bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of Tailed Phages: Insights from Comparative Phage Genomics
Authors: Brussow Harald , Desiere Frank 
Published: November 2023

Abstract
Many phage researchers believe that phages are as old as their bacterial hosts. If this hypothesis is true, then we have to postulate elements of vertical evolution for phages. In view of the postulated antiquity of these relationships we might not expect sequence similarities between more distantly related phages. Comparative phage genomics can reveal DNA sequence, protein sequence, or gene map similarities in the absence of sequence similarities between increasingly diverged phages. For even more distant relationships, data from structural biology can be informative. Recent genomics-based ideas on phage evolution are dominated by two interpretations. In one view all doublestranded DNA tailed phage genomes are mosaics with access, by horizontal exchange, to a large common genetic pool, but in which access to the gene pool is not uniform for all phages (22). In this hypothesis horizontal gene transfer dominates over vertical evolution. In fact, it is in some way an updated version of the classical modular theory of phage evolution developed 30 years ago on the basis of heteroduplex mapping with lambdoid coliphages (2, 7). Other investigators studying phages from dairy bacteria observed strong elements of vertical evolution in the structural gene cluster of phages that were not erased by horizontal gene transfer events (5).
Gene Regulatory Circuitry of Phage
Authors: Little John W 
Published: November 2023

Abstract
The gene regulatory circuitry of phage l was the first complex regulatory circuit to be analyzed in molecular detail. l was chosen as a model system for this purpose because it displays a wide range of interesting regulatory properties. It can adopt two alternative life-styles, the lytic and lysogenic states, and it can switch from the lysogenic state to the lytic state in the process of prophage induction, often called the ‘‘genetic switch’’ (13, 28). A choice is made between these two alternative pathways soon after infection; the lysogenic state, in particular, is highly stable, and the switch can be highly efficient. It was clear early on that these properties would be of general relevance to other organisms, including higher eukaryotes.
Lipid-Containing Bacteriophage PM2, the Type Organism of Corticoviridae
Authors: Bamford Dennis H Bamford Jaana K H 
Published: November 2023

Abstract
Bacteriophage PM2 is the only described member of the Corticoviridae family (1). It was isolated from seawater collected from a polluted bay off the coast of Chile (13). The original host was a common marine bacterium Pseudoalteromonas espejiana BAL-31 (originally Pseudomonas BAL-31; 14, 18), which is the source of the DNA exonuclease BAL-31. Alternatively, Pseudoalteromonas sp. ER72M2 obtained from the East River, New York, by Leonard Mindich (26) can be used as a host for PM2. PM2 is the first bacteriophage in which the presence of lipids in the virion was firmly demonstrated (7, 15). The mass of the virion ( 4.5 107 Da) is distributed among nucleic acid (14%), lipid (14%), and protein (72%) constituents (8, 9). The sedimentation coefficient (S20,w) of the particle is 293 S and buoyant density in sucrose and cesium chloride is 1.26 g/cm3 and 1.28 g/cm3, respectively (8, 26). The stability of the virion is dependent on sodium and calcium ions and the virion equilibrated in sucrose is inactive (26).
Bacteriophage SPP1
Authors: lurz Juan C Alonso paulo tavares rudi , Trautner Thomas A 
Published: November 2023

Abstract
The lytic Bacillus subtilis bacteriophage SPP1 was isolated in Pavia (Subtilis Phage Pavia) and first described by Riva et al. (99). Interest in this phage derived at first from the observation that the complementary DNA strands of the phage were separable into a heavy strand (r 1.725 g/cm3) and a light strand (r 1.713 g/cm3) following denaturation and isopycnic centrifugation (99, 109). This observation and the finding that the phage was highly active in transfection led to the use of SPP1 in studies of mismatch repair (109). In later experiments the molecular biology of the phage, including its structure, total DNA sequence, genetics, and life cycle were established.
N15: The Linear Plasmid Prophage
Authors: Ravin Nikolai V 
Published: November 2023

