Miracle-dz/UniFAR-FTUs huggingface dataset:
Using a nursing theory or a model in nursing PhD dissertations: a qualitative study from Turkey.

PURPOSE The aim of this study was to reveal experiences of nursing students and their advisors using theories and models in their PhD dissertations. METHODS The study adopted a descriptive qualitative approach. This study was performed with 10 PhD candidates and their five advisors from nursing faculty. RESULTS The results of the study were categorized into four. These are reasons for using a theory/model in a PhD dissertation, reasons for preferring a given model, causes of difficulties in using models in PhD dissertations, and facilitating factors of using theories and models in PhD of dissertations. CONCLUSIONS It was also reported to contribute to the methodology of research and professional development of the students and advisors.
CoreScope: Graph Mining Using k-Core Analysis — Patterns, Anomalies and Algorithms

How do the k-core structures of real-world graphs look like? What are the common patterns and the anomalies? How can we use them for algorithm design and applications? A k-core is the maximal subgraph where all vertices have degree at least k. This concept has been applied to such diverse areas as hierarchical structure analysis, graph visualization, and graph clustering. Here, we explore pervasive patterns that are related to k-cores and emerging in graphs from several diverse domains. Our discoveries are as follows: (1) Mirror Pattern: coreness of vertices (i.e., maximum k such that each vertex belongs to the k-core) is strongly correlated to their degree. (2) Core-Triangle Pattern: degeneracy of a graph (i.e., maximum k such that the k-core exists in the graph) obeys a 3-to-1 power law with respect to the count of triangles. (3) Structured Core Pattern: degeneracy-cores are not cliques but have non-trivial structures such as core-periphery and communities. Our algorithmic contributions show the usefulness of these patterns. (1) Core-A, which measures the deviation from Mirror Pattern, successfully finds anomalies in real-world graphs complementing densest-subgraph based anomaly detection methods. (2) Core-D, a single-pass streaming algorithm based on Core-Triangle Pattern, accurately estimates the degeneracy of billion-scale graphs up to 7× faster than a recent multipass algorithm. (3) Core-S, inspired by Structured Core Pattern, identifies influential spreaders up to 17× faster than top competitors with comparable accuracy.
Fundamental Studies on Biomachining of Carbon Steel by Iron Oxidizing Bacteria(Materials, Metallurgy & Weldability, INTERNATIONAL SYMPOSIUM OF JWRI 30TH ANNIVERSARY)

Bacteria living in natural environments usually attack metals leaving unacceptable corrosion and causing critical deterioration. This negative phenomena is studied in this paper in a positive sense by means of control of these bacteria for the purpose of biomachining of metals. The main objective of this research is the achievement of a low cost machining process at normal temperature with less energy involvement and more involvement of bacteria in biomachining without straining them. The main focus in this paper is on the effect of Thiobacillus ferrooxidans, iron oxidizing bacteria and their ability to oxidize iron. It has been found that the extent of corrosion of carbon steel in the presence of Thiobacillus ferrooxidans was remarkably large. A tendency towards preferential corrosion offerrite was also observed. The results of our experiments show that biomachining using Thiobacillus ferrooxidans is possible by controlling the structure of steel.
Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins

Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information.
On the Effect of Coarse Aggregate Fraction and Shape on the Rheological Properties of Self-Compacting Concrete

Rheological measurements have been undertaken to illustrate the applicability on fresh self-compacting concrete of a model for the relative viscosity and yield stress of suspensions. The model is based on linear viscoelasticity and classical theory for composite materials and it takes into account the amount, shape (aspect ratio of ellipsoids), and maximum packing density of the particles (here aggregates), as well as the rheological properties of the matrix (here mortar). Self-compacting concretes made from different types of coarse aggregates: spheres (glass beads), sea dredged, crushed, and a mix of sea dredged and crushed aggregates, have been tested in a coaxial cylinder concrete rheometer (BML). The investigations indicate that the aspect ratio, angularity, and surface texture of aggregates affect the viscosity and yield stress. The magnitude of these effects depends on the property in question, viscosity and yield stress.
Influence of Smart Cut™ technological steps on thickness uniformity of SOI wafers : multi-scale approach

