Miracle-dz/UniFAR-FTUs huggingface dataset:
Intestinal alkaline phosphatase has beneficial effects in mouse models of chronic colitis

Background: The brush border enzyme intestinal alkaline phosphatase (IAP) functions as a gut mucosal defense factor and is protective against dextran sulfate sodium (DSS)‐induced acute injury in rats. The present study evaluated the potential therapeutic role for orally administered calf IAP (cIAP) in two independent mouse models of chronic colitis: 1) DSS‐induced chronic colitis, and 2) chronic spontaneous colitis in Wiskott‐Aldrich Syndrome protein (WASP)‐deficient (knockout) mice that is accelerated by irradiation. Methods: The wildtype (WT) and IAP knockout (IAP‐KO) mice received four cycles of 2% DSS ad libitum for 7 days. Each cycle was followed by a 7‐day DSS‐free interval during which mice received either cIAP or vehicle in the drinking water. The WASP‐KO mice received either vehicle or cIAP for 6 weeks beginning on the day of irradiation. Results: Microscopic colitis scores of DSS‐treated IAP‐KO mice were higher than DSS‐treated WT mice (52 ± 3.8 versus 28.8 ± 6.6, respectively, P < 0.0001). cIAP treatment attenuated the disease in both groups (KO = 30.7 ± 6.01, WT = 18.7 ± 5.0, P < 0.05). In irradiated WASP‐KO mice cIAP also attenuated colitis compared to control groups (3.3 ± 0.52 versus 6.2 ± 0.34, respectively, P < 0.001). Tissue myeloperoxidase activity and proinflammatory cytokines were significantly decreased by cIAP treatment. Conclusions: Endogenous IAP appears to play a role in protecting the host against chronic colitis. Orally administered cIAP exerts a protective effect in two independent mouse models of chronic colitis and may represent a novel therapy for human IBD. (Inflamm Bowel Dis 2011)
Mg‐PSZ Reinforced TRIP‐Steel MMCs – In Situ CT Investigations of Cruciform Samples under Compressive Loading

Mechanical in situ CT investigations on cruciform members of square‐celled Mg‐PSZ reinforced TRIP‐steel honeycomb structures are presented. Furthermore, test series on a pure TRIP‐steel and MMC bulk material with 10 vol% Mg‐PSZ as well as macro‐scale compression tests on honeycomb structures are performed under quasi‐static loading. The measured stress–strain curves of the cruciform columns are related to their buckling and failure behaviour. The mechanical and structural characteristics of the cell wall node elements are compared to the damage mechanisms of the complete honeycombs. Differences in the damage patterns between the pure TRIP‐steel and the MMC are demonstrated. The phase transformation effect in the Mg‐PSZ particles is pointed out based on EBSD and EDX measurements.
Modeling the mighty maple

A method is presented for representing botanical trees, given three-dimensional points and connections. Limbs are modeled as generalized cylinders whose axes are space curves that interpolate the points. A free-form surface connects branching limbs. "Blobby" techniques are used to model the tree trunk as a series of non-circular cross sections. Bark is simulated with a bump map digitized from real world bark; leaves are textures mapped onto simple surfaces.
Microhardness of pore walls in porous titanium prepared with novel powder metallurgy

Abstract Owing to the adjustable mechanical properties, porous titanium as bone substitute can reduce the effect of stress shielding. Microhardness and its distribution on pore walls are good factors to determine the microstructure of porous titanium related to the wear and corrosion resistance in vivo. In the procedure of novel powder metallurgy, porous titanium was prepared after space holders as the second phase were removed during heat treatment. Through changing the compaction pressure, sintering temperature or holding time, porous bodies with different sintering index were prepared. The effect of the friction between die wall and powders or between powders themselves can be reduced by changing the compaction pressure. The mean hardness H m and homogeneous index HI are used to determine the homogeneity of porous structures. In order to gain specimens with high sintering index or high microhardness, sintering at higher temperature is preferred for longer holding time.
Limited reporting of major harms in studies of initial combination antiretroviral therapy: a systematic review

