Miracle-dz/UniFAR-FTUs huggingface dataset:
Congruence, non-homology, and the phylogeny of basal turtles

Joyce, W.G. and Sterli J. 2010. Congruence, non-homology, and the phylogeny of basal turtles. –Acta Zoologica (Stockholm) Modern cladistic analysis is characterized by the assembly of increasingly larger data sets coupled with the use of congruence as the final test of homology. Some critics of this development have recently called for a return to more detailed primary homology analysis while questioning the utility of congruence. This discussion appears to be central to the debate regarding the phylogenetic relationships of basal turtles, as the large data sets developed by us have been criticized recently for utilizing poorly constructed characters and including too many homoplasy-prone characters. Our analysis of this critique reveals that (1) new information regarding poorly understood taxa has a greater impact on the outcome of turtle phylogenies than the characters under dispute; (2) most current turtle phylogenies differ in taxon sampling, not character sampling, and so it appears illogical to condemn a particular analysis for its character sampling; (3) even evolutionary taxonomists should agree that key characters utilized to resolve basal turtle relationships cannot be thought to be ‘infallible’; (4) whereas various criteria provide positive evidence for homology, only congruence provides positive evidence for non-homology; and (5) a stalemate between conflicting camps within a congruence frame work is preferable to the ad hoc dismissal of data sets, because authoritative statements are untestable.
Penetrative Convection within the Anelastic Approximation

We present a method for studying penetrative convection within the anelastic approximation. This method is then applied to two-dimensional numerical simulations of a convective region bounded below by a stable (radiative) region. Descending plumes penetrate into the stable layer, exciting gravity waves with a spectrum of frequencies limited by the "Brunt-Väisäla" frequency. The depth of penetration depends sensitively on the "stiffness" of the boundary between the unstable and stable layers (quantified by S) and on the vigor of convection. We find scaling relations between the penetrative depth (Δ) and S, spanning 3 orders of magnitude in S. The reference state in these models is allowed to evolve; the convective region tends toward adiabaticity, and for low values of S, the stable region can be altered considerably (an extended superadiabatic region is developed). For high values of S, the stable region is left essentially unchanged.
Peripheral and central signals in the control of eating in normal, obese and binge-eating human subjects

The worldwide increase in the incidence of obesity is a consequence of a positive energy balance, with energy intake exceeding expenditure. The signalling systems that underlie appetite control are complex, and the present review highlights our current understanding of key components of these systems. The pattern of eating in obesity ranges from over-eating associated with binge-eating disorder to the absence of binge-eating. The present review also examines evidence of defects in signalling that differentiate these sub-types. The signalling network underlying hunger, satiety and metabolic status includes the hormonal signals leptin and insulin from energy stores, and cholecystokinin, glucagon-like peptide-1, ghrelin and peptide YY3-36 from the gastrointestinal tract, as well as neuronal influences via the vagus nerve from the digestive tract. This information is routed to specific nuclei of the hypothalamus and brain stem, such as the arcuate nucleus and the solitary tract nucleus respectively, which in turn activate distinct neuronal networks. Of the numerous neuropeptides in the brain, neuropeptide Y, agouti gene-related peptide and orexin stimulate appetite, while melanocortins and α-melanocortin-stimulating hormone are involved in satiety. Of the many gastrointestinal peptides, ghrelin is the only appetite-stimulating hormone, whereas cholecystokinin, glucagon-like peptide-1 and peptide YY3-36 promote satiety. Adipose tissue provides signals about energy storage levels to the brain through leptin, adiponectin and resistin. Binge-eating has been related to a dysfunction in the ghrelin signalling system. Moreover, changes in gastric capacity are observed, and as gastric capacity is increased, so satiety signals arising from gastric and post-gastric cues are reduced. Understanding the host of neuropeptides and peptide hormones through which hunger and satiety operate should lead to novel therapeutic approaches for obesity; potential therapeutic strategies are highlighted.
The Fate of the "Classic" Neanderthals: A Consideration of Hominid Catastrophism [and Comments and Reply]

