Miracle-dz/UniFAR-FTUs huggingface dataset:
Systems development philosophy

A philosophy book for systems developers is outlined, and it is argued that philosophy can play an important role in the education of professional practitioners. All systems developers acquire a philosophy in their education and practice. This philosophy is expressed in their views on the problems of their profession. But to what extent is this philosophy confornted with their personal practice? To what extent is it open to discussion and subject to change? Only some systems developers actively reflect on their practice. They do not accept problems at face value and they challenge traditions, concepts and methods. They philosophize as part of their practice and in doing so they develop a personal view on their profession.Our intention is to use philosophy to support inexperienced practitioners and students in becoming more professional. We do not want to make philosophers out of systems developers, but rather to encourage them to philosophize. Practitioners and students are invited to engage in a rational conversation about matters which they in their daily activities take for granted. The goal is to take a few steps in the direction of a richer, deeper, clearer, different, more truthful understanding of the activity of systems development.The paper discusses various ways to design a philosophy book for systems developers and concludes by proposing a book consisting of four parts, each dealing with a vital aspect of systems development: systems, development, quality, and perspectives.
Bioactive glass scaffolds for bone regeneration and their hierarchical characterisation

Abstract Scaffolds are needed that can act as temporary templates for bone regeneration and actively stimulate vascularized bone growth so that bone grafting is no longer necessary. To achieve this, the scaffold must have a suitable interconnected pore network and be made of an osteogenic material. Bioactive glass is an ideal material because it rapidly bonds to bone and degrades over time, releasing soluble silica and calcium ions that are thought to stimulate osteoprogenitor cells. Melt-derived bioactive glasses, such as the original Bioglass® composition, are available commercially, but porous scaffolds have been difficult to produce because Bioglass and similar compositions crystallize on sintering. Sol-gel foam scaffolds have been developed that avoid this problem. They have a hierarchical pore structure comprising interconnected macropores, with interconnect diameters in excess of the 100 μm that is thought to be needed for vascularized bone ingrowth, and an inherent nanoporosity of interconnected mesopores (2–50 nm) which is beneficial for the attachment of osteoprogenitor cells. They also have a compressive strength in the range of cancellous bone. This paper describes the optimized sol-gel foaming process and illustrates the importance of optimizing the hierarchical structure from the atomic through nano, to the macro scale with respect to biological response.
Pyrophosphatase is essential for growth of Escherichia coli

The ppa gene for inorganic pyrophosphatase is essential for the growth of Escherichia coli. A recombinant with a chromosomal ppa::Kanr lesion and a temperature-sensitive replicon with a ppa+ gene showed a temperature-sensitive growth phenotype, and a mutant with the sole ppa+ gene under control of the lac promoter showed inducer-dependent growth. When the lacp-ppa mutant was subcultured without inducer, the pyrophosphatase level decreased, the PPi level increased, and growth stopped. Cellular PPi reached 16 mM about 6 h after growth arrest without loss of cell viability.
Noninvasive quantification of principal strains in normal canine hearts using tagged MRI images in 3-D.

Previous studies of myocardial strains have been largely limited to invasive procedures in isolated regions. Utilizing images from tagged magnetic resonance imaging (MRI) in three dimensions (3-D), we noninvasively quantified in vivo endocardial (endo) and epicardial (epi) principal strains (PS) throughout the left ventricle (LV) and tested their uniformity. Seven normal hearts in paced reclosed-chest dogs were studied. Combining long- and short-axis images, 24 myocardial cuboids were tagged at end diastole (ED), imaged at end systole and ED, and reconstructed in 3-D. The cuboids were circumferentially arranged in three parallel approximately 1-cm-thick short-axis slices (8 cuboids/slice). By application of finite strain analysis to each cuboid, the major PS (i.e., magnitude and angle with respect to the circumferential direction of maximal shortening) was calculated for each face. when strains are averaged globally (i.e., using all regions), the average magnitude of endo PS exceeded epi PS approximately twofold: -0.24 +/- 0.07 (SD) vs. -0.11 +/- 0.05 (P < 0.05). On the other hand, the PS angle with respect to the circumferential direction at epi exceeded the angle at endo (P < 0.05) by 33 +/- 36 degrees. Average PS direction at epi, 59 +/- 32 degrees, aligned with the expected fiber direction but was perpendicular to it at endo, 26 +/- 30 degrees. However, significant regional variations were observed from wall to wall and from apex to base. When variations in location were accounted for, the pooled SD for the PS magnitudes dropped to 0.032 and for the direction to only 15 degrees. Furthermore, it was found that the anterior-posterior pair of walls contracted differently (P < 0.05) from the septal-lateral pair of walls. These observations indicate that regional myocardial function is heterogeneous and is location dependent.
Ultrastructural modifications of the cell surface and intercellular contacts of some transformed cell strains.

