Miracle-dz/UniFAR-FTUs huggingface dataset:
Smoothing an overlay grid to minimize linear distortion in texture mapping

Texture is an essential component of computer generated models. For a texture mapping procedure to be effective it has to generate continuous textures and cause only small mapping distortion. The Angle Based Flattening (ABF) parameterization method is guaranteed to provide a continuous (no foldovers) mapping. It also minimizes the angular distortion of the parameterization, including locating the optimal planar domain boundary. However, since it concentrates on minimizing the angular distortion of the mapping, it can introduce relatively large linear distortion.In this paper we introduce a new procedure for reducing length distortion of an existing parameterization and apply it to ABF results. The linear distortion reduction is added as a second step in a texture mapping computation. The new method is based on computing a mapping from the plane to itself which has length distortion very similar to that of the ABF parameterization. By applying the inverse mapping to the result of the initial parameterization, we obtain a new parameterization with low length distortion. We notice that the procedure for computing the inverse mapping can be applied to any other (convenient) mapping from the three-dimensional surface to the plane in order to improve it.The mapping in the plane is computed by applying weighted Laplacian smoothing to a Cartesian grid covering the planar domain of the initial mapping. Both the mapping and its inverse are provably continuous. Since angle preserving (conformal) mappings, such as ABF, locally preserve distances as well, the planar mapping has small local deformation. As a result, the inverse mapping does not significantly increase the angular distortion.The combined texture mapping procedure provides a mapping with low distance and angular distortion, which is guaranteed to be continuous.
The new indirubin derivative inhibitors of glycogen synthase kinase‐3, 6‐BIDECO and 6‐BIMYEO, prevent tau phosphorylation and apoptosis induced by the inhibition of protein phosphatase‐2A by okadaic acid in cultured neurons

Alterations in glycogen synthase kinase‐3β (GSK3β) and protein phosphatase‐2A (PP2A) have been proposed to be involved in the abnormal tau phosphorylation and aggregation linked to Alzheimer's disease (AD). Interconnections between GSK3β and PP2A signaling pathways are well established. Targeting tau kinases was proposed to represent a therapeutic strategy for AD. However, which tau kinases should be blocked and to what extent, keeping in mind that kinases have physiological roles? Because most kinase inhibitors are relatively specific and many of them interfere with the cell cycle, it is necessary to develop more specific tau kinase inhibitors devoid of cell toxicity. Here, we used the PP2A inhibition by okadaic acid (OKA) in primary cultured cortical neurons as an in vitro model of increased tau phosphorylation and apoptosis. We tested the effects of two newly characterized indirubin derivative inhibitors of GSK3, 6‐BIDECO (6‐bromoindirubin‐3′‐[O‐(N,N‐diethylcarbamyl)‐oxime] and 6‐BIMYEO (6‐bromoindirubin‐3′‐[O‐(2‐morpholin‐1‐ylethyl)‐oxime] hydrochloride) on OKA‐induced tau phosphorylation and neuronal apoptosis. Both compounds exhibit higher selectivity toward GSK3 compared with other tau kinases (for 6‐BIDECO, IC50 is 0.03 μM for GSK3, >10 μM for CDK1, and 10 μM for CDK5; for 6‐BIMYEO, IC50 is 0.11 μM for GSK3, 1.8 μM for CDK1, and 0.9 μM for CDK5). We show that 6‐BIDECO and 6‐BIMYEO used at micromolar concentrations are not neurotoxic and potently reversed tau phosphorylation and apoptosis induced by OKA. The neuroprotection by these compounds should be further validated in animal models of AD. © 2011 Wiley‐Liss, Inc.
Onset of type 1 diabetes: a dynamical instability.

