led Intervention for People With Dementia
Authors: Huang Kuei Hsiang , Saragih Ita Daryanti , Suarilah Ira , Son Nguyen Thi , Lee Bih-O 
Published: November 2023

Background
Nurses’ primary role in clinical settings for persons living with dementia is to lessen the strain of dementia on daily life, monitor comorbidities, and manage medications. However, no comprehensive literature review has investigated the effectiveness of nurse-led interventions for persons living with dementia.

Objective
The purpose of this study was to evaluate randomized controlled trials on the efficacy of nurse-led dementia interventions and provide an extended range of outcomes related to cognitive function, depression, and quality of life.

Methods
A comprehensive literature search of six databases was conducted from database inception to August 10, 2022. Methodologies were evaluated, followed by a pooled analysis using random effects models to explain the effects of nurse-led dementia interventions on patients.

Results
Nurse-led interventions were more effective than standard care in alleviating depression and improving quality of life. However, they did not enhance cognitive performance.

Discussion
Nurse-led interventions for dementia alleviate depression and improve quality of life. However, because of lack of randomized controlled trials, the analysis found less effectiveness in improving cognitive function. Therefore, further trials are needed to corroborate these findings.