bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin structure and epigenetic regulation in yeast
Authors: Pillus Lorraine , Grunstein Michael 
Published: November 2023

Abstract
Although the genetic information of each cell in a yeast colony is identical, the transcriptional patterns of individual cells within that colony may be very different. These variable, or epigenetic, transcriptional patterns arise at least in part from local differences in chromatin structure. The focus of this chapter is a discussion of how chromatin structure contributes to epigenetic transcriptional states. We begin with a brief description of how chromatin structure contributes to transcriptional regulation in multicellular eukaryotes, particularly the form of regulation known as position effect variegation (a topic considered in depth in Chapter 8). We then move on to consider in greater detail the role of chromatin structure in position effect transcriptional regulation in yeast.
Multiple Pin Peptide Scanning (“Pepscan”)
Authors: Sumar Nazira 
Published: November 2023

Abstract
The identification of regions of interaction between an antigen and antibody is an important area of research in molecular immunology. The correct identification of epitopes not only allows one to map where the important regions of an antigen are located in its three-dimensional structure but more importantly, it is instrumental in the diagnosis and prognosis of disease, in immunointervention, and in the design of drugs and generation of vaccines where specific peptides are used to induce antibodies to pathogenic organisms.
The elements of Drosophila biology and genetics
Authors: Roberts David B , Standen Graeme N 
Published: November 2023

Abstract
If you want to work with Drosophila the best start is to spend a couple of weeks in a good Drosophila laboratory learning how to handle and keep the flies. For many reasons this may not be possible and so we present this chapter as an alternative which can only be second best. When you have worked with Drosophila for many years there is still much to be gained in visiting other ‘fly labs’ to see how they have made the keeping and handling of flies easier. Indeed this chapter is a mixture of techniques, protocols, and tricks, many of which have been picked up on visits to colleagues and few if any developed by us. It is impossible at this late date to attribute these techniques to any one person but if you learn to handle flies with care and interest we are sure that this will be considered thanks enough.
Cell culture
Authors: Cherbas Lucy , Cherbas Peter 
Published: November 2023

Abstract
In recent years cell lines have emerged as important tools for Drosophila research, tools that are being applied in such diverse projects as promoter analysis, studies of signal transduction mechanisms and hormone action, somatic cell genetics, and even as substrates for the development in vitro of the malarial parasite Plasmodium (1). In this chapter we introduce the Drosophila cell lines and provide those detailed protocols needed to maintain, transfect, and clone, and otherwise manipulate Drosophila cells. Our direct experience has been almost exclusively with the embryonic cell lines (e.g. Kc and S2 cells) that are in widespread use, and our laboratory protocols reproduced here were developed for those lines. Recently imaginal disc and CNS-derived lines have become available, and promise to become important research tools. Lacking direct experience with those lines we have, for the most part, elected to direct the reader to the appropriate literature.
Evolution des activités lipoxygénasique et polyphénoloxydasique de différentes variétés d’orge au cours du maltage
Authors: Billaud Catherine , Garcia Rebeca , Boivin Patrick , Nicolas Jacques 
Published: November 2023

Abstract
Lipoxygenase (LOχ) and polyphenoloxidase (PPO) were measured in ten barley varieties during malting and kilning. A rapid method of determination is described, following separation of the two isoenzymes LOχ1 and LOχ2. LOχ3 showed preferential production in both barley and malt of a 9- hydroperoxide precursor of trans-2-nonenal, while LOX2, which appeared during germination, formed a 13-hydroperoxide. During kilning, variable quantities were formed of inhibitory compounds to LOχ, shown by dialysis before the estimation. PPO activity.
Hydrolysis of barley starch by malt limit dextrinase
Authors: Stenholrn K , Horne S , Lauro M , Perttula M , Suortti T 
Published: November 2023

Abstract
The reaction mechanism of malt limit dextrinase was studied in comparison to that of microbial pullulanase using gel permeation chromatography and high performance anion exchange chromatography with pulsed amperometric detection.
Wort stripping
Authors: Seldeslachts Dirk , Eynde Erik Van den , Degelin Ludo 
Published: November 2023