The Current View That the "Classic" Neanderthals Were an aberrant, specialized, or otherwise peculiar side branch which eventually became extinct without descendants has its origins in anti-evolutionary interpretations placed upon the available hominid fossils by the french palaeontologist marcellin boule in the early part of the current century. The theoretical bases of boule's thinking stem from the early nineteenth century position of George Cuvier who attempted to explain sequence in the fossil record by a series of catastrophes with their attendant extinctions and subsequent invasions. Without specifically labelling it as such, Boule applied the concept of catastrophism to explain the sequence of forms in the hominid fossil record, assuming that none of the fossil men discovered which differed from modern man could be regarded as ancestral to modern man. The proof of this assumption lay in the claim that modern forms of man already existed as exemplified by the Grimaldi skeletons. Although these skeletons were shown to be more recent than the Neanderthals, the conviction remained that ancient moderns would be found, and, guided by the ideals of what is here labelled hominid catastrophism, a disproportionate amount of the efforts of subsequent prehistorians has been devoted to their discovery. In fact, far more time has been expended in the attempt to deny the evidence for human evolution than in trying to show how man could have evolved. attempts to interpret the available hominid fossils from a frankly evolutionary point of view have been offered by Schwalbe, Weinert, Weidenreich, and Hrdlicka, but because of the eclipse of German anthropology as a result of the First World War and subsequent political history, both Schwalbe's and Weinert's views have been ignored. Hrdlicka and Weidenreich were museum men and failed to have the impact on anthropological thinking which was enjoyed by the views of Boule via Keith, Hooton, Vallois, and their numerous students. As a result, the Neanderthals are denied any role in the ancestry of modern man despite the fact that all of the candidates for ancient moderns are open to serious doubts-either of date or morphology or both. Recognizing the Australopithecines as the earliest ancestors of modern man, this paper suggests that the initial three stage scheme of Gustav Schwalbe be expanded to four stages with the Australopithecines as the first stage, the Pithecanthropines as the second, the Neanderthals as the third, and finally modern man as the result. Changes in brain size are related to the supposed selective advantage conferred by cerebral increase, while progressive reduction of the dentition and hence the entire facial skeleton is related to the suspension of the advantage in possessing a large face which occurred as a result of increasingly effective cultural adaptation-particularly refinements in cutting tools in the later part of human cultural and physical evolution.
Transactional Memory Repair

Transactional memory (TM) [9, 8] is an alternative to fine-grained and coarse-grained locking that provides users with an abstraction called a transaction. Transactions are atomic pieces of code that appear as if they are executed at some point in time. They can be aborted or committed. If a transaction is committed, then all changes made by operations within the transaction are made visible to other transactions, otherwise all the changes are rolled back. A transactional memory implementation can be used by many applications. Correctness of applications using a TM implementation depends on the correctness of the implementation [7]. Therefore, it is important to make sure that the implementation itself is correct, i.e. that it satisfies safety and liveness properties. A safety property property states that some ’bad’ events will never happen, while a liveness property states that some ’good’ events will eventually happen [1]. In the TM context a liveness property states when some processes (threads) executing transactions eventually commit their transactions, while a safety property states when some transactional operations should not occur and the transaction should be aborted. It is possible to verify if a TM implementation satisfies some safety property [6, 3, 2, 4]. If a TM implementation does not satisfy some desirable safety property, then how to change the implementation so that it satisfies the safety property? This problem is similar to the problem of a system repair in supervisory control [10]. Supervisory control deals with the problem by finding an external entity called a supervisor which interacts with the system to be repaired and prevents the system from executing some actions so that the resulting system satisfies the desirable safety property. However, such approach, if applied directly to a TM implementation, prevents the implementation from ensuring a liveness property because responses of some operations are blocked by the supervisor, i.e. some operations never return. Since blocking operations reduces liveness and aborting transactions
Medicinal Plants Qua Glucagon-Like Peptide-1 Secretagogue via Intestinal Nutrient Sensors

Glucagon-like peptide-1 (GLP-1) participates in glucose homeostasis and feeding behavior. Because GLP-1 is rapidly inactivated by the enzymatic cleavage of dipeptidyl peptidase-4 (DPP4) long-acting GLP-1 analogues, for example, exenatide and DPP4 inhibitors, for example, liraglutide, have been developed as therapeutics for type 2 diabetes mellitus (T2DM). However, the inefficient clinical performance and the incidence of side effects reported on the existing therapeutics for T2DM have led to the development of a novel therapeutic strategy to stimulate endogenous GLP-1 secretion from enteroendocrine L cells. Since the GLP-1 secretion of enteroendocrine L cells depends on the luminal nutrient constituents, the intestinal nutrient sensors involved in GLP-1 secretion have been investigated. In particular, nutrient sensors for tastants, cannabinoids, and bile acids are able to recognize the nonnutritional chemical compounds, which are abundant in medicinal plants. These GLP-1 secretagogues derived from medicinal plants are easy to find in our surroundings, and their effectiveness has been demonstrated through traditional remedies. The finding of GLP-1 secretagogues is directly linked to understanding of the role of intestinal nutrient sensors and their recognizable nutrients. Concurrently, this study demonstrates the possibility of developing novel therapeutics for metabolic disorders such as T2DM and obesity using nutrients that are readily accessible in our surroundings.
Atomic Basic Blocks - Eine Abstraktion für die gezielte Manipulation der Echtzeitsystemarchitektur

