Miracle-dz/UniFAR-FTUs huggingface dataset:
A Glucurono(arabino)xylan Synthase Complex from Wheat Contains Members of the GT43, GT47, and GT75 Families and Functions Cooperatively1[C][W][OA]

Glucuronoarabinoxylans (GAXs) are the major hemicelluloses in grass cell walls, but the proteins that synthesize them have previously been uncharacterized. The biosynthesis of GAXs would require at least three glycosyltransferases (GTs): xylosyltransferase (XylT), arabinosyltransferase (AraT), and glucuronosyltransferase (GlcAT). A combination of proteomics and transcriptomics analyses revealed three wheat (Triticum aestivum) glycosyltransferase (TaGT) proteins from the GT43, GT47, and GT75 families as promising candidates involved in GAX synthesis in wheat, namely TaGT43-4, TaGT47-13, and TaGT75-4. Coimmunoprecipitation experiments using specific antibodies produced against TaGT43-4 allowed the immunopurification of a complex containing these three GT proteins. The affinity-purified complex also showed GAX-XylT, GAX-AraT, and GAX-GlcAT activities that work in a cooperative manner. UDP Xyl strongly enhanced both AraT and GlcAT activities. However, while UDP arabinopyranose stimulated the XylT activity, it had only limited effect on GlcAT activity. Similarly, UDP GlcUA stimulated the XylT activity but had only limited effect on AraT activity. The [14C]GAX polymer synthesized by the affinity-purified complex contained Xyl, Ara, and GlcUA in a ratio of 45:12:1, respectively. When this product was digested with purified endoxylanase III and analyzed by high-pH anion-exchange chromatography, only two oligosaccharides were obtained, suggesting a regular structure. One of the two oligosaccharides has six Xyls and two Aras, and the second oligosaccharide contains Xyl, Ara, and GlcUA in a ratio of 40:8:1, respectively. Our results provide a direct link of the involvement of TaGT43-4, TaGT47-13, and TaGT75-4 proteins (as a core complex) in the synthesis of GAX polymer in wheat.
Associations of age, adiposity, alcohol intake, menstrual status, and estrogen therapy with high-density lipoprotein subclasses.

We used nondenaturing polyacrylamide gradient gel electrophoresis to examine the associations of age, adiposity, alcohol intake, and exogenous estrogen with high-density lipoprotein (HDL) subclasses in 427 members of 51 principally Mormon kindreds. The absorbency of protein stain was used as an index of mass concentrations at intervals of 0.01 nm within five HDL subclasses: HDL3c (7.2 to 7.8 nm), HDL3b (7.8 to 8.2 nm), HDL3a (8.2 to 8.8 nm), HDL2a (8.8 to 9.7 nm), and HDL2b (9.7 to 12 mm). Age and alcohol intake were obtained from questionnaires, and body mass index was computed from clinic measurements as weight (kg)/height (m)2. The results suggest that HDL3b concentrations were higher after menopause than before. Adult men (> or = 18 years old) had significantly higher HDL3c and HDL3b and significantly lower HDL2b and HDL2a levels than younger boys. Compared with the women, adult men had higher levels of HDL3c and HDL3b and lower levels of HDL2b, HDL2a, and larger-diameter HDL3a particles. There were no significant differences between the HDL profiles of women and younger boys, suggesting that divergence in HDL occurs during puberty. Eighty-eight percent of the increase in HDL associated with estrogen replacement in postmenopausal women occurred within HDL3a and HDL2a. Reported alcohol intake in adult men correlated with two HDL regions: one within the HDL2b region and a second within the HDL3a/2a region, whereas in women the positive correlation between alcohol and HDL levels was within the HDL2b region only. In both men and premenopausal adult women, increasing levels of body mass index were associated with higher levels of HDL3b and lower levels of HDL2b. (ABSTRACT TRUNCATED AT 250 WORDS)
Evaluating the Effectiveness of Conservation on Mangroves: A Remote Sensing-Based Comparison for Two Adjacent Protected Areas in Shenzhen and Hong Kong, China

