Miracle-dz/UniFAR-FTUs huggingface dataset:
Microvascular changes in radiation-induced oral mucositis.

BACKGROUND Mucositis is one of the most debilitating side effects of head and neck cancer therapy and is currently believed to arise from an inflammatory cascade leading to cellular damage. However, no effective treatment has been identified despite extensive attempts with anti-inflammatory medications. OBJECTIVE To compare real-time microvascular inflammatory changes with oral mucositis levels in patients undergoing radiotherapy or chemoradiotherapy for head and neck tumours. DESIGN Prospective, longitudinal, cohort, observational study. SETTING Regional cancer program. METHODS Twenty patients with head and neck tumours were assessed on a weekly basis throughout the course of radiotherapy. Levels of mucositis were graded objectively using the Oral Mucositis Assessment Scale and subjectively using a patient symptom questionnaire. Video imaging of the sublingual microcirculation was obtained using orthogonal polarized spectral imaging to quantify inflammatory markers such as microcirculatory velocity, white blood cell margination, and extravasation. RESULTS Despite very high levels of objective and subjective mucositis, inflammatory changes were not present in the microcirculation. CONCLUSIONS Typical microvascular inflammatory changes are not demonstrated in radiation-induced mucositis. These findings contradict the currently proposed mechanism of mucosal damage and may therefore have important implications in the development of novel therapeutic interventions.
Contacts-based prediction of binding affinity in protein–protein complexes

Almost all critical functions in cells rely on specific protein–protein interactions. Understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack a thorough understanding of the energetics of association of proteins. Here, we introduce a new and simple approach to predict binding affinity based on functional and structural features of the biological system, namely the network of interfacial contacts. We assess its performance against a protein–protein binding affinity benchmark and show that both experimental methods used for affinity measurements and conformational changes have a strong impact on prediction accuracy. Using a subset of complexes with reliable experimental binding affinities and combining our contacts and contact-types-based model with recent observations on the role of the non-interacting surface in protein–protein interactions, we reach a high prediction accuracy for such a diverse dataset outperforming all other tested methods. DOI: http://dx.doi. org/10.7554/eLife.07454. 001
Miami classification for probe-based confocal laser endomicroscopy

An essential element for any new advanced imaging technology is standardization of indications, terminology, categorization of images, and research priorities. In this review, we propose a state-of-the-art classification system for normal and pathological states in gastrointestinal disease using probe-based confocal laser endomicroscopy (pCLE). The Miami classification system is based on a consensus of pCLE users reached during a meeting held in Miami, Florida, in February 2009.
Tunable millimeter-wave generation with subharmonic injection locking in two-section strongly gain-coupled DFB lasers

Using two-section dual-mode strongly gain-coupled (SGC) distributed feedback (DFB) lasers, tunable millimeter-wave (mm-wave) generation from 18 to 40 GHz can he achieved under CW bias conditions. Due to its high speed and excellent dynamic single-mode yield in SGC DFB lasers, each section can be individually modulated to beyond 10 GHz. Using subharmonic injection locking, the linewidth of the generated mm-wave can be significantly reduced and is found to be less than 30 Hz which is limited by stability of the microwave source and the resolution of the spectrum analyzer. This device provides a useful source to high-bit-rate optical systems and/or high-frequency wireless communications.
Mechanical testing of a selective laser melted superalloy

Selective laser melting is an additive manufacturing technology where metal powder is melted by a laser source layer-wise, forming a solid, dense metallic component. With the selective laser meting process, near net shape components can be manufactured directly from a 3D-model. The model is sliced into thin layers and a powder is spread onto a build platform. In the next step, the powder is fused by a laser as dictated by the model. The laser energy is intense enough to permit full melting (welding) of the particles to form solid metal. The process is repeated layer by layer until the part is complete. A number of materials are available, including steel, aluminium, titanium and, in recent time, also superalloys. The material investigated in the current project is a nickel base superalloy composition-wise equivalent to Hastelloy X, a solution strengthened superalloy typically used in large welded components exposed to high temperatures in oxidizing as well as reducing environments. Microstructurally, the material is different from both a hot-rolled, as well as a cast material due to the manufacturing process. Since the SLM process involves laser melting of powder particles in the size range of <50μm, the structure resembles of a weld structure, however on a smaller scale. Due to the layer-by-layer build strategy, the material will exhibit anisotropy. In the current project, high temperature mechanical fatigue and creep tests are performed. The microstructure is evaluated and the influence on the mechanical properties is discussed. Anisotropy in mechanical properties is discussed and the underlying factors of the anisotropy are analyzed.
Application of a colorimeter for turbidity measurement