The internal composition of a real-time system is significantly affected by the structural elements of the underlying real-time systems architecture. These elements control how tasks are attached to external events and how cooperating tasks interact with each other. Research and industry have brought up two fundamentally different manifestations of such realtime systems architectures: On the hand, there are event-triggered systems and on the other hand, there are time-triggered systems. Event-triggered systems perform tasks directly in response to external events. As a consequence, it depends on the occurrence of these events at which time certain computations are carried out. Time-triggered systems, in contrast, use a static, precomputed schedule table that is executed cyclically. Thus, at any given time, the task that is currently executed is known. It is easy to figure out that the event-triggered paradigm can deal much better with events whose precise temporal specification is not known beforehand than its time-triggered counterpart. Such systems, on the other hand, are to be preferred if cyclic tasks are predominant. In that case, time-triggered systems offer a fully predictable behaviour. Thus, application scenarios that have different temporal characteristics are not supported equally well by these paradigms. Hence, it is logical to go for that paradigm that suits the current application scenario best. Provided a real-time system is built from scratch, this is not a problem, as one can easily choose the ideal real-time paradigm. This is different if some parts of this system already exist; either because some components of other systems should be reused, or because the requirements of the real-time system currently being developed have changed. In that case, changing the real-time paradigm is a challenging undertaking, since the real-time systems architecture heavily influences the internal structure of a real-time system. Thus, you can find its structural elements spread all over the application. This normally demands for a manual and labour-intensive porting in most cases. This thesis presents a tool to purposefully manipulate the real-time systems architecture and to replace that manual porting process by an automated transformation. This tool is called the Real-Time Systems Compiler (RTSC). The RTSC uses Atomic Basic Blocks (ABBs) to abstract from the real-time systems architecture’s structural elements and notes down the internal structure of a real-time system by a global dependency graph made up by ABBs. Finally, it maps that dependency graph to the desired real-time systems architecture. Furthermore, this transformation takes into account the temporal requirements of the real-time system taken down in a system model connecting them to the internal structure of the real-time system. Therefore, the core contributions of this thesis are the abstraction Atomic Basic Block, the system model and the Real-Time Systems Compiler enabling the directed and automated manipulation of the real-time systems architecture as sketched above.
Bayesian inversion with α-stable priors

We propose using Lévy α-stable distributions to construct priors for Bayesian inverse problems. The construction is based on Markov fields with stable-distributed increments. Special cases include the Cauchy and Gaussian distributions, with stability indices α = 1, and α = 2, respectively. Our target is to show that these priors provide a rich class of priors for modeling rough features. The main technical issue is that the α-stable probability density functions lack closed-form expressions, and this limits their applicability. For practical purposes, we need to approximate probability density functions through numerical integration or series expansions. For Bayesian inversion, the currently available approximation methods are either too time-consuming or do not function within the range of stability and radius arguments. To address the issue, we propose a new hybrid approximation method for symmetric univariate and bivariate α-stable distributions that is both fast to evaluate and accurate enough from a practical viewpoint. In the numerical implementation of α-stable random field priors, we use the constructed approximation method. We show how the constructed priors can be used to solve specific Bayesian inverse problems, such as the deconvolution problem and the inversion of a function governed by an elliptic partial differential equation. We also demonstrate hierarchical α-stable priors in the one-dimensional deconvolution problem. For all numerical examples, we use maximum a posteriori estimation. To that end, we exploit the limited-memory BFGS and its bounded variant for the estimator.
Engraftment of Pancreatic Islets in Alternative Transplantation Sites and the Feasibility of in vivo Monitoring of Native and Transplanted Beta-Cell Mass