Normal contact-inhibited and transformed cell cultures have been fixed and embedded in situ for an electron microscopic study of the cell surface and intercellular connections. In a number of experiments, ruthenium red was added to the fixatives following Luft's technic for visualizing the mucopolysaccharide layer on the cell surface. Cultures of normal rat, Chinese and Syrian hamster embryo cells were compared with 5 different strains of transformed cell lines: Chinese hamster cells transformed in vitro by adenovirus 12, Syrian hamster cells transformed in vitro by adenovirus 12, Syrian hamster cells transformed in vivo by SV40 virus, spontaneously transformed BHK21 cell line, and finally a spontaneously transformed rat fibroblast strain. Two main observations are reported: ( a ) The character of intercellular contacts was changed in the transformed cells. Whereas close junctions and desmosome-like structures are as frequent as in controls, the so-called tight junctions practically disappeared in the transformed cultures. ( b ) The ruthenium red layer was considerably increased in all the five transformed strains compared to the normal controls, suggesting an increase of the mucopolysaccharide deposit at the cell surface.
Responses of Gut Microbiota and Glucose and Lipid Metabolism to Prebiotics in Genetic Obese and Diet-Induced Leptin-Resistant Mice

OBJECTIVE To investigate deep and comprehensive analysis of gut microbial communities and biological parameters after prebiotic administration in obese and diabetic mice. RESEARCH DESIGN AND METHODS Genetic (ob/ob) or diet-induced obese and diabetic mice were chronically fed with prebiotic-enriched diet or with a control diet. Extensive gut microbiota analyses, including quantitative PCR, pyrosequencing of the 16S rRNA, and phylogenetic microarrays, were performed in ob/ob mice. The impact of gut microbiota modulation on leptin sensitivity was investigated in diet-induced leptin-resistant mice. Metabolic parameters, gene expression, glucose homeostasis, and enteroendocrine-related L-cell function were documented in both models. RESULTS In ob/ob mice, prebiotic feeding decreased Firmicutes and increased Bacteroidetes phyla, but also changed 102 distinct taxa, 16 of which displayed a >10-fold change in abundance. In addition, prebiotics improved glucose tolerance, increased L-cell number and associated parameters (intestinal proglucagon mRNA expression and plasma glucagon-like peptide-1 levels), and reduced fat-mass development, oxidative stress, and low-grade inflammation. In high fat–fed mice, prebiotic treatment improved leptin sensitivity as well as metabolic parameters. CONCLUSIONS We conclude that specific gut microbiota modulation improves glucose homeostasis, leptin sensitivity, and target enteroendocrine cell activity in obese and diabetic mice. By profiling the gut microbiota, we identified a catalog of putative bacterial targets that may affect host metabolism in obesity and diabetes.
Metric learning by directly minimizing the k-NN training error

This paper presents an approach for computing global distance metrics that minimize the k-NN leave-one-out (LOO) error. The approach optimizes an energy function that corresponds to a smoothened version of the k-NN LOO error. The generalization of the proposed approach is further improved by controlling the k parameter through a heuristic. Evaluation of the proposed approach on several public datasets showed that it was able to compete with an established state-of-the art approach.
Selective Over-Expression of Endothelin-1 in Endothelial Cells Exacerbates Inner Retinal Edema and Neuronal Death in Ischemic Retina