This paper describes a new turbidity transducer based on color measurement. The absorbance of solutions reflects the absorption and scattering of suspended particle for incident light which could determine the turbidity of solutions. The experimental results indicate that there are good linear relationships between chromaticity and turbidity. The new way is suitable for continuous monitoring of water turbidity in the wide range.
TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis

Environmental stresses such as drought, salinity, and cold are major factors that significantly limit agricultural productivity. NAC transcription factors play essential roles in response to various abiotic stresses. However, the paucity of wheat NAC members functionally characterized to date does not match the importance of this plant as a world staple crop. Here, the function of TaNAC2 was characterized in Arabidopsis thaliana. A fragment of TaNAC2 was obtained from suppression subtractive cDNA libraries of wheat treated with polyethylene glycol, and its full-length cDNA was obtained by searching a full-length wheat cDNA library. Gene expression profiles indicated that TaNAC2 was involved in response to drought, salt, cold, and abscisic acid treatment. To test its function, transgenic Arabidopsis lines overexpressing TaNAC2–GFP controlled by the cauliflower mosaic virus 35S promoter were generated. Overexpression of TaNAC2 resulted in enhanced tolerances to drought, salt, and freezing stresses in Arabidopsis, which were simultaneously demonstrated by enhanced expression of abiotic stress-response genes and several physiological indices. Therefore, TaNAC2 has potential for utilization in transgenic breeding to improve abiotic stress tolerances in crops.
Rationing in health systems: A critical review

Background: It is difficult to provide health care services to all those in need of such services due to limited resources and unlimited demands. Thus, priority setting and rationing have to be applied. This study aimed at critically examining the concept of rationing in health sector and identifying its purposes, influencing factors, mechanisms, and outcomes. Methods: The critical interpretive synthesis methodology was used in this study. PubMed, Cochrane, and Proquest databases were searched using the related key words to find related documents published between 1970 and 2015. In total, 161 published reports were reviewed and included in the study. Thematic content analysis was applied for data analysis. Results: Health services rationing means restricting the access of some people to useful or potentially useful health services due to budgetary limitation. The inherent features of the health market and health services, limited resources, and unlimited needs necessitate health services rationing. Rationing can be applied in 4 levels: health care policy- makers, health care managers, health care providers, and patients. Health care rationing can be accomplished through fixed budget, benefit package, payment mechanisms, queuing, copayments, and deductibles. Conclusion: This paper enriched our understanding of health services rationing and its mechanisms at various levels and contributed to the literature by broadly conceptualizing health services rationing.
Towards an understanding of tailoring scrum in global software development: a multi-case study

There is growing interest in applying Scrum practices in Global Software Development to leverage the advantages of both. However, the effective use of Scrum practices largely depends on close interactions between project stakeholders. The distribution of project stakeholders in GSD provides significant challenges related to project collaboration processes that may limit the use of Scrum. However, project managers increasingly seek to use the Scrum model in their distributed projects. While there is an emerging body of industrial experience, there are limited empirical studies that discuss Scrum tailoring in GSD. The paper reports a multi-case study that investigates the impact of key project contextual factors on the use of Scrum practices in GSD. This study is relevant to researchers and practitioners who are seeking ways to use Scrum in GSD and improve project effectiveness.
SEER: A Secure and Efficient Service Review System for Service-Oriented Mobile Social Networks

In this paper, we consider service-oriented mobile social networks (S-MSNs) and propose a Secure and Efficient service Review (SEER) system to enable user feedback. Each service provider independently maintains a SEER system for itself, which collects and stores user reviews about its services without requiring any central trusted authority. The service reviews can then be made available to interested users in making wise service selection decisions. We identify three unique service review attacks and then develop sophisticated security mechanisms for SEER to deal with these attacks. Specifically, SEER enables users to distributedly and cooperatively submit their reviews in an integrated chain form by using hierarchical and aggregate signature techniques. It discourages service providers to reject, modify or delete their reviews. The integrity of reviews is therefore improved. Through security analysis and performance evaluation, we show that SEER effectively resists the service review attacks and achieves significantly better performance in terms of submission rate and delay than a service review system that does not adopt user cooperation or the chain review structure.
Associations between objectively assessed and questionnaire-based sedentary behaviour with BMI-defined obesity among general population children and adolescents living in England