Abstract
During classical wort boiling generally high total evaporation rates (7 to 10 percent) are applied, mainly to eliminate unwanted volatiles. However, a big classical wort kettle is not designed for efficient evaporation. Hence we developed a new wort boiling system that devides the wort boiling process into 2 phases. In a first phase - during which the wort is held at boiling temperature without any significant evaporation - the volatiles are accumulated. In a second phase - after wort clarification - the hot wort is sent over a wortstripping column with an open packing. Using life steam volatiles are eliminated very efficiently.
Relation between lipoxygenase extraction during brewing, reducing capacity of the wort and the organoleptical stability of beer
Authors: Buck A De , Aerts G , Bonte S , Dupire S , Eynde E Van den 
Published: November 2023

Abstract
The production of stale off-flavours caused by trans-2-nonenal during beer storage has to be related with lipid oxidation during wort production. Although the two LOX isoenzymes contribute to the nonenal potential in wort, it is LOX1 that produces mainly the 9-hydroperoxide of linoleic acid, a precursor of trans-2-nonenal.
Main fermentation with immobilized yeast - a breakthrough?
Authors: Linko Matti , Virkajarvi Ilkka , Pohjaia Nana , Lindborgl Katri , Kronlof’l Jukka , Pajunen Esko 
Published: November 2023

Abstract
The successful rapid maturation of beer with immobilized yeast has encouraged further research on main fermentation with immobilized yeast, too. Investigations have been carried out both in laboratory and in pilot scale. A feasibility study revealed clearly that the carrier costs are crucial because of the relatively large reactor volumes needed, compared with those for maturation. Very strongly flocculating yeasts hold promise. With proper reactor design it may be possible to operate even without true immobilization, possibly using suitab!e filling particles or supporting structures to ensure high yeast concentration and smooth plug-flow type flux.
The use of ultrasonic radiation to suppress foaming in fermenters
Authors: Freeman G J , Reid A I , Martfnez C Valdecantos , Lynch F J , Juárez J A Gallego 
Published: November 2023

Abstract
The geometry of cylindroconical fermenters causes foam formation to reduce maximum wort fill level significantly. Accordingly a technology which removes foam without risk to beer quality would increase fermenter room capacity. Patented power ultrasound equipment has been shown to break beer foam. Pilot trials demonstrated that the ultrasound was able to break older foam much more effectively than freshly formed foam. There was a beneficial effect of reverberation around the vessel headspace. The technology showed enough potential for scale-up to full-size fermenters to be considered.
Innovation in yeast cell filtration: cost saving technology with high flux membranes
Authors: Rijn C J M van , Nijdam W , Stappen L A V G van der , Raspe OJ A , Broens L , Hoof S van 
Published: November 2023

Abstract
Common yeast cell filtration systems are based on diatomaceous earth. An alternative yeast cell filtration system has been tested using high flux microsieves made with silicon micromachining. The microsieves have been tested in a cross-flow filtration system with back-pulse techniques. The flux observed during the filtration of beer after maturation was at least 12,000 Vm%ar/hour without significant fiux decline. For cost saving high volume filtration a number of microsieves can be stacked to a compact micro filtration system. The developed system is chemical inert to most cleaning agents and therefore suitable for in-line cleaning.
Hydroxyl radical footprinting
Authors: Kolb Annie 
Published: November 2023

Abstract
Hydroxyl radicals have now been used for more than 15years to probe the structure of various macromolecules. They have also been widely used to footprint DNA-protein and RNA-protein complexes (1, 2). Hydroxyl radicals are w1y small, comparable in size to a water molecule, are most commonly generated from FeEDTA in solution by an innocuous and inexpensive procedure (see Protocols 2 and 3) &lt;md are capable of cutting the DNA or RNA backbone at eve1y accessible nucleotide without sequence specificity (3-5). A footprinting reagent in which the .EDTA moiety is coupled to an intercalator can also be used to generate hydroxyl radicals (6). This reactant. methidium-propyl Fe-EDTA, binds to some preferred positions along the DNA, and consequently the pattern of DNA backbone cleavage is much less random than with Fee-EDTA alone.
Biochemistry of C. elegans
Authors: Mains Paule E , McGhee James D 
Published: November 2023