Les substrats de silicium sur isolant (SOI) sont tres prometteurs pour la technologie CMOS. Un substrat SOI est notamment forme d'une couche extremement fine de silicium cristallin. Il a ete demontre que les caracteristiques des transistors dependent fortement de l'epaisseur de cette couche. Il est indispensable que les variations d'epaisseur soient parfaitement controlees et caracterisees sur une large gamme spatiale ce qui represente un grand defi. Des methodes d'analyse de donnees, obtenues par differentes techniques experimentales ont ete developpees, ceci permet de caracteriser la rugosite et l'epaisseur de couches fines sur la bande spectrale d'interet. L'analyse approfondie de l'impact des principales etapes technologiques de la fabrication de substrats FD-SOI, sur l'uniformite d'epaisseur de la couche de silicium a permis de determiner l'empreinte spectrale de ces etapes. En outre, nous avons etudie les phenomenes physiques a l'origine du lissage thermique. Un model statistique base sur la diffusion surfacique des ad-atomes d'un cristal a ete developpe. Ce model permet de predire l'evolution de la topographie des surfaces de silicium traitees par un recuit thermique.
SNAP-23 regulates phagosome formation and maturation in macrophages

Using macrophages overexpressing or reducing SNAP-23, this study shows that SNAP-23 is implicated in phagosome formation and maturation, presumably by mediating SNARE-based membrane traffic. Indeed, a conformational change in SNAP-23 structure based on FRET signal is observed on the phagosome membrane of cells overexpressing the lysosomal SNARE VAMP7.
Neuroprotection of the developing brain by systemic administration of vasoactive intestinal peptide derivatives.

Periventricular leukomalacia (PVL), a necrotic and often cystic lesion of the cerebral white matter occurring in very premature babies, is the leading cause of cerebral palsy in this population. Increased glutamate release and the excitotoxic cascade thus triggered may be critical factors in the development of PVL. The glutamatergic analog ibotenate injected intracerebrally into newborn mice produces white matter cysts that mimic human PVL. Concomitant injection of vasoactive intestinal peptide (VIP), a trophic factor, protects the white matter against excitotoxic lesions. The goal of the present study was to assess the protective properties of systemically injected VIP analogs against ibotenate-induced excitotoxic white matter lesions in newborn mice. VIP analogs were selected on the basis of their low susceptibility to endopeptidases and their potential ability to cross biological membranes. RO-25-1553, a long-lasting cyclic VIP analog, and stearyl-norleucine-VIP, a fatty derivative of VIP, reduced ibotenate-induced white matter cysts by up to 87% and 84%, respectively, when injected i.p. immediately after ibotenate. By comparison, i.p. coadministration of VIP and ibotenate was not protective against the excitotoxic insult. Furthermore, RO-25-1553 and stearyl-norleucine-VIP still induced significant neuroprotection of the developing white matter when injected systemically 8 and 12 h, respectively, after ibotenate, establishing these peptides as therapeutic agents in this murine model. VIP analogs may have therapeutic potential in human premature babies at high risk for PVL.
Weight-averaged consistency targets improve semi-supervised deep learning results

The recently proposed temporal ensembling has achieved state-of-the-art results in several semi-supervised learning benchmarks. It maintains an exponential moving average of label predictions on each training example, and penalizes predictions that are inconsistent with this target. However, because the targets change only once per epoch, temporal ensembling becomes unwieldy when using large datasets. To overcome this problem, we propose a method that averages model weights instead of label predictions. As an additional benefit, the method improves test accuracy and enables training with fewer labels than earlier methods. We report state-of-the-art results on semi-supervised SVHN, reducing the error rate from 5.12% to 4.41% with 500 labels, and achieving 5.39% error rate with 250 labels. By using extra unlabeled data, we reduce the error rate to 2.76% on 500-label SVHN.
Review article: steatosis, the metabolic syndrome and cancer

The incidence of hepatocellular carcinoma is increasing, but the temporal changes of risk factors remain unclear. A significant proportion of hepatocellular carcinoma (7–30%) develops in cryptogenic cirrhosis, and may represent the most worrisome complication of non‐alcoholic steatohepatitis. Non‐alcoholic steatohepatitis is tightly related to insulin resistance and several features of the metabolic syndrome, i.e obesity, type 2 diabetes and dyslipidaemia. Nearly two‐thirds of adults in the United States and an increasing percentage of the population worldwide are overweight or obese. Diabetes prevalence is increasing as well. The rising prevalence of risk factors associated with non‐alcoholic steatohepatitis can partially account for the increasing incidence of cryptogenic cirrhosis and subsequent hepatocellular carcinoma. Moreover, recent evidence demonstrates that both obesity and diabetes are per se associated with an increased cancer risk. Large prospective studies show a significant association with obesity for several cancers, including cancers of the colon, female breast, endometrium, kidney, oesophagus and liver (hepatocellular carcinoma). Type 2 diabetes is also related with increased risks of colon, endometrial, kidney, pancreatic cancer and hepatocellular carcinoma. In western countries, the insulin resistance syndrome is emerging as a risk factor for a wide variety of cancers, including hepatocellular carcinoma.
Mechanisms of High Temperature Resistance of Synechocystis sp. PCC 6803: An Impact of Histidine Kinase 34

Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying responses and acclimation to different abiotic stresses. Changes in transcriptome, proteome, lipidome, and photosynthesis in response to short term heat stress are well studied in this organism, and histidine kinase 34 (Hik34) is shown to play an important role in mediating such response. Corresponding data on long term responses, however, are fragmentary and vary depending on parameters of experiments and methods of data collection, and thus are hard to compare. In order to elucidate how the early stress responses help cells to sustain long-term heat stress, as well as the role of Hik34 in prolonged acclimation, we examined the resistance to long-term heat stress of wild-type and ΔHik34 mutant of Synechocystis. In this work, we were able to precisely control the long term experimental conditions by cultivating Synechocystis in automated photobioreactors, measuring selected physiological parameters within a time range of minutes. In addition, morphological and ultrastructural changes in cells were analyzed and western blotting of individual proteins was used to study the heat stress-affected protein expression. We have shown that the majority of wild type cell population was able to recover after 24 h of cultivation at 44 °C. In contrast, while ΔHik34 mutant cells were resistant to heat stress within its first hours, they could not recover after 24 h long high temperature treatment. We demonstrated that the early induction of HspA expression and maintenance of high amount of other HSPs throughout the heat incubation is critical for successful adaptation to long-term stress. In addition, it appears that histidine kinase Hik34 is an essential component for the long term high temperature resistance.
Stored-Trace Reactivation in Rat Prefrontal Cortex Is Correlated with Down-to-Up State Fluctuation Density

Spontaneous reactivation of previously stored patterns of neural activity occurs in hippocampus and neocortex during non-rapid eye movement (NREM) sleep. Notable features of the neocortical local field potential during NREM sleep are high-amplitude, low-frequency thalamocortical oscillations including K-complexes, low-voltage spindles, and high-voltage spindles. Using combined neuronal ensemble and local field potential recordings, we show that prefrontal stored-trace reactivation is correlated with the density of down-to-up state transitions of the population of simultaneously recorded cells, as well as K-complexes and low-voltage spindles in the local field potential. This result strengthens the connection between reactivation and learning, as these same NREM sleep features have been correlated with memory. Although memory trace reactivation is correlated with low-voltage spindles, it is not correlated with high-voltage spindles, indicating that despite their similar frequency characteristics, these two oscillations serve different functions.
Harvester Ant Colony Variation in Foraging Activity and Response to Humidity

Collective behavior is produced by interactions among individuals. Differences among groups in individual response to interactions can lead to ecologically important variation among groups in collective behavior. Here we examine variation among colonies in the foraging behavior of the harvester ant, Pogonomyrmex barbatus. Previous work shows how colonies regulate foraging in response to food availability and desiccation costs: the rate at which outgoing foragers leave the nest depends on the rate at which foragers return with food. To examine how colonies vary in response to humidity and in foraging rate, we performed field experiments that manipulated forager return rate in 94 trials with 17 colonies over 3 years. We found that the effect of returning foragers on the rate of outgoing foragers increases with humidity. There are consistent differences among colonies in foraging activity that persist from year to year.
Dynamic constitutive response of tantalum at high strain rates

Pressure-shear plate impact experiments were conducted on annealed and rolled tantalum foils to determine the dynamic constitutive response of the material at high strain rates between 105s−1 and 106s−1 and pressures between 4 and 8 GPa. The experiments were performed to determine the strain rate sensitivity of the flow stress of the metal. The results suggest that both texture and strain rate play an important role in determining the flow stress of tantalum.
A Language Modeling Approach to Information Retrieval