Objectives:Risk–benefit assessment of combination antiretroviral therapy (cART) requires consideration of all potential serious harms. Studies of initial cART may permit identification of associations between particular regimens and uncommon harms, but only if comprehensively reported in the public domain. Design:Study-based, systematic review of published initial cART studies (in adult patients) for completeness of serious harms reporting. Methods:Electronic databases, abstracts, and regulatory/sponsor reports were searched (1 January 1996 – 31 December 2012). Reporting of pre-specified harms – deaths, new/recurrent AIDS events, serious non-AIDS events (2010 INSIGHT classification) and serious adverse events (SAEs) – were assessed as the proportion of studies providing data (reporting frequency). Pharmaceutical sponsors were approached for unreported data. Results:103 studies (86% randomized, 54% industry-sponsored) were included. Deaths, AIDS events, serious non-AIDS events and SAEs were reported for 85 (83%), 55 (53%), 26 (25%) and 43 (42%) studies, respectively. Deaths were better reported for academic than industry-sponsored studies (91 vs. 75%; P = 0.03); the converse applied for SAEs (26 vs. 55%; P = 0.002). SAEs were better reported for randomized than cohort studies (46 vs. 14%; P = 0.03), and for phase 3 than phase 2 or 4 studies (58 vs. 32 and 29%, respectively; P = 0.02). SAE reporting increased over time [&rgr; = 0.704, P = 0.002 (Spearman)]. Unreported data acquired for 34 (61%) of 56 industry-sponsored studies improved ascertainment in these studies to between 82 and 100% (P < 0.001). Conclusion:Public domain reporting of serious harms for initial cART studies is limited. Insufficient data exist to determine if particular ART drugs/regimens are associated with most serious harms.
Harmonization of PCR-based detection of intestinal pathogens: experiences from the Dutch external quality assessment scheme on molecular diagnosis of protozoa in stool samples

Abstract Background: Real-time PCR methods are increasingly used in routine patient care settings not only to determine the presence or absence of pathogens in patient materials, but also to obtain semiquantitative results to estimate the pathogen load. However, it is so far unknown how well these methods are harmonized among different laboratories. Methods: Sets of stool samples were distributed three to four times per year to ca. 25–40 participating laboratories within the European Union as part of an external quality assessment scheme (EQAS) for the detection of gastrointestinal protozoa. This paper presents the results obtained over a 3-year period for Entamoeba histolytica, Entamoeba dispar, Giardia lamblia, Cryptosporidium species and Dientamoeba fragilis. Results: Although both false-positive and false-negative results were reported, the overall sensitivity and specificity were high. The substantial differences in the quantitative output of the real-time PCR assays could be traced back to differences in DNA isolation procedures between different laboratories. Conclusions: Participation in an EQAS proved to be important as it provides information on how the real-time PCR methods used by the participant compares to the generally reported results and indicates how procedures could be improved. Semiquantitative results of real-time PCR methods are not exchangeable between laboratories as long as the diagnostic procedures are not harmonized. Intralaboratory comparison of semiquantitative real-time PCR results seems only possible by the use of calibration curves derived from well-validated standards in clinical material and not by spiking solutions with purified DNA.
Possible mechanisms of postprandial physiological alterations following flavan 3-ol ingestion

Foods rich in flavan 3-ols are known to prevent cardiovascular diseases by reducing metabolic syndrome risks, such as hypertension, hyperglycemia, and dyslipidemia. However, the mechanisms involved in this reduction are unclear, particularly because of the poor bioavailability of flavan 3-ols. Recent metabolome analyses of feces produced after repeated ingestion of foods rich in flavan 3-ols may provide insight into the chronic physiological changes associated with the intake of flavan 3-ols. Substantial postprandial changes have been reported after flavan 3-ol ingestion, including hemodynamic and metabolic changes as well as autonomic and central nervous alterations. Taken together, the evidence suggests that flavan 3-ols have both postprandial and chronic effects, which could involve different or common mechanisms. In general, the accumulation of acute functional changes induces chronic physiological alteration. Therefore, this review highlights the postprandial action of flavan 3-ols in order to address the yet unknown mechanism(s) for their physiological function.
Structure learning for natural language processing

We applied a structure learning model, Max-Margin Structure (MMS), to natural language processing (NLP) tasks, where the aim is to capture the latent relationships within the output language domain. We formulate this model as an extension of multi-class Support VectorMachine (SVM) and present a perceptron-based learning approach to solve the problem. Experiments are carried out on two related NLP tasks: part-of-speech (POS) tagging and machine translation (MT), illustrating the effectiveness of the model.
Slide-based laser scanning cytometry.