Abstract
Notwithstanding the virtues of C. elegans as an experimental system and extolled in the earlier chapters of this book, it is probably only fair to say that C. elegans is not an ideal organism in which to study biochemistry. It is tedious to grow and disrupt worms in the large quantities that are the usual starting point for conventional biochemistry, at least for the isolation of rare molecules. It is also difficult to produce tightly synchronized populations on a large scale eggshells and cuticles present impressive barriers and it is essentially impossible to produce biochemically useful quantities of pure tissues. There are two exceptions to this last statement, i.e. the production of sperm (1) and the production of oocytes (2, 3; and see below).
Comparison of protein three-dimensional structures
Authors: Johnson Mark S , Lehtonen Jukka V 
Published: November 2023

Abstract
In this chapter we define the different types of questions that may be asked through the comparison of the three-dimensional (3-D) structures of proteins, how to make the comparisons necessary to answer each question, and how to interpret them. We shall focus on the different strategies used, and the assumptions made within typical computer programs that are available.
Cell line preservation and authentication
Authors: Hay R J , Miranda-Cleland M , Durkin S , Miranda-Cleland M , Reid Y A 
Published: November 2023

Abstract
Literally thousands of different cell lines have been derived from human and other metazoan tissues. Many of these originate from normal tissues and exhibit a definable, limited doubling potential. Other cell lines may be propagated continuously, either having gone through an engineered or spontaneous genetic change from the normal primary population. or having been developed initially from turn over our tissue. Both finite lines of sufficient doubling potential and continuous lines can be expanded to produce a large number of aliquots, frozen, and authenticated for widespread use in research. Note: use of the terms cell line and cell strain is as recommended by The Tissue Culture Association committee on nomenclature (1).
Mindfulness and Social Work: Paying Attention to Ourselves, Our Clients, and Society
Authors: Hick Steven F 
Published: November 2023

Abstract
What is mindfulness? What are its foundations, and how can it help social workers in their practice? Mindfulness is an orientation to our everyday experiences that can be cultivated by means of various exercises and practices. By opening up in a particular way to their internal and external experiences, social workers and clients are better able to understand what is happening to them in both a psychological and sociological sense. With this understanding, people are better able to see the variety of ways in which they can respond. Habitual reactions are more easily avoided, and inner peace and balance are developed. Social workers are increasingly using aspects of mindfulness in three ways: (1) as a means of self-care, looking inward, and cultivating mindfulness within themselves; (2) directly in their practice as an intervention within micro-practice (direct intervention with individuals, families, and groups) and in mezzo- and macro-practice (community work and policy); and (3) as a means to positively affect the helping or therapeutic relationship between social worker and client.
Nonoperative treatment of multiple rib fractures, the results to beat: International multicenter prospective cohort study among 845 patients
Authors: Peuker Felix , Hoepelman Ruben J. , Beeres Frank J.P. , Balogh Zsolt J. , Beks Reinier B. , Sweet Arthur A.R. , IJpma Frank F.A. , Lansink Koen W.W. , van Wageningen Bas , Tromp Tjarda N. , Minervini Fabrizio , van Veelen Nicole M. , Hoogendoorn Jochem M. , de Jong Mirjam B. , van Baal Mark C.P.M. , Leenen Luke P.H. , Groenwold Rolf H.H. , Houwert R. Marijn 
Published: November 2023

BACKGROUND
Optimal treatment (i.e., nonoperative or operative) for patients with multiple rib fractures remains debated. Studies that compare treatments are rationalized by the alleged poor outcomes of nonoperative treatment.

METHODS
The aim of this prospective international multicenter cohort study (between January 2018 and March 2021) with 1-year follow-up, was to report contemporary outcomes of nonoperatively treated patients with multiple rib fractures. Including 845 patients with three or more rib fractures. Primary outcome was in-hospital mortality. Secondary outcomes included hospital length of stay (HLOS), (pulmonary) complications, and quality of life.

RESULTS
Mean age was 57.7 ± 17.0 years, median Injury Severity Score was 17 (13–22) and the median number of rib fractures was 6 (4–8). In-hospital mortality rate was 1.5% (n = 13), 112 (13.3%) patients had pneumonia and four (0.5%) patients developed a symptomatic nonunion. The median HLOS was 7 days (4–13 days), and median intensive care unit length of stay was 2 days (1–5 days). Mean 5-Level Quality of Life Questionnaire index value was 0.83 ± 0.18 1 year after trauma. Polytrauma patients had a median HLOS of 10 days (6–18 days), a pneumonia rate of 17.6% (n = 77) and mortality rate of 1.7% (n = 7). Elderly patients (≥65 years) had a median HLOS of 9 days (5–15 days), a pneumonia rate of 19.7% (n = 57) and mortality rate of 4.1% (n = 12).