Mangroves are ecologically important ecosystems and globally protected. The purpose of this study was to evaluate the effectiveness of mangrove conservation efforts in two adjacent protected areas in China that were under the management policies of the Ramsar Convention (Mai Po Marshes Nature Reserve (MPMNR), Hong Kong) and China’s National Nature Reserve System (Futian Mangrove National Nature Reserve (FMNNR), Shenzhen). To achieve this goal, eleven Landsat images were chosen and classified, areal extent and landscape metrics were then calculated. The results showed that: from 1973–2015, the areal extent of mangroves in both reserves increased, but the net change for the MPMNR (281.43 hm2) was much higher than those of the FMNNR (101.97 hm2). In general, the area-weighted centroid of the mangroves in FMNNR moved seaward by approximately 120 m, whereas in the MPMNR, the centroid moved seaward even farther (410 m). Although both reserves saw increased integrality and connectivity of the mangrove patches, the patches in the MPMNR always had higher integrality than those in the FMNNR. We concluded that the mangroves in the MPMNR were more effectively protected than those in the FMNNR. This study may provide assistance to the formulation of generally accepted criteria for remote sensing-based evaluation of conservation effectiveness, and may facilitate the development of appropriate mangrove forest conservation and management strategies in other counties.
ISOLATION, CHARACTERIZATION, AND DISTRIBUTION OF ACID MUCOPOLYSACCHARIDES IN RABBIT LEUCOCYTES

Acid mucopolysaccharides have been extracted from whole rabbit polymorphonuclear leucocytes and from the cytoplasmic granules of these cells. The leucocyte acid mucopolysaccharides can be separated into two fractions by the solubility of their CPC complexes in solutions of differing salt concentration. One of these fractions appears to be identical with hyaluronic acid; the other appears to be an atypical chondroitin sulfate. On both a dry weight and total protein basis the polymorphonuclear leucocyte granule contains approximately 2.6 times as much acid mucopolysaccharide as does the whole cell. Hyaluronic acid is concentrated in the granules in particular; its function is unknown. These results do not indicate that all lysosomes contain abundant acid mucopolysaccharides, for no detectable carbohydrate of this class could be extracted from lysosome-rich alveolar macrophages.
Enterprise search through automatic synthesis of tag clouds

In a large organization, finding the right expert who can provide knowledge needed in a particular work context is critical to achieving higher levels of quality and productivity especially in the present scenario of a rapidly evolving technology and business environment where knowledge plays a vital role in value creation. Previous approaches to the problem of reliably finding experts in an area of knowledge focus on mapping employees to their knowledge based primarily on voluntary data inputs by users and minimally supplemented by data derived from enterprise systems. However, the generation of employee profiles through inputs is usually not based on a controlled vocabulary and therefore results in poor precision and recall in expertise search in addition to posing difficulties in integration with content search. In this paper, a novel approach that addresses some of these limitations is described wherein tag clouds for members are automatically generated from enterprise data. The paper also outlines the use of such tag clouds in an integrated search system that aims to provide an optimal set of experts as well as relevant content corresponding to a knowledge need.
Congenital cholesteatoma

Since the late 1970s, the author has had the opportunity to prospectively study, document, and surgically manage 40 cases of congenital cholesteatoma. All cases met strict criteria for inclusion in the study, all were surgically and pathologically confirmed, and were definitively followed. During that same period, 38 cases were managed by other members of the otolaryngology department.
slab: smart labeling of family photos through an interactive interface

A novel technique for semi-automatic photo annotation is proposed and evaluated. The technique, sLab, uses face processing algorithms and a simplified user interface for labeling family photos. A user study compared our system with two others. One was Adobe Photoshop Element. The other was an in-house implementation of a face clustering interface recently proposed in the research community. Nine participants performed an annotation task with each system on faces extracted from a set of 150 images from their own family photo albums. As the faces were all well known to participants, accuracy was near perfect with all three systems. On annotation time, sLab was 25% faster than Photoshop Element and 16% faster than the face clustering interface.
Bcl2 as a surrogate prognostic and predictive marker in triple-negative breast cancer.

1024 Background: TNBC patients have a relatively poor prognosis and the optimal choice of chemotherapy for this subgroup has not yet been defined. Studies have shown TNBC is a heterogeneous group of tumours and certain subgroups of TNBC could benefit from neoadjuvant therapy. In this study, we hypothesized that Bcl2 immunohistochemical expression could accurately stratified TNBC into low- and high risk patients and predict their response to chemotherapy. METHODS Three independent series of BC were immunohistochemically profiled for Bcl2; a) 296 and 153 of primary TNBC and non TNBC respectively, in which adjuvant CMF chemotherapy was given, b) 63 TNBC and 160 non-TNBC locally advanced primary BC treated with anthracycline-based chemotherapy c) 31 TNBC and 209 non-TNBC in which all patients were primarily treated with surgery followed by anthracycline-based chemotherapy. RESULTS In patients with TNBC who received CMF chemotherapy, multivariate Cox regression models demonstrated that Bcl2 was significantly associated with patient outcome; TNBC/ low Bcl2 tumours were associated with a three-fold increased risk of death ((p=0.000039) and recurrence ( p =0.0001) compared to TNBC/high Bcl2 tumours. In patients with BC treated with neoadjuvant anthracycline based chemotherapy, 18/63 (28%) TNBC achieved a pathological complete response (pCR) vs. 17/144 (12%) of non-TNBC (p=0.006). 42% of TNBC with low level of Bcl2 achieved pCR compared with 11% of TNBC with high Bcl2 expression (p=0.02). After neoadjuvant treatment, patients with TNBC with low and high Bcl2 expression had similar clinical outcome. CONCLUSIONS In patients with TNBC who received CMF chemotherapy, Bcl2 expression reclassified patients into two groups: low risk (Bcl2+) versus high risk (Bcl2-) of BC mortality and recurrence. Anthracycline based neoadjuvant therapy is an effective treatment for TNBC with low levels of Bcl2 expression and is associated with a higher pCR rate. Adding Bcl2 to the panel of TNBC phenotype markers could help guide treatment decisions in this group of patients and ultimately lead to better patient outcome.
Hepatitis C Virus Nonstructural 5A Protein (HCV-NS5A) Inhibits Hepatocyte Apoptosis through the NF-κb/miR-503/bcl-2 Pathway