OBJECTIVE To show that laser scanning cytometry (LSCM) can provide data equivalent to flow cytometry (FCM) data and furnish a number of benefits, including cell relocation for visualization and several additional measurement features that may make it more suitable than FCM for pathology laboratories. STUDY DESIGN A laser scanning cytometer, the LSC, was developed. Several instruments, at sites in the United States and Japan during the last two years, provided data characterizing the instrument and its usefulness. RESULTS Data describing the sensitivity, precision, accuracy, utility of added measurement features and cell relocation capabilities of the LSC are presented. The data illustrate the applicability of the LSC to multiparameter DNA ploidy studies, resolution of phases of the cell cycle and cytogenetics. CONCLUSION Because it is microscope based and measures cells on a slide, not in a flow chamber; records the position of each cell on the slide; and has higher resolution, LSCM provides a number of benefits that may make it more suitable than FCM for pathology laboratories.
Energy-based design criterion of dissipative bracing systems for the seismic retrofit of frame structures

Direct sizing criteria represent useful tools in the design of dissipative bracing systems for the advanced seismic protection of existing frame structures, especially when incorporated dampers feature a markedly non-linear behaviour. An energy-based procedure is proposed herein to this aim, focusing attention on systems including fluid viscous devices. The procedure starts by assuming prefixed reduction factors of the most critical response parameters in current conditions, which are evaluated by means of a conventional elastic finite element analysis. Simple formulas relating the reduction factors to the equivalent viscous damping ratio of the dampers, ξeq, are proposed. These formulas allow calculating the ξeq values that guarantee the achievement of the target factors. Finally, the energy dissipation capacity of the devices is deduced from ξeq, finalizing their sizing process. A detailed description of the procedure is presented in the article, by distinguishing the cases where the prevailing structural deficiencies are represented by poor strength of the constituting members, from the cases having excessive horizontal displacements. A demonstrative application to the retrofit design of a reinforced concrete gym building is then offered to explicate the steps of the sizing criterion in practice, as well as to evaluate the enhancement of the seismic response capacities generated by the installation of the dissipative system.
Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis

ABSTRACT Anaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound “prokaryotic organelle” called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacterium Kuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway. IMPORTANCE Anammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures.
A Fast Recommender System for Cold User Using Categorized Items

In recent years, recommender systems (RS) provide a considerable progress to users. RSs reduce the cost of a user’s time in order to reach to desired results faster. The main issue of RSs is the presence of cold users which are less active and their preferences are more difficult to detect. The aim of this study is to provide a new way to improve recall and precision in recommender systems for cold users. According to the available categories of items, prioritization of the proposed items is improved and then presented to the cold user. The obtained results show that in addition to increased speed of processing, recall and precision have an acceptable improvement.
Dynamic attack detection and mitigation in IoT using SDN

With the advent of smart devices and lowering prices of sensing devices, adoption of Internet of Things (IoT) is gaining momentum. These IoT devices come with greater threat of being attacked or compromised that could lead to Denial of Service (DoS) and Distributed Denial of Service (DDoS). The high volume of IoT devices with high level of heterogeneity, magnify the possibility of security threats. So far, there is no protocol to guarantee the security of IoT devices. But to enable resilience, continuous monitoring is required along with adaptive decision making. These challenges can be addressed with the help of Software Defined Networking (SDN) which can effectively handle the security threats to the IoT devices in dynamic and adaptive manner without any burden on the IoT devices. In this paper, we propose an SDN-based secure IoT framework called SoftThings to detect abnormal behaviors and attacks as early as possible and mitigate as appropriate. Machine Learning is used at the SDN controller to monitor and learn the behavior of IoT devices over time. We have conducted experiments on Mininet emulator. Initial results show that this framework is capable to detect attacks on IoT with around 98% precision.
Realization of complex three-dimensional free-standing structures on silicon substrates using controllable underetching in a deep reactive ion etching

We report the realization of three-dimensional free-standing structures with high complexity on silicon substrates without using surface micromachining. The etching is feasible using the reactive ion etching method in which three gases are used in a two-step etching process. The passivation step is carried out by means of hydrogen, oxygen and sulfur-hexafluoride (SF6) while the etching step uses SF6 in a low-density capacitive-coupled radio frequency reactor. The overall etching process can be adjusted to arrive at three-dimensional structures with desired underetchings. The formation of partially and fully suspended structures is reported. Multi-level floated structures have been realized using this method.
An Improved MbICP Algorithm for Mobile Robot Pose Estimation