CONCLUSION
Overall, nonoperative treatment of patients with multiple rib fractures shows low mortality and morbidity rate and good quality of life after 1 year. Future studies evaluating the benefit of operative stabilization should use contemporary outcomes to establish the therapeutic margin of rib fixation.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level III.
Automated single-cell omics end-to-end framework with data-driven batch inference
Authors: Wang Yuan , Thistlethwaite William , Tadych Alicja , Ruf-Zamojski Frederique , Bernard Daniel J , Cappuccio Antonio , Zaslavsky Elena , Chen Xi , Sealfon Stuart C. , Troyanskaya Olga G. 
Published: November 2023

SummaryTo facilitate single-cell multi-omics analysis and improve reproducibility, we present SPEEDI (Single-cell Pipeline for End to End Data Integration), a fully automated end-to-end framework for batch inference, data integration, and cell type labeling. SPEEDI introduces data-driven batch inference and transforms the often heterogeneous data matrices obtained from different samples into a uniformly annotated and integrated dataset. Without requiring user input, it automatically selects parameters and executes pre-processing, sample integration, and cell type mapping. It can also perform downstream analyses of differential signals between treatment conditions and gene functional modules. SPEEDI’s data-driven batch inference method works with widely used integration and cell-typing tools. By developing data-driven batch inference, providing full end-to-end automation, and eliminating parameter selection, SPEEDI improves reproducibility and lowers the barrier to obtaining biological insight from these valuable single-cell datasets. The SPEEDI interactive web application can be accessed athttps://speedi.princeton.edu/.
ModrRNA1: A tool for possible RNA modification site identification with associated putative enzymes in bacterial rRNA
Authors: Thilanka Uvindu , Warushavithana Paaramitha Sithumini 
Published: November 2023

AbstractRibosomal RNA modifications play a crucial role in bacteria, impacting function, ribosome formation, and antibiotic resistance. ModrRNA1 replaces manual methods and introduces a user-friendly, streamlined bioinformatics tool for the identification of potential rRNA modification sites and associated enzymes, across various bacteria.This tool utilizes a curated database of known bacterial rRNA modifications and enzymes, employing sequence alignment with a customized scoring system for precise site identification. High-confidence alignments generate annotated RNA sequence plots. Subsequently, enzyme detection is facilitated through structural comparisons, phylogenetics, and BLAST.ModrRNA1 boasts a user-friendly web interface hosted athttps://modrrna.biotechie.orgwith the open-source code for customization available athttps://github.com/sciguysl/ModrRNA1. The results demonstrate ModrRNA1’s efficacy in identifying potential non-species-specific bacterial rRNA modification sites and species-specific associated enzymes.
Human neural stem cells restore spatial memory in a transgenic Alzheimer’s disease mouse model by an immunomodulating mechanism
Authors: Chen Kevin S. , Noureldein Mohamed H. , McGinley Lisa M. , Hayes John M. , Rigan Diana M. , Kwentus Jacquelin F. , Mason Shayna N. , Mendelson Faye E. , Savelieffd Masha G. , Feldman Eva L. 
Published: November 2023