Objectives Sedentary behaviour (SB) is an emerging candidate risk factor for obesity in young people. Evidence to date is conflicting and it is unclear how different SB types are associated with obesity independently of physical activity. The objective of this study was to examine associations between a range of objectively measured and questionnaire-based SB indicators with obesity and body mass index (BMI) to assess whether these associations were independent of physical activity. Participants 4469 (705 with accelerometer data) children aged 5–15 years from the 2008 Health Survey for England. Outcomes The outcome was adiposity, classified using age-specific and sex-specific BMI SD scores (continuous) and obesity cut-offs (binary). Questionnaire-based measures comprised TV time, non-TV sitting time (such as homework, drawing, time at a computer or playing video games), total sitting time (TV time+non-TV sitting time) and average daily MVPA time. Objective SB and moderate to vigorous physical activity (MVPA) time were measured using an Actigraph GT1M accelerometer, with cut-offs of 100 and 200 counts per minute for SB, and 2802 counts per minute for MVPA. Multiple logistic and multiple linear regression models examined associations between each indicator of sedentary time with obesity and BMI SD scores. Results TV time (but not non-TV sitting or objectively-measured SB) was consistently associated with higher levels of obesity and BMI SD score, even after adjusting for MVPA and other potential confounders. Weaker associations were observed for total sitting time. Conclusions TV viewing (but not other forms of objectively-measured or questionnaire-based sedentary time) was associated with obesity in children and adolescents. Although a causal relationship cannot be established, TV time may be a reasonable target for obesity prevention in young populations.
An Empirical Study of RefactoringChallenges and Benefits at Microsoft

It is widely believed that refactoring improves software quality and developer productivity. However, few empirical studies quantitatively assess refactoring benefits or investigate developers' perception towards these benefits. This paper presents a field study of refactoring benefits and challenges at Microsoft through three complementary study methods: a survey, semi-structured interviews with professional software engineers, and quantitative analysis of version history data. Our survey finds that the refactoring definition in practice is not confined to a rigorous definition of semantics-preserving code transformations and that developers perceive that refactoring involves substantial cost and risks. We also report on interviews with a designated refactoring team that has led a multi-year, centralized effort on refactoring Windows. The quantitative analysis of Windows 7 version history finds the top 5 percent of preferentially refactored modules experience higher reduction in the number of inter-module dependencies and several complexity measures but increase size more than the bottom 95 percent. This indicates that measuring the impact of refactoring requires multi-dimensional assessment.
The plant phosphoinositide system.

The discovery of the mammalian phosphoinositide signalling system has led to tremendous progress in the understanding of how extracellular signals are perceived by cells and converted into intracellular responses. This advance has naturally led to the question of whether similar types of signalling systems also are present in other eukaryotes. Three often stated differences between plant and animal cells are: the limited discernable movement of plants, the very wide variety of environmental signals plant cells need to respond to and the continuous organogenesis of plant tissues. The presence of the plant cell wall means that movement of cells within tissues is very limited. The considerable constraint upon plant cells by their walls is likely to influence significantly both the need and ability to perceive, and respond to, extracellular signals. It may also be one of the determining factors for the developmental plasticity offered to plants by the potential for perpetual organogenesis-a feature dominant in sessile organisms. If an overall consideration is made of both the major types of signals that plants need to respond to, and of the responses they display, it nevertheless becomes clear that many features are similar to those found in animals, and current evidence suggests that several of the basic molecular aspects of cellular signal transduction have been highly conserved during evolution and are shared by most, if not all, eukaryotes. One example is the use of Ca2l as a second messenger.
Optimal Design of Composite Stiffened Panel with Cohesive Elements using Micro-Genetic Algorithm

A postbuckling analysis for composite stiffened structures is a representative nonlinear analysis, but is difficult to obtain analysis results and a lengthy computational time is required. In this study, an accurate and realistic postbuckling model for a stiffened composite panel is made, and optimization module is studied. In order to predict the realistic behavior in the postbuckling region, cohesive elements were introduced to the analysis model to account for skin-stiffener debonding. The global behaviors and failure loads of the analysis results were found to be similar to the experimental results. Based on this analysis model, the optimal layer design of a composite stiffened panel up to postbuckling failure was performed using micro genetic algorithm. The optimized result showed a higher maximum failure load in the postbuckling region.
The Role of Shear-Induced Transforming Growth Factor-&bgr; Signaling in the Endothelium

Objective—Vascular endothelial cells (ECs) are continuously exposed to blood flow that contributes to the maintenance of vessel structure and function; however, the effect of hemodynamic forces on transforming growth factor-&bgr; (TGF-&bgr;) signaling in the endothelium is poorly described. We examined the potential role of TGF-&bgr; signaling in mediating the protective effects of shear stress on ECs. Approach and Results—Human umbilical vein ECs (HUVECs) exposed to shear stress were compared with cells grown under static conditions. Signaling through the TGF-&bgr; receptor ALK5 was inhibited with SB525334. Cells were examined for morphological changes and harvested for analysis by real-time polymerase chain reaction, Western blot analysis, apoptosis, proliferation, and immunocytochemistry. Shear stress resulted in ALK5-dependent alignment of HUVECs as well as attenuation of apoptosis and proliferation compared with static controls. Shear stress led to an ALK5-dependent increase in TGF-&bgr;3 and Krüppel-like factor 2, phosphorylation of endothelial NO synthase, and NO release. Addition of the NO donor S-nitroso-N-acetylpenicillamine rescued the cells from apoptosis attributable to ALK5 inhibition under shear stress. Knockdown of TGF-&bgr;3, but not TGF-&bgr;1, disrupted the HUVEC monolayer and prevented the induction of Krüppel-like factor 2 by shear. Conclusions—Shear stress of HUVECs induces TGF-&bgr;3 signaling and subsequent activation of Krüppel-like factor 2 and NO, and represents a novel role for TGF-&bgr;3 in the maintenance of HUVEC homeostasis in a hemodynamic environment.
Numerical simulation of reaction injection molding with polyurethane foam