Type 1 diabetes is a disease characterized by progressive loss of beta-cell function due to an autoimmune reaction affecting the islets of Langerhans. It is now generally accepted that cytokines are implicated in the pathogenesis of autoimmune diseases. Animal studies have shown that interleukin-1beta, tumor necrosis factor-alpha, and interferon-gamma affect type 1 diabetes development profoundly. It has been suggested that beta-cells are destroyed by cytokine-induced free radical formation before cytotoxic T-helper (Th)-lymphocytes and/or autoantibody-mediated cytolysis. This hypothesis is known as the "Copenhagen model. " We introduce a mathematical model encompassing the various processes within this framework. The model is expressed in rate equations describing the changes in numbers of beta-cells, macrophages, and Th-lymphocytes. Being concerned with the earliest events, we explore the conditions necessary to maintain self-sustained beta-cell elimination based on the feedback between immune cells and insulin-producing cells. The motivation for this type of analysis becomes clear when we consider the multifactorial and complicated nature of the disease. Indeed, recent research has provided detailed information about the different factors that contribute to the development of the disease, stressing the importance of incorporating these findings into a more general picture. A mathematical formalism allows for a more comprehensive description of the biological problem and can reveal nonintuitive properties of the dynamics. Despite the rather complicated structure of the equations, our main conclusion is simple: onset of type 1 diabetes is due to a collective, dynamical instability, rather than being caused by a single etiological factor.
Comparison of precoding schemes for digital subscriber lines

Precoding at the transmitter side is a practicable method for transmission over intersymbol interference channels. In contrast to decision-feedback equalization no error propagation occurs and coded modulation can be applied as for the intersymbol interference free channel. Tomlinson-Harashima (1971, 1972) precoding and flexible precoding are analyzed and compared. The dualities and differences are discussed. The focus of interest is the application of precoding to fast digital transmission over twisted pair lines, such as high-rate or asymmetric digital subscriber lines. It turns out that flexibility-which is not necessary in the specific application, digital subscriber lines-of flexible precoding is paid with a performance loss compared to Tomlinson-Harashima precoding.
Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation

Phytoplankton growth rates are limited by the supply of iron (Fe) in approximately one third of the open ocean, with major implications for carbon dioxide sequestration and carbon (C) biogeochemistry. To date, understanding how alteration of Fe supply changes phytoplankton physiology has focused on traditional metrics such as growth rate, elemental composition, and biophysical measurements such as photosynthetic competence (Fv/Fm). Researchers have subsequently employed transcriptomics to probe relationships between changes in Fe supply and phytoplankton physiology. Recently, studies have investigated longer-term (i.e. following acclimation) responses of phytoplankton to various Fe conditions. In the present study, the coastal diatom, Thalassiosira pseudonana, was acclimated (10 generations) to either low or high Fe conditions, i.e. Fe-limiting and Fe-replete. Quantitative proteomics and a newly developed proteomic profiling technique that identifies low abundance proteins were employed to examine the full complement of expressed proteins and consequently the metabolic pathways utilized by the diatom under the two Fe conditions. A total of 1850 proteins were confidently identified, nearly tripling previous identifications made from differential expression in diatoms. Given sufficient time to acclimate to Fe limitation, T. pseudonana up-regulates proteins involved in pathways associated with intracellular protein recycling, thereby decreasing dependence on extracellular nitrogen (N), C and Fe. The relative increase in the abundance of photorespiration and pentose phosphate pathway proteins reveal novel metabolic shifts, which create substrates that could support other well-established physiological responses, such as heavily silicified frustules observed for Fe-limited diatoms. Here, we discovered that proteins and hence pathways observed to be down-regulated in short-term Fe starvation studies are constitutively expressed when T. pseudonana is acclimated (i.e., nitrate and nitrite transporters, Photosystem II and Photosystem I complexes). Acclimation of the diatom to the desired Fe conditions and the comprehensive proteomic approach provides a more robust interpretation of this dynamic proteome than previous studies.
Partners in care: investigating community nurses' understanding of an interdisciplinary team-based approach to primary care.