Abstract
The temperate bacteriophage N15 is unique among Escherichia coli phages in that its prophage is not integrated into the bacterial chromosome but instead is a linear plasmid molecule with covalently closed ends. Linear plasmids are very unusual in the Enterobacteria and only two others have been reported: phiKO2 in Klebsiella oxytoca (4, 43) and pY54 inYersinia enterocolitica (16). However, such replicons are common in the spirochete genus, Borrelia (1). Here I will summarize the most relevant work on phage N15 with a special emphasis on the mechanism of replication, telomere formation, and control of lysogeny.
Phages of Cyanobacteria
Authors: Mann Nicholas H 
Published: November 2023

Abstract
The scientific importance of the phages of cyanobacteria (cyanophages) is intimately associated with the ecological significance of their hosts. Cyanobacteria are arguably the most diverse and widely distributed group of eubacteria on the planet and play central roles in major biogeochemical processes, such as the carbon and nitrogen cycles. Cyanobacteria exist in a wide range of freshwater and marine environments, ranging from thermophilic to psycrophilic, and terrestrial environments, including those subject to periodic desiccation. By virtue of their higher plant-like oxygenic photosynthetic apparatus they contribute significantly to the maintenance of the Earth’s atmosphere, in terms of both oxygen production and carbon dioxide fixation. Consequently, the ability of cyanophages to determine the population structures and genetic diversity of cyanobacteria, as well as to potentially influence the dynamics of biogeochemical processes, gives them a unique ecological significance.
Yersinia Phages
Authors: Appel Stefan Hertwig Mikael Skurnik Bernd 
Published: November 2023

Abstract
The genus Yersinia contains 11 species, of which Yersinia enterocolitica,Yersinia pestis, and Yersinia pseudotuberculosis are pathogenic for humans and animals (5). While Y. pestis is the causative agent of plague, Y. enterocolitica and Y. pseudotuberculosis are mainly enteropathogenic. In comparison with the other pathogenic Yersinia species, Y. enterocolitica is very heterogeneous, comprising pathogenic and nonpathogenic strains which belong to about 70 serogroups. In order to differentiateYersinia strains, a number of phages were isolated and used for typing. Several phage typing sets have been worked out for Y. enterocolitica (4, 30, 38). The sets contain temperate phages isolated from Yersinia strains (37, 39) or phages isolated from sewage (2, 8), whose origin is unknown. Three yersiniophages have been sequenced: phages fA1122, fYeO3-12, and PY54. This chapter is primarily an overview of the properties of those three phages.
Phages of Lactococcus lactis
Authors: Hammer Lone Brąndsted Karin 
Published: November 2023

Abstract
Lactococci are Gram-positive mesophilic bacteria with low G-C content that belong to the group of lactic acid bacteria. They are aerotolerant and live by means of fermentation, as they are lacking a respiratory chain, and the main end product during fermentation is lactic acid. In nature lactococci are mainly found on plant material (100). Some lactococci have apparently adapted to multiply in milk and contain a plasmid-encoded milk protease and enzymes responsible for catabolism of lactose. Lactococcus lactis is used world-wide as starter culture for large-scale milk fermentations producing cheese such as cheddar and other fermented milk products. It has been estimated that approximately 107 tonnes of cheese are made annually, leading to human consumption of close to 1018 lactococci (41). In the genus Lactococcus five species are currently found: L. lactis, L. garviae, L. plantarum, L. piscium, L. raffinolactis (101, 118).
The Use of Phage as Diagnostic Systems
Authors: Rees Cath 
Published: November 2023

Abstract
The most common use of bacteriophage in detection methodology is phage typing. When developing panels of phage which will discriminate between isolates of the same species on the basis of lytic spectrum, phage are chosen specifically because of their narrow (and there-fore discriminatory) host range. Since this is the use of phage most commonly encountered, a general impression has been created that phage have a narrow host range. Hence, one of the most commonly voiced criticisms of phage-based detection methods is that the host range of phage - and therefore any test - is limited, but this is far from the truth. When phage are selected for detection of species or of whole genera, those with the widest host range are chosen. A classic example of this is the phage Felix 01, first described as a broad-host-range phage infecting Salmonella enterica by Cherry et al. (8).
Diagnosing Depersonalization Disorder
Authors: Simeon Daphne , Abugel Jeffrey 
Published: November 2023