The level of endothelin-1 (ET-1), a potent vasoconstrictor, was associated with retinopathy under ischemia. The effects of endothelial endothelin-1 (ET-1) over-expression in a transgenic mouse model using Tie-1 promoter (TET-1 mice) on pathophysiological changes of retinal ischemia were investigated by intraluminal insertion of a microfilament up to middle cerebral artery (MCA) to transiently block the ophthalmic artery. Two-hour occlusion and twenty-two-hour reperfusion were performed in homozygous (Hm) TET-1 mice and their non-transgenic (NTg) littermates. Presence of pyknotic nuclei in ganglion cell layer (GCL) was investigated in paraffin sections of ipsilateral (ischemic) and contralateral (non-ischemic) retinae, followed by measurement of the thickness of inner retinal layer. Moreover, immunocytochemistry of glial fibrillary acidic protein (GFAP), glutamine synthetase (GS) and aquaporin-4 (AQP4) peptides on retinal sections were performed to study glial cell reactivity, glutamate metabolism and water accumulation, respectively after retinal ischemia. Similar morphology was observed in the contralateral retinae of NTg and Hm TET-1 mice, whereas ipsilateral retina of NTg mice showed slight structural and cellular changes compared with the corresponding contralateral retina. Ipsilateral retinae of Hm TET-1 mice showed more significant changes when compared with ipsilateral retina of NTg mice, including more prominent cell death in GCL characterized by the presence of pyknotic nuclei, elevated GS immunoreactivity in Müller cell bodies and processes, increased AQP-4 immunoreactivity in Müller cell processes, and increased inner retinal thickness. Thus, over-expression of endothelial ET-1 in TET-1 mice may contribute to increased glutamate-induced neurotoxicity on neuronal cells and water accumulation in inner retina leading to edema.
Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry

MED12 is a key component of the transcription‐regulating Mediator complex. Specific missense and in‐frame insertion/deletion mutations in exons 1 and 2 have been identified in uterine leiomyomas, breast tumors, and chronic lymphocytic leukemia. Here, we characterize the first MED12 5′ end nonsense mutation (c.97G>T, p.E33X) identified in acute lymphoblastic leukemia and show that it escapes nonsense‐mediated mRNA decay (NMD) by using an alternative translation initiation site. The resulting N‐terminally truncated protein is unable to enter the nucleus due to the lack of identified nuclear localization signal (NLS). The absence of NLS prevents the mutant MED12 protein to be recognized by importin‐α and subsequent loading into the nuclear pore complex. Due to this mislocalization, all interactions between the MED12 mutant and other Mediator components are lost. Our findings provide new mechanistic insights into the MED12 functions and indicate that somatic nonsense mutations in early exons may avoid NMD.
Enterprise Social Networks from a Manager's Perspective

The increasing use of Enterprise Social Networks (ESN) has been resulting in important changes in individual work practices, and is subject of numerous studies. From both a theoretical and a practical perspective, there is a lack of well-founded knowledge on how the implementation of ESN can be supported best to trigger both learning and change processes in the enterprise. For such processes, managers have a strong multiplying and "role model" effect. Therefore, following a case study approach, we conducted 15 interviews with managers at different hierarchical levels at a financial services provider to identify factors obstructing the successful ESN introduction and implementation. Understanding these obstructing factors is an important prerequisite for the competency development of both management and staff for a successful ESN implementation.
A Cooperative Creative Conceptual Design System

Lots of geographically distributed designers are usually involved to accomplish a complex design task and creativity and amenity of artifacts are more and more emphasized, so researches on cooperative creative conceptual design system are valuable both theoretically and practically. This paper firstly identifies some major requirements of cooperative creative conceptual design system. Then, creative genetic algorithm based on simple genetic algorithm is proposed to serve as creative mechanisms and methods. The design and development of prototype TripleCDS is described and some typical design images are shown, so the creative mechanisms and methods and prototype are validated
Wind Effects on Asphalt Shingles