AIM This study investigated community nurses understanding of teamwork in primary care. BACKGROUND Internationally trends indicate a movement towards the development of primary care as a key element in health service delivery. This will have implications for the organisation of community nursing services by creating the need for more coherent integrated structures for service delivery. In this context, teamwork is associated with a range of positive outcomes including higher levels of quality care and job satisfaction. DESIGN A research study was undertaken to investigate community nurses' understanding of an interdisciplinary team-based approach to primary care using a qualitative research design. Focus groups were held with community nurses working in the areas of public health nursing, general nursing and practice nursing. METHODS Three focus groups were established. Twenty seven participants were recruited to form three groups comprising public health nurses (n = 10), general nurses (n = 10) and practice nurses (n = 7). A sequenced-questioning framework guided the systematic process of data collection. Data analysis engaged a thematic content analysis framework. RESULTS The analysis of the data revealed the following themes: teamwork, promoting community services, promoting health, professional roles and skills and knowledge for primary care. CONCLUSION Nurses can contribute significantly to the re-orientation and development of primary care services. There must be greater efforts to encourage interdisciplinary approaches. The outcomes of this study can inform strategies for effective team working in primary care. Collective team efforts enhance patient care and effective teamwork requires a greater understanding of group processes and team development. RELEVANCE TO CLINICAL PRACTICE Nurses clearly articulated their contribution to primary care, but recognised that there are many challenges to overcome. An enhanced primary care team has the potential to allow the public access to both the individual and collective skills and knowledge of team members.
Evolution of ultraviolet vision in shorebirds (Charadriiformes)

Diurnal birds belong to one of two classes of colour vision. These are distinguished by the maximum absorbance wavelengths of the SWS1 visual pigment sensitive to violet (VS) and ultraviolet (UVS). Shifts between the classes have been rare events during avian evolution. Gulls (Laridae) are the only shorebirds (Charadriiformes) previously reported to have the UVS type of opsin, but too few species have been sampled to infer that gulls are unique among shorebirds or that Laridae is monomorphic for this trait. We have sequenced the SWS1 opsin gene in a broader sample of species. We confirm that cysteine in the key amino acid position 90, characteristic of the UVS class, has been conserved throughout gull evolution but also that the terns Anous minutus, A. tenuirostris and Gygis alba, and the skimmer Rynchops niger carry this trait. Terns, excluding Anous and Gygis, share the VS conferring serine in position 90 with other shorebirds but it is translated from a codon more similar to that found in UVS shorebirds. The most parsimonious interpretation of these findings, based on a molecular gene tree, is a single VS to UVS shift and a subsequent reversal in one lineage.
Chitosan Nanoparticles as a Mucoadhesive Drug Delivery System for Ocular Administration

Pharmaceutical approaches based on nanotechnologies and the development of eye drops composed of the mucoadhesive polymers chitosan and hyaluronic acid are emerging strategies for the efficient treatment of ocular diseases. These innovative nanoparticulate systems aim to increase drugs’ bioavailability at the ocular surface. For the successful development of these systems, the evaluation of mucoahesiveness (the interaction between the ocular delivery system and mucins present on the eye) is of utmost importance. In this context, the aim of the present work was to investigate the mucoadhesivity of a novel nanoparticle eye drop formulation containing an antibiotic (ceftazidime) intended to treat eye infections. Eye drop formulations comprised a polymer (hydroxypropyl) methyl cellulose (HPMC) 0.75% (w/v) in an isotonic solution incorporating chitosan/sodium tripolyphosphate (TPP)-hyaluronic acid-based nanoparticles containing ceftazidime. The viscosity of the nanoparticles, and the gels incorporating the nanoparticles were characterized in contact with mucin at different mass ratios, allowing the calculation of the rheological synergism parameter (∆η). Results showed that at different nanoparticle eye formulation:mucin weight ratios, a minimum in viscosity occurred which resulted in a negative rheological synergism. Additionally, the results highlighted the mucoadhesivity of the novel ocular formulation and its ability to interact with the ocular surface, thus increasing the drug residence time in the eye. Moreover, the in vitro release and permeation studies showed a prolonged drug release profile from the chitosan/TPP-hyaluronic acid nanoparticles gel formulation. Furthermore, the gel formulations were not cytotoxic on ARPE-19 and HEK293T cell lines, evaluated by the metabolic and membrane integrity tests. The formulation was stable and the drug active, as shown by microbiological studies. In conclusion, chitosan/TPP-hyaluronic acid nanoparticle eye drop formulations are a promising platform for ocular drug delivery with enhanced mucoadhesive properties.
Gram-positive three-component antimicrobial peptide-sensing system