The nonstructural protein 5A (NS5A) encoded by the human hepatitis C virus (HCV) RNA genome is a multifunctional phosphoprotein. To analyse the influence of NS5A on apoptosis, we established an Hep-NS5A cell line (HepG2 cells that stably express NS5A) and induced apoptosis using tumour necrosis factor (TNF)-α. We utilised the MTT assay to detect cell viability, real-time quantitative polymerase chain reaction and Western blot to analyse gene and protein expression, and a luciferase reporter gene experiment to investigate the targeted regulatory relationship. Chromatin immunoprecipitation was used to identify the combination of NF-κB and miR-503. We found that overexpression of NS5A inhibited TNF-αinduced hepatocellular apoptosis via regulating miR-503 expression. The cell viability of the TNF-α induced Hep-mock cells was significantly less than the viability of the TNF-α induced Hep-NS5A cells, which demonstrates that NS5A inhibited TNF-α-induced HepG2 cell apoptosis. Under TNF-α treatment, miR-503 expression was decreased and cell viability and B-cell lymphoma 2 (bcl-2) expression were increased in the Hep-NS5A cells. Moreover, the luciferase reporter gene experiment verified that bcl-2 was a direct target of miR-503, NS5A inhibited TNF-α-induced NF-κB activation and NF-κB regulated miR-503 transcription by combining with the miR-503 promoter. After the Hep-NS5A cells were transfected with miR-503 mimics, the data indicated that the mimics could reverse TNF-α-induced cell apoptosis and blc-2 expression. Collectively, our findings suggest a possible molecular mechanism that may contribute to HCV treatment in which NS5A inhibits NF-κB activation to decrease miR-503 expression and increase bcl-2 expression, which leads to a decrease in hepatocellular apoptosis.
Natural Language Processing: many questions, no answers

Computational Linguistics, as a subfield of Linguistics, or Natural Language Processing (NLP), as a subfield of Artificial Intelligence (two research areas that nowadays can be safely considered as merged) concentrate on the “study of computer systems for understanding and generating natural language” [10], in order to develop “a computational theory of language, using the notions of algorithms and data structures from Computer Science” [2]. Typical problems for these research fields are [2]: How is the structure of sentences identified? How can knowledge and reasoning be modelled? How can language be used to accomplish specific tasks? In more recent times, these problems are being studied not so much from the traditional linguistic viewpoint (syntax and semantics) but with a focus on problems of belief models, planning processes, and functional properties of both discourse and text. I will focus my discussion on three problems in NLP. The choice of the problems to address is admittedly biased by my personal research interests, but I do believe that these problems in particular can (and should) most benefit from considerations coming from the Argumentation theory field. This paper is merely an attempt to build up a canvas of issues, on which further discussion is needed.
A Mechanism for the Major Histocompatibility Complex–linked Resistance to Autoimmunity

Certain major histocompatibility complex (MHC) class II haplotypes encode elements providing either susceptibility or dominant resistance to the development of spontaneous autoimmune diseases via mechanisms that remain undefined. Here we show that a pancreatic beta cell–reactive, I-Ag7–restricted, transgenic TCR that is highly diabetogenic in nonobese diabetic mice (H-2g7) undergoes thymocyte negative selection in diabetes-resistant H-2g7/b, H-2g7/k, H-2g7/q, and H-2g7/nb1 NOD mice by engaging antidiabetogenic MHC class II molecules on thymic bone marrow–derived cells, independently of endogenous superantigens. Thymocyte deletion is complete in the presence of I-Ab, I-Ak + I-Ek or I-Anb1 + I-Enb1 molecules, partial in the presence of I-Aq or I-Ak molecules alone, and absent in the presence of I-As molecules. Mice that delete the transgenic TCR develop variable degrees of insulitis that correlate with the extent of thymocyte deletion, but are invariably resistant to diabetes development. These results provide an explanation as to how protective MHC class II genes carried on one haplotype can override the genetic susceptibility to an autoimmune disease provided by allelic MHC class II genes carried on a second haplotype.
Ballistic Inas Nanowire Transistors