In this study, numerical approach for simulation of mold filling is presented. Polyurethane foam formation includes several complex phenomena such as chemical reactions, heat generation and blowing agent evaporation. Foam properties are variable during formation, foam viscosity increases and conductivity reduces. Foam phase is considered compressible and two phases are immiscible. Foam front will be captured by volume of fluid and appropriate governing equations will be implemented in OpenFOAM. This study prepares a numerical model to reduce several experimental runs with expensive prototypes for mold design.
Using Image Attributes for Human Identification Protocols

A secure human identification protocol aims at authenticating human users to a remote server when even the users' inputs are not hidden from an adversary. Recently, the authors proposed a human identification protocol in the RSA Conference 2007, which is loosely based on the ability of humans to efficiently process an image. The advantage being that an automated adversary is not effective in attacking the protocol without human assistance. This paper extends that work by trying to solve some of the open problems. First, we analyze the complexity of defeating the proposed protocols by quantifying the workload of a human adversary. Secondly, we propose a new construction based on textual CAPTCHAs (Reverse Turing Tests) in order to make the generation of automated challenges easier. We also present a brief experiment involving real human users to find out the number of possible attributes in a given image and give some guidelines for the selection of challenge questions based on the results. Finally, we analyze the previously proposed protocol in detail for the relationship between the secrets. Our results show that we can construct human identification protocols based on image evaluation with reasonably ``quantified'' security guarantees based on our model.
On region merging: the statistical soundness of fast sorting, with applications

This work explores a statistical basis for a process often described in computer vision: image segmentation by region merging following a particular order in the choice of regions. We exhibit a particular blend of algorithmics and statistics whose error is, as we formally show, close to the best possible. This approach can be approximated in a very fast segmentation algorithm for processing images described using most common numerical feature spaces. Simple modifications of the algorithm allow us to cope with occlusions and/or hard noise levels. Experiments on grey-level and color images, obtained with a short C-code, display the quality of the segmentations obtained.
A Novel HTS Flux-Reversal Linear Permanent Magnet Machine With a Lower Number of Mover Teeth and Higher Thrust Density

Compared to the conventional flux-reversal linear permanent magnet machine (FRLPM), a novel high-temperature superconducting (HTS) FRLPM with a lower number of mover teeth and higher thrust density is proposed in this paper. In order to explain the superiority of the proposed machine, the back electromotive force of the regular FRLPM, the lower mover teeth number FRLPM (LMT-FRLPM), and the LMT-FRLPM with HTS bulks (HTS LMT-FRLPM) are derived in this paper. The analytical results are validated by the finite-element method (FEM). Furthermore, the thrust performances of the regular FRLPM, LMT-FRLPM, and HTS LMT-FRLPM at rated load are also calculated by the FEM, which verifies the outstanding thrust performances of the proposed HTS LMT-FRLPM.
Adaptive sex differences in growth of pre-ovulation oocytes in a passerine bird

Maternal modification of offspring sex in birds has strong fitness consequences, however the mechanisms by which female birds can bias sex of their progeny in close concordance with the environment of breeding are not known. In recently established populations of house finches (Carpodacus mexicanus), breeding females lay a sex-biased sequence of eggs when ambient temperature causes early onset of incubation. We studied the mechanisms behind close association of incubation and sex-determination strategies in this species and discovered that pre-ovulation oocytes that produce males and females differed strongly in the temporal patterns of proliferation and growth. In turn, sex-specific exposure of oocytes to maternal secretion of prolactin and androgens produced distinct accumulation of maternal steroids in oocyte yolks in relation to oocyte proliferation order. These findings suggest that sex difference in oocyte growth and egg-laying sequence is an adaptive outcome of hormonal constraints imposed by the overlap of early incubation and oogenesis in this population, and that the close integration of maternal incubation, oocytes' sex-determination and growth might be under control of the same hormonal mechanism. We further document that population establishment and the evolution of these maternal strategies is facilitated by their strong effects on female and offspring fitness in a recently established part of the species range.