To survive during colonization or infection of the human body, microorganisms must circumvent mechanisms of innate host defense. Antimicrobial peptides represent a key component of innate host defense, especially in phagocytes and on epithelial surfaces. However, it is not known how the clinically important group of Gram-positive bacteria sense antimicrobial peptides to coordinate a directed defensive response. By determining the genome-wide gene regulatory response to human β-defensin 3 in the nosocomial pathogen Staphylococcus epidermidis, we discovered an antimicrobial peptide sensor system that controls major specific resistance mechanisms of Gram-positive bacteria and is unrelated to the Gram-negative PhoP/PhoQ system. It contains a classical two-component signal transducer and an unusual third protein, all of which are indispensable for signal transduction and antimicrobial peptide resistance. Furthermore, our data indicate that a very short, extracellular loop with a high density of negative charges in the sensor protein is responsible for antimicrobial peptide binding and the observed specificity for cationic antimicrobial peptides. Our study shows that Gram-positive bacteria have developed an efficient and unique way of controlling resistance mechanisms to antimicrobial peptides, which may provide a promising target for antimicrobial drug development.
Hub Promiscuity in Protein-Protein Interaction Networks

Hubs are proteins with a large number of interactions in a protein-protein interaction network. They are the principal agents in the interaction network and affect its function and stability. Their specific recognition of many different protein partners is of great interest from the structural viewpoint. Over the last few years, the structural properties of hubs have been extensively studied. We review the currently known features that are particular to hubs, possibly affecting their binding ability. Specifically, we look at the levels of intrinsic disorder, surface charge and domain distribution in hubs, as compared to non-hubs, along with differences in their functional domains.
B2B eContract Handling- A Survey of Projects, Papers and Standards

The rapid development of IT gives rise to changes in many industries and different spheres of life. It simplifies and speeds up processes and data processing. As a result, it changes the processes and the data involved in them. The area of commerce and contracting in particular undergoes similar changes. The new developments aim at speeding up, facilitating and globalizing the process of contracting. This inevitably leads to new contracting processes and changes the standard approach for contracting. This report presents a survey of the research, development, and standardization efforts in the area of business-to-business e-contracting. The report is divided into three parts. The first part presents a multi-dimensional contracting framework. The second part reviews current standardization processes and developments in the e-commerce field. The third part provides summaries and comments on a selected set of papers on e-contracting. Depending on their goals, focus and content, the papers are categorized in accordance with the contract cycle phases described in one of the dimensions of the contracting framework. Where appropriate, the content of the papers is related to the dimensions of the contracting framework. This report further provides an acronym list of the most common abbreviations in e-commerce terminology.
What Does Control Flow Really Look Like? Eyeballing the Cyclomatic Complexity Metric

Assessing the understandability of source code remains an elusive yet highly desirable goal for software developers and their managers. While many metrics have been suggested and investigated empirically, the McCabe cyclomatic complexity metric (CC) - which is based on control flow complexity - seems to hold enduring fascination within both industry and the research community despite its known limitations. In this work, we introduce the ideas of Control Flow Patterns (CFPs) and Compressed Control Flow Patterns (CCFPs), which eliminate some repetitive structure from control flow graphs in order to emphasize high-entropy graphs. We examine eight well-known open source Java systems by grouping the CFPs of the methods into equivalence classes, and exploring the results. We observed several surprising outcomes: first, the number of unique CFPs is relatively low, second, CC often does not accurately reflect the intricacies of Java control flow, and third, methods with high CC often have very low entropy, suggesting that they may be relatively easy to understand. These findings challenge the widely-held belief that there is a clear-cut causal relationship between CC and understandability, and suggest that CC and similar measures need to be reconsidered as metrics for code understandability.
The Introduction of a New Screening Tool for the Identification of Cognitively Impaired Medically At-Risk Drivers