Espes, D. 2016. Engraftment of Pancreatic Islets in Alternative Transplantation Sites and the Feasibility of in vivo Monitoring of Native and Transplanted Beta-Cell Mass. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1211. 88 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9551-0. Islet transplantation is a possible curative treatment for type 1 diabetes (T1D). Currently the liver dominates as implantation site, despite the many challenges encountered at this site. Acute hypoxia in islets transplanted to muscle and omentum, two possible alternative sites, was prevailing. However, it was rapidly reversed at both implantation sites, in contrast to when islets were transplanted intraportally. At the intramuscular site hypoxia was further relieved by co-transplantation of an oxygen carrier, polymerized hemoglobin, which also improved the functional outcome. The complement system was activated after islet transplantation to muscle, but did not hamper graft function. Both mouse and human islets transplanted to omentum become well re-vascularized and have a functional blood flow and oxygenation comparable with that of endogenous islets. Animals transplanted with islets to the omentum had a superior graft function compared with animals receiving intraportal islet grafts. Alloxan-diabetic animals were cured with a low number of islets both when the islets were implanted in the omentum and muscle. The islet grafts responded adequately to both glucose and insulin and displayed a favorable mRNA gene expression profile. A challenge in diabetes research and in islet transplantation is that there are no established techniques for quantifying beta-cell mass in vivo. By using radiolabeled Exendin-4, a GLP-1 receptor agonist, beta-cell mass after transplantation to muscle of mice was quantified. The results may well be translated to the clinical setting. By comparing the pancreatic accumulation of [C]5-hydroxy tryptophan ([C]5-HTP) as detected by positron emission tomography (PET) in T1D patients with that of healthy controls, a 66% decrease was observed. This may in fact represent the loss of beta-cells, taking into account that other cells within the islets of Langerhans are largely unaffected in T1D. In conclusion, the data presented support the use of alternative implantation sites for islet transplantation. In addition to improving the functional outcome this may enable more transplantations since the number of transplanted islets may be reduced. The techniques investigated for quantifying transplanted and endogenous beta-cell mass may greatly improve our knowledge of the pathophysiology of T1D and become a valuable tool for evaluation of beta-cell mass.
Farmland features in the European Union : a description and pilot inventory of their distribution

National and regional datasets on landscape features can be used to analyse the stock and change of farmland features. However, these landscape datasets are not categorised according to farmland features, farmed features or unfarmed features. The available national level datasets are used to obtain information on the extent and distribution of farmland features within the major Member States of the European Union. Data on farmland features is extracted from nationally-focused projects and datasets. These projects have been carried out for governments to analyse stock and change in the country for policy purposes, and have been carried out in Great Britain, Sweden and Spain. Extra datasets exist that also plot stock and change in a country, and have been carried out in the Netherlands and in Austria, but these studies do not have a national policy objective. The lack of universal definitions of landscape features means that comparisons between national datasets in not always reliable. There is particularly sparse data on the lengths of linear features and point features, as these surveys established set rules on what should be recorded, and what should not. This has caused differences in data available from different projects. In addition, the presence of solitary trees and small patches of natural grasslands are not collected in all of these surveys. Alterra developed a typology suitable for use with the available data. This typology proposes eight main classes of farmed and unfarmed features. Among these classes, two (class 5 and 6) fulfil the definition of a ‘farmland feature on EU farmland’, as defined for this study, as follows: - Linear or point features on, or adjacent to, farmland, that are managed directly e.g. hedges on farmland or terrace walls in managed vineyards. - Linear or point features on, or adjacent to, farmland, that are indirectly influenced by agriculture but are not managed actively e.g. field corners and small woodlands surrounded by agricultural land. During the analysis of the datasets we have harmonised and refined this typology as far as possible given the different structures, designs and underlying methodologies of the various datasets. However, examining the entire landscape matrix is essential to obtain a clear perception of the relative proportion of farmland features across the entire land surface. As national datasets do not discern between farmland and forest, it is important in this project to make such a distinction. This distinction sets the baseline between (currently) farmed land and land out of farming, such as land abandoned in the past and now under forest.
Changes in vaginal microbiota following antimicrobial and probiotic therapy

Background The composition of the vaginal microbiota is known to be important for health. When infections occur, antimicrobial therapy is often poorly efficacious. Objective and design We used 16S rRNA gene sequencing to characterize changes in the bacterial microbiota following oral antimicrobial and probiotic interventions. Results While the bacterial vaginal profiles of women with vulvovaginal candidiasis were dominated by lactobacilli as in healthy women, and unchanged by therapy, Gardnerella vaginalis, Prevotella, Atopobium, Sneathia, and Megasphaera dominated the vagina of women with bacterial vaginosis (BV), and treatment with tinidazole plus Lactobacillus reuteri RC-14+L. rhamnosus GR-1 resulted in an increased relative abundance of indigenous L. iners or L. crispatus. Conclusions The ability to restore homeostasis provides a rationale for conjoint use of probiotics with antibiotic treatment of BV.
Obsolete Fill Materials Found on Ceramics

AbstractFills on ceramics have a long history, associated either with covering up an adhesive line or replacing a large loss. Numerous materials have been employed in loss compensation, from thickened adhesives, pastes, and putties to substituted fragments from other vessels, manufactured ceramic replacements, and cast resins and waxes. Many of the early materials and methods of filling losses that have given way to more efficient, predictable, and reversible techniques can now be classified as “obsolete. ” Even so, the ceramics conservator will encounter these materials in re-treatment for centuries to come.