Abstract
Like any other psychiatric condition, the diagnosis of depersonalization disorder (DPD) is made clinically, by meeting with the patient and conducting a thorough evaluation interview. Descriptions of the symptoms, as we have described throughout this book, and as spelled out in the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV), serve as the point of departure—symptoms that are not just fleeting, but recurrent or persistent. The symptoms must also not be occurring exclusively and only in the context of some other condition, be it psychiatric, medical, or related to substance use. If, for example, the depersonalization happened only when the person was deeply depressed, or during a panic attack, or a seizure, or because a person has a brain tumor, he or she would not be diagnosed as having DPD. Likewise, regular substance users (daily drinkers or marijuana users) who experience depersonalization only in that context would not be diagnosed with DPD.
The Blow of the Void: Depersonalization in Literature and Philosophy
Authors: Simeon Daphne , Abugel Jeffrey 
Published: November 2023

Abstract
The idea that reality is subjective, constructed from our own perceptions, is quite an ancient concept. “We are what we think. All that we are arises with our thoughts. With our thoughts, we make the world,” said the Buddha. Depersonalization, a serious disruption in a person’s thoughts or sensations about their individual self, understandably alters their entire world. A person may feel as if everything he or she has ever believed must be somehow reconstructed back to what it was, or made afresh, since little of what was once taken for granted remains solid or safe. People may find themselves in a Never Neverland with an altered sense of self, or a distinct sensation of having no self at all. Struggling with this mental change can lead down many paths, sometimes implying a spiritual awakening, while at other times the path may lead to anxiety, fruitless rumination, and, on occasion, works of art.
Kim Jong Il—The Terrorist Master
Authors: Becker Jasper 
Published: November 2023

Abstract
When a mysterious vessel was spotted lurking close to Japan’s shores in 2001, a naval patrol gave chase. When the intruder refused to stop, there was a brief fire fight, and the vessel sank to the bottom of the sea. Later the Japanese navy managed to raise it and put it on public display in 2002. To any casual observer it looked like an ordinary fishing boat, but up close it was possible to see that it was heavily armed with weapons that included a surface-to-air missile launcher. Closer examination revealed that a special door fitted into the hull could open to release a tiny submersible scooter big enough to carry three men for a few miles. It enabled special agents to sneak ashore undetected.
Nuclear Warlord
Authors: Becker Jasper 
Published: November 2023

Abstract
The plan to bomb North Korea’s nuclear facilities seemed simple. President William Clinton sat with his advisers in the West Wing as his Defense Secretary William J. Perry laid out satellite photographs of North Korea’s plutonium reprocessing facility. They showed a long narrow two-story fac-tory next to a small experimental reactor at Yongbyon, some 60 miles north of Pyongyang. A wave of cruise missiles and F-117 stealth fighters flying high beyond the reach of the North’s air defenses dropping laser guided bombs could easily blast it.
Kim Jong Il—The Reformer
Authors: Becker Jasper 
Published: November 2023

Abstract
The first executions in Songrim City took place at nine o’clock one morning in February 1998. A truck carrying five condemned men, all senior executives of the Hwanghae Iron and Steel Works, all blindfolded, bound, and dressed in thick padded cotton clothing, halted before the crowd of steel workers and their families who had been summoned to watch. As the guards pulled the prisoners off the truck the crowd noticed that the men were limping so badly that the guards had to half drag each of them to the execution posts erected on the municipal sports ground.
Grappling with a Rogue State
Authors: Becker Jasper 
Published: November 2023