The number of drivers with a cognitive impairment due to dementia or other age-associated pathologies will increase significantly over the next 3 decades. Physicians are well placed to identify medically at-risk drivers, but are hampered by the lack of a valid, easy to administer screening tool. This research develops and validates a brief screening tool for use in the primary care setting to identify drivers with cognitive impairment with or without dementia. Initial Study Participants: A cohort of 146 consecutive referrals from community-based family physicians, diagnosed with an undifferentiated cognitive impairment or dementia, as well as 35 community dwelling healthy controls. Validation Study: A cohort of 192 consecutive referrals carrying the same diagnosis as above and 52 community dwelling healthy controls. Criterion Measure: Pass/fail on an On-Road evaluation. Predictor Measures: Subtests of the DemTect, a screening test for cognitive impairment or dementia developed by Kalbe and colleagues. 1 Initial Study: Three of the DemTect measures predicted On-Road outcomes (R2 = .262). Regression results were used to develop a simple scoring algorithm, with cut-points then derived by identifying those most at risk for failing and passing the On-Road assessment, and those needing a driving assessment for determination of driving competency. 89 individuals scored in the indeterminate range, with 49 and 43 predicted to fail and pass, respectively—86% and 84% of those predicted to fail and pass did subsequently fail and pass. Validation Study: 123 individuals scored in the indeterminate range, with 66 and 55 predicted to fail and pass, respectively—80% and 87% of those predicted to fail and pass did subsequently fail and pass. Conclusions: The SIMARD A Modification of the DemTect (Screen for the Identification of cognitively impaired Medically At-Risk Drivers) is a brief paper and pencil screening tool with a high degree of accuracy that can be used for immediate decisions in the clinical setting.
Omeprazole before endoscopy in patients with gastrointestinal bleeding.

BACKGROUND A neutral gastric pH is critical for the stability of clots over bleeding arteries. We investigated the effect of preemptive infusion of omeprazole before endoscopy on the need for endoscopic therapy. METHODS Consecutive patients admitted with upper gastrointestinal bleeding underwent stabilization and were then randomly assigned to receive either omeprazole or placebo (each as an 80-mg intravenous bolus followed by an 8-mg infusion per hour) before endoscopy the next morning. RESULTS Over a 17-month period, 638 patients were enrolled and randomly assigned to omeprazole or placebo (319 in each group). The need for endoscopic treatment was lower in the omeprazole group than in the placebo group (60 of the 314 patients included in the analysis [19.1%] vs. 90 of 317 patients [28.4%], P=0.007). There were no significant differences between the omeprazole group and the placebo group in the mean amount of blood transfused (1.54 and 1.88 units, respectively; P=0.12) or the number of patients who had recurrent bleeding (11 and 8, P=0.49), who underwent emergency surgery (3 and 4, P=1.00), or who died within 30 days (8 and 7, P=0.78). The hospital stay was less than 3 days in 60.5% of patients in the omeprazole group, as compared with 49.2% in the placebo group (P=0.005). On endoscopy, fewer patients in the omeprazole group had actively bleeding ulcers (12 of 187, vs. 28 of 190 in the placebo group; P=0.01) and more omeprazole-treated patients had ulcers with clean bases (120 vs. 90, P=0.001). CONCLUSIONS Infusion of high-dose omeprazole before endoscopy accelerated the resolution of signs of bleeding in ulcers and reduced the need for endoscopic therapy. (ClinicalTrials.gov number, NCT00164866 [ClinicalTrials.gov] .).