This paper presents an improved version of the metric-based iterative closest point algorithm to estimate robot poses by matching 2D laser scans with different overlapping percentages. Because of the greatly varied density distribution of realistic point clouds, a resampling method is used to accelerate the iteration process and protect the calculation of the rejection threshold from being distorted by reducing dense but unhelpful points. A new procedure that combines point-to-point and point-to-line metrics is used to determine the correct correspondence between partially overlapping scans, which maintains both efficiency and accuracy. In addition, a rejection threshold that is based on the MAD-from-median method is utilized to discard correspondences with large distances, which are likely to be incorrect. Experiments show that the improved algorithm is more accurate and robust than the standard algorithm with respect to the existence of non-overlapping areas, and testing demonstrates that it is valid in practice.
Alignment between Protostellar Outflows and Filamentary Structure

We present new Submillimeter Array (SMA) observations of CO(2–1) outflows toward young, embedded protostars in the Perseus molecular cloud as part of the Mass Assembly of Stellar Systems and their Evolution with the SMA (MASSES) survey. For 57 Perseus protostars, we characterize the orientation of the outflow angles and compare them with the orientation of the local filaments as derived from Herschel observations. We find that the relative angles between outflows and filaments are inconsistent with purely parallel or purely perpendicular distributions. Instead, the observed distribution of outflow-filament angles are more consistent with either randomly aligned angles or a mix of projected parallel and perpendicular angles. A mix of parallel and perpendicular angles requires perpendicular alignment to be more common by a factor of ∼3. Our results show that the observed distributions probably hold regardless of the protostar’s multiplicity, age, or the host core’s opacity. These observations indicate that the angular momentum axis of a protostar may be independent of the large-scale structure. We discuss the significance of independent protostellar rotation axes in the general picture of filament-based star formation.
Upper and lower bounds for dynamic data structures on strings

We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give both conditional and unconditional lower bounds for variants of exact matching with wildcards, inner product, and Hamming distance computation via a sequence of reductions. As an example, we show that there does not exist an $O(m^{1/2-\varepsilon})$ time algorithm for a large range of these problems unless the online Boolean matrix-vector multiplication conjecture is false. We also provide nearly matching upper bounds for most of the problems we consider.
Diagnostic accuracy of optical coherence tomography for diagnosing glaucoma: secondary analyses of the GATE study

Background/Aims To assess the diagnostic performance of retinal nerve fibre layer (RNFL) data of optical coherence tomography (OCT) for detecting glaucoma. Methods Secondary analyses of a prospective, multicentre diagnostic study (Glaucoma Automated Tests Evaluation (GATE)) referred to hospital eye services in the UK were conducted. We included data from 899 of 966 participants referred to hospital eye services with suspected glaucoma or ocular hypertension. We used both eyes’ data and logistic regression-based receiver operator characteristics analysis to build a set of models to measure the sensitivity and specificity of the average and inferior quadrant RNFL thickness data of OCT. The reference standard was expert clinician examination including automated perimetry. The main outcome measures were sensitivity at 0.95 specificity and specificity at 0.95 sensitivity and the corresponding RNFL thickness thresholds. We explored the possibility of accuracy improvement by adding measures of within-eye and between-eye variation, scan quality, intraocular pressure (IOP) and age. Results Glaucoma was diagnosed in at least one eye in 17% of participants. Areas under the curve were between 0.83 and 0.88. When specificity was fixed at 0.95, the sensitivity was between 0.38 and 0.55, and the highest values were reached with models including the inferior quadrant rather than the average RNFL thickness. Fixing sensitivity at 0.95, the specificity was between 0.36 and 0.58. The addition of age, refractive error, IOP or within-subject variation did not improve the accuracy. Conclusion RNFL thickness data of OCT can be used as a diagnostic test, but accuracy estimates remain moderate even in exploratory multivariable modelling of aiming to improve accuracy.
Reducing Interruptions at Work: A Large-Scale Field Study of FlowLight

Due to the high number and cost of interruptions at work, several approaches have been suggested to reduce this cost for knowledge workers. These approaches predominantly focus either on a manual and physical indicator, such as headphones or a closed office door, or on the automatic measure of a worker's interruptibilty in combination with a computer-based indicator. Little is known about the combination of a physical indicator with an automatic interruptibility measure and its long-term impact in the workplace. In our research, we developed the FlowLight, that combines a physical traffic-light like LED with an automatic interruptibility measure based on computer interaction data. In a large-scale and long-term field study with 449 participants from 12 countries, we found, amongst other results, that the FlowLight reduced the interruptions of participants by 46%, increased their awareness on the potential disruptiveness of interruptions and most participants never stopped using it.