Asphalt shingles have been utilized as a roofing material for more than one hundred years. The first asphalt shingles were manufactured in 1901 but were not mass produced until 1911 (Snoke 1941). Asphalt shingles were originally made from cotton rags that were coated with asphalt and surfaced with slate particles (McNulty 2000). In the early 1960s, glass fiber mats were introduced as the base material for asphalt shingles which made the shingles lighter and less apt to retain detrimental moisture (Cullen 1993). Relatively inexpensive asphalt along with advancements in mat and sealant technology quickly led to asphalt shingles becoming the primary choice for steep slope roofing. In 2009, asphalt shingles comprised 57 percent of the roofing market covering 138.5 million roofing squares (The Freedonia Group 2010). (Note: A square in roofing is 100 sq. ft. or 9.3 m.) Today, there are literally billions of roofing squares covered by asphalt shingles in the United States (Noone and Blanchard 1993). Not surprising, a large percentage of steep slope roofing in hurricane prone regions is asphalt shingles because asphalt shingles are more economical than their tile or metal counterparts. Further, stringent building codes and standards have led to tougher demands on the asphalt shingle industry. Today, asphalt shingles can be rated for high wind zones up to 67 m s (150 mph) as a three-second gust. However, there remain problems at the basic level with the design, manufacture, installation, and durability of asphalt shingles. Assessments of asphalt shingle roofs by the authors after hurricanes have revealed deficiencies in each of these areas. Similar findings have been made by McDonald and Smith (1990) after Hurricane Hugo, Smith (1995) after Hurricane Andrew, Rash (2006) after Hurricane Ivan, and the Roofing Industry Committee on Weather Issues (RICOWI) (2006, 2007, and 2009) after Hurricanes Charley and Ivan, Katrina, and Ike, respectively.
Historical and Future Changes of Snowfall Events in China under a Warming Background

Using station data and Regional Climate Model version 4 (RegCM4) simulations under the representative concentration pathway 4.5 (RCP4.5) scenario, this article addresses historical and future changes of the wintertime snowfall over China. The observational results generally show a decrease in the frequency and an increase in the mean intensity of snowfalls in northwestern China (NWC), northeastern China (NEC), the eastern Tibetan Plateau (ETP), and southeastern China (SEC) since the 1960s. The total amount of wintertime snowfall, however, has increased in NWC, NEC, and ETP but decreased in SEC. The decrease in snow days is primarily due to the reduction of light snowfall events. The increase in the total amount is primarily explained by increases in heavy snowfalls, and the corresponding decrease is the result of decreases in light-to-heavy snowfalls. The RegCM4 ensemble, which can well simulate the observed snowfall climatology, projects that the snow days will be further reduced by the end of the twenty-first century relative to 1986–2005, primarily owing to the decline of light snowfall events. The total amount is projected to increase in NWC but decrease in the other three subregions. The increase in the total amount in NWC is attributed to increases in heavy and large snowfalls. Decreases in light snowfalls play a leading role in the decrease of the total amount in NEC. In ETP and SEC, the decrease in the total amount is the result of overall decreases in light-to-heavy snowfalls. The mechanism for such changes is an interesting topic to study in the future.
Critical appraisal of a fixed combination of esomeprazole and low dose aspirin in risk reduction

Low dose aspirin (≤325 mg) is routinely used for primary and secondary prophylaxis of cardiovascular and cerebrovascular events. The use of low dose aspirin is associated with two- to four-fold greater risk of symptomatic or complicated peptic ulcers. Risk factors associated with low dose aspirin induced gastrointestinal toxicity includes prior history of ulcer or upper gastrointestinal (GI) bleeding, concomitant use of other nonsteroidal anti-inflammatory drugs, corticosteroid or warfarin, dual antiplatelet therapy, Helicobacter pylori (H. pylori) infection, and advanced age. Esomeprazole, like other proton pump inhibitors (PPIs) is very effective in decreasing the risk of aspirin induced gastrointestinal toxicity. Although evidence to support esomeprazole or other PPIs for primary prophylaxis in aspirin induced gastrointestinal toxicity is limited, its role in secondary prophylaxis is well established.
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts

Marine sponges contain complex bacterial communities of considerable ecological and biotechnological importance, with many of these organisms postulated to be specific to sponge hosts. Testing this hypothesis in light of the recent discovery of the rare microbial biosphere, we investigated three Australian sponges by massively parallel 16S rRNA gene tag pyrosequencing. Here we show bacterial diversity that is unparalleled in an invertebrate host, with more than 250 000 sponge-derived sequence tags being assigned to 23 bacterial phyla and revealing up to 2996 operational taxonomic units (95% sequence similarity) per sponge species. Of the 33 previously described ‘sponge-specific’ clusters that were detected in this study, 48% were found exclusively in adults and larvae – implying vertical transmission of these groups. The remaining taxa, including ‘Poribacteria’, were also found at very low abundance among the 135 000 tags retrieved from surrounding seawater. Thus, members of the rare seawater biosphere may serve as seed organisms for widely occurring symbiont populations in sponges and their host association might have evolved much more recently than previously thought.
Comparative biology of sperm factors and fertilization‐induced calcium signals across the animal kingdom

Fertilization causes mature oocytes or eggs to increase their concentrations of intracellular calcium ions (Ca2+) in all animals that have been examined, and such Ca2+ elevations, in turn, provide key activating signals that are required for non‐parthenogenetic development. Several lines of evidence indicate that the Ca2+ transients produced during fertilization in mammals and other taxa are triggered by soluble factors that sperm deliver into oocytes after gamete fusion. Thus, for a broad‐based analysis of Ca2+ dynamics during fertilization in animals, this article begins by summarizing data on soluble sperm factors in non‐mammalian species, and subsequently reviews various topics related to a sperm‐specific phospholipase C, called PLCζ, which is believed to be the predominant activator of mammalian oocytes. After characterizing initiation processes that involve sperm factors or alternative triggering mechanisms, the spatiotemporal patterns of Ca2+ signals in fertilized oocytes or eggs are compared in a taxon‐by‐taxon manner, and broadly classified as either a single major transient or a series of repetitive oscillations. Both solitary and oscillatory types of fertilization‐induced Ca2+ signals are typically propagated as global waves that depend on Ca2+ release from the endoplasmic reticulum in response to increased concentrations of inositol 1,4,5‐trisphosphate (IP3). Thus, for taxa where relevant data are available, upstream pathways that elevate intraoocytic IP3 levels during fertilization are described, while other less‐common modes of producing Ca2+ transients are also examined. In addition, the importance of fertilization‐induced Ca2+ signals for activating development is underscored by noting some major downstream effects of these signals in various animals. Mol. Reprod. Dev. 80: 787–815, 2013. © 2013 Wiley Periodicals, Inc.
Chemokine receptor expression and modulation by Mycobacterium tuberculosis antigens on mononuclear cells from human lymphoid tissues

Chemokine receptor switching on lymphoid cells is an important factor regulating migration and homing, but little is known about the expression of such molecules during Mycobacterium tuberculosis infection in humans. We describe CCR2, CCR5 and CCR7 expression on human cells from blood, spleen and pulmonary hilar lymph nodes (PHLN) stimulated by M. tuberculosis antigens. CCR2 was not expressed by CD3+ cells regardless of the presence of antigen, but was highly expressed on CD14+ CD63+ monocytes/macrophages. CCR2 decreased on splenic monocytes/macrophages by nearly 50% in culture, independent of antigen, but remained high in blood and PHLN. CCR5 was low in CD3+ cells and was down‐regulated by M. tuberculosis antigens on blood and splenic cells but not in PHLN. CCR5 was highly expressed on monocytes/macrophages and was down‐regulated by M. tuberculosis antigens at 48 hr only in blood. Less than 15% of CD3+ cells from spleen and PHLN were CCR7+, whereas nearly 40% from blood expressed this receptor on primary isolation. However, CCR7 in PHLN increased in culture, independent of antigen. Monocytes/macrophages did not express CCR7. Thus, we characterize, for the first time, chemokine receptor expression and differential modulation by M. tuberculosis antigens on human mononuclear cells from spleen, blood and PHLN. Knowledge of chemokine receptor switching in human lymphoid tissue provides novel insight into mechanisms of the immune response to M. tuberculosis with potential effects on directing cell trafficking.