Abstract
U.S. Secretary of State Madeleine Albright was in Pyongyang in the last months of the second Clinton Administration holding talks with Kim Jong Il when he announced he had prepared a special surprise for her. That evening they arrived at the May Day Stadium for a performance by 100,000 citizens, which Kim confided would help the Americans understand North Korea. A huge crowd gave forth a volcano of rapturous sounds as they arrived. “It began with a giant image of a hammer for workers, a brush for intellectuals, and a sickle for farmers.
Huntington’s Disease
Authors: Ogden Jenni A 
Published: November 2023

Abstract
Huntington’s disease is the focus of one of the most remarkable stories of discovery in medical history. In 1872, George Huntington, a North American general practitioner, published the first unambiguous description of this unrelenting neurodegenerative disorder in The Medical and Surgical Reporter (Huntington 1872). The title of his article was simply “On Chorea,” and his description of this type of chorea as a specific hereditary disorder became quickly and widely accepted and became known as Huntington’s disease (HD). HD is a chronic, progressive hereditary disease, usually of adult onset, and is typified by a number of motor abnormalities, most obviously the excessive, spontaneous irregular movements called chorea, but also other motor disorders such as rigidity. Accompanying these motor disorders is a range of psychiatric, behavioral and cognitive disturbances and a progressive decline to a severe dementia is almost inevitable if the patient lives long enough.
Dementia
Authors: Ogden Jenni A 
Published: November 2023

Abstract
In most Western countries, the proportion of elderly to young in the population is increasing rapidly because of the dual factors of improving health care, leading to longer life expectancy, and decreasing family size. The incidence (number of newly diagnosed cases) of dementia rises with increasing age and exceeds one new case per 100 in the 70–80 age group and two new cases per 100 in the over 80 age group. As patients with dementia tend to live for a number of years, the prevalence (total number of sufferers in a specified population at any one time) is higher than the incidence. The prevalence of dementia doubles every 5 years after the age of 60 years. In the age bracket 60–65 years, 1% have dementia, and in the age bracket 85 years and older, 35%–40% suffer dementia (Hendrie 1998). Therefore, the number of elderly people with dementia that the population must support is increasing dramatically (McLean 1987a). In 1999, the World Health Organization estimated that there were 20 million people suffering from dementia (of all types) worldwide, a figure estimated to reach 40 million by 2025, and that 66% of these dementia victims live in developing countries (Richter and Richter 2002; Walker and Salek 2002).
Interpreting the results of linear regression
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
Linear regression finds the best-fit values of the slope and intercept, and reports these values along with a standard errors and confidence intervals. The standard error values of the slope and intercept can be hard to interpret intuitively, but their main usefulness is to compute the 95% confidence intervals. If you accept the assumptions oflinear regression, there is a 95% chance that the true value of the slope lies within the 95% confidence interval of the slope. Similarly, there is a 95% chance that the true value of the intercept lies within the 95% confidence interval of the intercept.
Tips on choosing a model
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
In many cases, picking a model will be easy, as you will likely be choosing a model that is conventionally used in your field. Later in the book, we discuss in detail some of the models commonly used in experimental biology. If you aren’t sure about the model, take the time to learn. If you pick a model that isn’t right for your experimental situation, the regression results won’t be helpful.
Unequal weighting of data points
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
As outlined in the previous chapter, regression is most often done by minimizing the sum­ of-squares of the vertical distances of the data from the line or curve. Points farther from the curve contribute more to the sum-of-squares. Points close to the curve contribute little. This makes sense, when you expect experimental scatter to be the same, on average, in all parts of the curve.
Testing whether a parameter differs from a hypothetical value
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
The approaches for comparing models described in the previous chapters can also be used to perform statistical testing on individual model parameters. The key is to recast the problem as a choice between two models, one where the parameter of interest is estimated, and another where the same model is refitted to the data with the parameter of interest constrained to a specified value. This concept is illustrated with an example below. The null hypothesis is that the standard Hill slope of 1.0 is correct. To fit the model corresponding to the null hypothesis (simpler model), you constrain the slope to equal 1.0; you are thus fitting a three-parameter Hill equation (Top, Bottom, and LogEC50 being estimated). The alternative hypothesis is that the Hill slope has some other value. To fit this model, fit the variable slope sigmoidal dose-response curve equation (also called a four-parameter Hill equation). The program will find best-fit values of Top, Bottom, LogEC50 and HillSlope. For these data, the best-fit Hill slope is 0.7535.
Using a paired t test to test for a treatment effect in a series of matched experiments
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
Chapter 25 explained how to compare two curves obtained in one experiment. But if you really want to know how a treatment changes the parameters of a curve, you’ll want to repeat the experiment several times. This chapter explains how to pool the results from several experiments. The first step is to focus on what you really want to know. In most cases, you’ll care most about a best-fit parameter from curve fitting.
Analyzing radioligand binding data
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
A radioligand is a radioactively labeled drug that can associate with a receptor, transporter, enzyme, or any site of interest. Measuring the rate and extent of binding provides information on the number of binding sites, and their affinity and accessibility for various drugs. There are three kinds of experimental protocols for radioligand binding, discussed in the next three chapters.
Complex dose-response curves
Authors: Motulsky Harvey , Christopoulos Arthur 
Published: November 2023