In today's world, there is no shortage of information. However, for a specific information need, only a small subset of all of the available information will be useful. The field of information retrieval (IR) is the study of methods to provide users with that small subset of information relevant to their needs and to do so in a timely fashion. Information sources can take many forms, but this thesis will focus on text based information systems and investigate problems germane to the retrieval of written natural language documents. Central to these problems is the notion of "topic. " In other words, what are documents about? However, topics depend on the semantics of documents and retrieval systems are not endowed with knowledge of the semantics of natural language. The approach taken in this thesis will be to make use of probabilistic language models to investigate text based information retrieval and related problems. One such problem is the prediction of topic shifts in text, the topic segmentation problem. It will be shown that probabilistic methods can be used to predict topic changes in the context of the task of new event detection. Two complementary sets of features are studied individually and then combined into a single language model. The language modeling approach allows this problem to be approached in a principled way without complex semantic modeling. Next, the problem of document retrieval in response to a user query will be investigated. Models of document indexing and document retrieval have been extensively studied over the past three decades. The integration of these two classes of models has been the goal of several researchers but it is a very difficult problem. Much of the reason for this is that the indexing component requires inferences as to the semantics of documents. Instead, an approach to retrieval based on probabilistic language modeling will be presented. Models are estimated for each document individually. The approach to modeling is non-parametric and integrates the entire retrieval process into a single model. One advantage of this approach is that collection statistics, which are used heuristically for the assignment of concept probabilities in other probabilistic models, are used directly in the estimation of language model probabilities in this approach. The language modeling approach has been implemented and tested empirically and performs very well on standard test collections and query sets. In order to improve retrieval effectiveness, IR systems use additional techniques such as relevance feedback, unsupervised query expansion and structured queries. These and other techniques are discussed in terms of the language modeling approach and empirical results are given for several of the techniques developed. These results provide further proof of concept for the use of language models for retrieval tasks.
Nonketotic hyperglycinemia A genetic study of 13 Finnish families

In Finland, 19 children, born 1964–1977, from 13 families, have been diagnosed as suffering from nonketotic hyperglycinemia (NKH). This gives an incidence for NKH in the Finnish population of 1:55,000 newborns. The majority of these children were born in the northern part of the country, where the incidence is 1:12,000. The geographical distribution of the birth‐places of the grandparents also seems to point towards an enrichment of the gene in northern Finland. An autosomal recessive mode of inheritance for this disease seems probable, since the corrected proportion of affected siblings (Apert's a priori method) is 0.288. Abnormally high plasma glycine concentration and elevated glycine urinary excretion in the parents of the NKH‐children suggest the existence of a minor metabolic defect in heterozygotes of this disease. Some of the healthy siblings of the NKH‐patients also show similary elevated levels. However, a definite diagnosis of the NKH‐heterozygote state cannot easily be made on the basis of these laboratory findings, as the levels in some individuals are very close to, or even overlap corresponding values in a normal material.
Repression of the hindbrain developmental program by Cdx factors is required for the specification of the vertebrate spinal cord

The spinal cord is a unique vertebrate feature that originates, together with the hindbrain, from the caudal neural plate. Whereas the hindbrain subdivides into rhombomeres, the spinal cord remains unsegmented. We have identified Cdx transcription factors as key determinants of the spinal cord region in zebrafish. Loss of Cdx1a and Cdx4 functions causes posterior expansion of the hindbrain at the expense of the unsegmented spinal cord. By contrast, cdx4 overexpression in the hindbrain impairs rhombomere segmentation and patterning and induces the expression of spinal cord-specific genes. Using cell transplantation, we demonstrate that Cdx factors function directly within the neural ectoderm to specify spinal cord. Overexpression of 5′ Hox genes fails to rescue hindbrain and spinal cord defects associated with cdx1a/cdx4 loss-of-function, suggesting a Hox-independent mechanism of spinal cord specification. In the absence of Cdx function, the caudal neural plate retains hindbrain characteristics and remains responsive to surrounding signals, particularly retinoic acid, in a manner similar to the native hindbrain. We propose that by preventing the posterior-most region of the neural plate from following a hindbrain developmental program, Cdx factors help determine the size of the prospective hindbrain and spinal cord territories.
Distributed Call Admission Control for a Heterogeneous PCS Network

Personal communication service (PCS) networks offer mobile users multimedia applications with different quality-of-service (QoS) and bandwidth requirements. This paper proposes a distributed call admission algorithm to provide QoS guarantees for multimedia traffic carried in a heterogeneous PCS network, where the parameters (e.g., number of channels, new and hand-off call arrival rates) of cells can be varied. The algorithm is based on the moveable boundary scheme that dynamically adjusts the number of channels for different types of traffic. With the moveable boundary scheme, the bandwidth can be utilized efficiently while satisfying the QoS requirements for different types of traffic. In addition, by taking the effect of hand-off traffic into account, we develop an analytical model for the network using the proposed algorithm. Using our model, the impact of hot-spot traffic caused by hand-offs can be effectively analyzed. The analytical model is validated by simulation.