ABSTRACTINTRODUCTIONStem cells are a promising therapeutic in Alzheimer’s disease (AD) given the complex pathophysiologic pathways involved. However, the therapeutic mechanisms of stem cells remain unclear. Here, we used spatial transcriptomics to elucidate therapeutic mechanisms of human neural stem cells (hNSCs) in an animal model of AD.METHODShNSCs were transplanted into the fimbria fornix of the hippocampus using the 5XFAD mouse model. Spatial memory was assessed by Morris water maze. Amyloid plaque burden was quantified. Spatial transcriptomics was performed and differentially expressed genes (DEGs) identified both globally and within the hippocampus. Subsequent pathway enrichment and ligand-receptor network analysis was performed.RESULTShNSC transplantation restored learning curves of 5XFAD mice. However, there were no changes in amyloid plaque burden. Spatial transcriptomics showed 1061 DEGs normalized in hippocampal subregions. Plaque induced genes in microglia, along with populations of stage 1 and stage 2 disease associated microglia (DAM), were normalized upon hNSC transplantation. Pathologic signaling between hippocampus and DAM was also restored.DISCUSSIONhNSCs normalized many dysregulated genes, although this was not mediated by a change in amyloid plaque levels. Rather, hNSCs appear to exert beneficial effects in part by modulating microglia-mediated neuroinflammation and signaling in AD.
Regional interneuron transcriptional changes reveal pathologic markers of disease progression in a mouse model of Alzheimer’s disease
Authors: Chen Kevin S. , Noureldein Mohamed H. , Rigan Diana M. , Hayes John M. , Savelieff Masha G. , Feldman Eva L. 
Published: November 2023

ABSTRACTAlzheimer’s disease (AD) is a progressive neurodegenerative disorder and leading cause of dementia, characterized by neuronal and synapse loss, amyloid-β and tau protein aggregates, and a multifactorial pathology involving neuroinflammation, vascular dysfunction, and disrupted metabolism. Additionally, there is growing evidence of imbalance between neuronal excitation and inhibition in the AD brain secondary to dysfunction of parvalbumin (PV)- and somatostatin (SST)-positive interneurons, which differentially modulate neuronal activity. Importantly, impaired interneuron activity in AD may occur upstream of amyloid-β pathology rendering it a potential therapeutic target. To determine the underlying pathologic processes involved in interneuron dysfunction, we spatially profiled the brain transcriptome of the 5XFAD AD mouse model versus controls, across four brain regions, dentate gyrus, hippocampal CA1 and CA3, and cortex, at early-stage (12 weeks-of-age) and late-stage (30 weeks-of-age) disease. Global comparison of differentially expressed genes (DEGs) followed by enrichment analysis of 5XFAD versus control highlighted various biological pathways related to RNA and protein processing, transport, and clearance in early-stage disease and neurodegeneration pathways at late-stage disease. Early-stage DEGs examination found shared,e.g., RNA and protein biology, and distinct,e.g., N-glycan biosynthesis, pathways enriched in PV-versus somatostatin SST-positive interneurons and in excitatory neurons, which expressed neurodegenerative and axon- and synapse-related pathways. At late-stage disease, PV-positive interneurons featured cancer and cancer signaling pathways along with neuronal and synapse pathways, whereas SST-positive interneurons showcased glycan biosynthesis and various infection pathways. Late-state excitatory neurons were primarily characterized by neurodegenerative pathways. These fine-grained transcriptomic profiles for PV- and SST-positive interneurons in a time- and spatial-dependent manner offer new insight into potential AD pathophysiology and therapeutic targets.
The L27 Domain of MPP7 enhances TAZ-YY1 Cooperation to Renew Muscle Stem Cells
Authors: Shao Anwen , Kissil Joseph L. , Fan Chen-Ming 
Published: November 2023

SUMMARYStem cells regenerate differentiated cells to maintain and repair tissues and organs. They also replenish themselves, i.e. self-renewal, for the regenerative process to last a lifetime. How stem cells renew is of critical biological and medical significance. Here we use the skeletal muscle stem cell (MuSC) to study this process. Using a combination of genetic, molecular, and biochemical approaches, we show that MPP7, AMOT, and TAZ/YAP form a complex that activates a common set of target genes. Among these targets,Carm1can direct MuSC renewal. In the absence of MPP7, TAZ can support regenerative progenitors and activateCarm1expression, but not to a level needed for self-renewal. Facilitated by the actin polymerization-responsive AMOT, TAZ recruits the L27 domain of MPP7 to up-regulateCarm1to the level necessary to drive MuSC renewal. The promoter ofCarm1, and those of other common downstream genes, also contain binding site(s) for YY1. We further demonstrate that the L27 domain of MPP7 enhances the interaction between TAZ and YY1 to activateCarm1. Our results define a renewal transcriptional program embedded within the progenitor program, by selectively up-regulating key gene(s) within the latter, through the combination of protein interactions and in a manner dependent on the promoter context.