Abstract
The standard (Hill) sigmoidal dose-response model is based on the assumption that the log(dose) vs. response curve is symmetrical around its midpoint. But some dose-response curves are not symmetrical. In a recent study, Van der Graaf and Schoemaker (J. Pharmacol. Toxicol. Meth., 41: 107-115, 1999) showed that the application of the Hill equation to asymmetric dose-response data can lead to quite erroneous estimates of drug potency (EC50). They suggested an alternative model, known as the Richards equation, which could provide a more adequate fit to asymmetric dose-response data. Here is the Richards model shown both as an equation and as computer code.
The Parkinson’s Disease Treatment Book
Authors: Ahlskog J Eric 
Published: November 2023

Abstract
Over 4 million people worldwide and 1 in every 500 people in the UK, suffer from Parkinson's Disease. Now, a leader in the fight against Parkinson’s, Dr. J. Eric Ahlskog of the Mayo Clinic, has written the definitive guide for patients and their families. Dr. Alhskog offers a crystal-clear, nuts-and-bolts approach to the treatment of PD, distilled from over twenty years of experience as a clinician and researcher. His goal is to educate the patient so that they can better team with their doctor to do battle with the disease, streamlining the decision-making process and enhancing their treatment. To do this, Dr. Ahlskog offers a gold mine of information: How do I know if I have PD? What kinds of tests can I take? What medications slow the progress of the disease? What if medications don’t help my tremor? What kinds of movement problems may develop later? How can I cope with insomnia and daytime sleepiness, dizziness and depression, memory problems, paranoia, and delusions? Indeed, the book covers virtually every topic related to Parkinson’s, from sexual impotence and skin rashes, to the role of nutrition, exercise, and physical therapy. In addition, Dr. Ahlskog discusses brain surgery (though he urges that patients only consider this as a last resort) and such experimental therapies as stem cell transplantation and gene therapy. There are also lists of support and advocacy groups and Internet sites that focus on Parkinson’s. The ultimate guide to symptoms and treatment, this superb book is the first place patients should turn for reliable, easy-to-grasp information on Parkinson’s disease.
Background and Rationale
Authors: Ahlskog J Eric 
Published: November 2023

Abstract
Parkinson’s disease (PD) is a treatable condition. Medical treatment increases longevity and allows most people with PD to remain active and productive for many years. We don’t have a cure (yet), but some of the responses to available drugs are striking and occasionally border on the miraculous. PD is one of the most treatable of all neurological conditions. The medical treatment of PD, unfortunately, is not always simple. There are multiple medications and they can be used in a variety of ways. The choice of the drug, the dose, and the timing often are crucial; therapy must be individualized to meet each person’s unique requirements. Also, the distinction between PD symptoms and medication side effects frequently causes confusion, with potential for ineffective or inappropriate treatment. Sometimes, treatable symptoms are not even recognized as part of PD. The difference between optimal versus ineffective therapy may be the difference between a nursing home and independent living. The goal of this book is to help each and every person with PD achieve the best treatment.