Ballistic transport of electrons at room temperature in top-gated InAs nanowire (NW) transistors is experimentally observed and theoretically examined. From length dependent studies, the low-field mean free path is directly extracted as ∼150 nm. The mean free path is found to be independent of temperature due to the dominant role of surface roughness scattering. The mean free path was also theoretically assessed by a method that combines Fermi's golden rule and a numerical Schrö dinger−Poisson simulation to determine the surface scattering potential with the theoretical calculations being consistent with experiments. Near ballistic transport (∼80% of the ballistic limit) is demonstrated experimentally for transistors with a channel length of ∼60 nm, owing to the long mean free path of electrons in InAs NWs. T he scaling of electronic transistors for performance and density enhancement has been a major driving force behind the advancement of modern integrated circuit technology. As scaling becomes increasingly difficult, the electronics industry is moving toward unconventional materials and nonplanar structures. Both of these aspects are inherent in InAs nanowire (NW) transistors, making them a promising platform for future high-performance transistors. 1−5 One critical goal in scaling is to obtain ballistic devices, 6−9 where carriers are transported through the channel without undergoing scattering events. Ballistic devices are highly desirable as they offer minimal resistive voltage drop in the channel. Hence, ballistic operation presents the upper limit for the ON-state conductance of a transistor. InAs can potentially be used to fabricate ballistic transistors given its relatively long bulk electron mean free path (λ). 10 In this regard, detailed characterization of λ of InAs NWs is required, 11,12 especially as a function of subband population. Recently, we reported the direct observation of one-dimensional (1D) subbands in the electrical transfer characteristics of long-channel (L ∼ 8 μm) InAs NW field-effect transistors (FETs). 13 Given the large Bohr radius of InAs (∼34 nm), 14 strong quantization with prominent subband spacing is readily observed for sub-50 nm diameter NWs. The devices were passivated by a ZrO 2 dielectric that resulted in the lowering of surface disorder, and thereby allowing for the direct mapping of the transport in individual 1D subbands. Given that for a ballistic NW, each 1D subband contributes a quantum unit of conductance of G o = 2e 2 /h, 15 the transmission probability and thereby λ can be directly assessed from electrical measurements. Here, by fabricating InAs NW FETs with …
Localized electromagnetic analysis of RO PUFs

Among all proposed Physical Unclonable Functions (PUFs), those based on Ring Oscillators (ROs) are a popular solution for ASICs as well as for FPGAs. However, compared to other PUF architectures, oscillators emit electromagnetic (EM) signals over a relatively long run time, which directly reveal their unique frequencies. Previous work by Merli et al. exploited this fact by global EM measurements and proposed a countermeasure for their attack. In this paper, we first demonstrate that it is feasible to measure and locate the EM emission of a single tiny RO consisting of only three inverters, implemented within a single configurable logic block of a Xilinx Spartan-3A. Second, we present a localized EM attack for standard and protected RO PUFs. We practically investigate the proposed side-channel attack on a protected FPGA RO PUF implementation. We show that RO PUFs are prone to localized EM attacks and propose two countermeasures, namely, randomization of RO measurement logic and interleaved placement.
Hyperketonemia (Acetoacetate) Upregulates NADPH Oxidase 4 and Elevates Oxidative Stress, ICAM-1, and Monocyte Adhesivity in Endothelial Cells

Background/Aims: The incidence of developing microvascular dysfunction is significantly higher in type 1 diabetic (T1D) patients. Hyperketonemia (acetoacetate, β-hydroxybutyrate) is frequently found along with hyperglycemia in T1D. Whether hyperketonemia per se contributes to the excess oxidative stress and cellular injury observed in T1D is not known. Methods: HUVEC were treated with ketones in the presence or absence of high glucose for 24 h. NOX4 siRNA was used to specifically knockdown NOX4 expression in HUVEC. Results: Ketones alone or in combination with high glucose treatment cause a significant increase in oxidative stress, ICAM-1, and monocyte adhesivity to HUVEC. Using an antisense approach, we show that ketone induced increases in ROS, ICAM-1 expression, and monocyte adhesion in endothelial cells were prevented in NOX4 knockdown cells. Conclusion: This study reports that elevated levels of ketones upregulate NOX, contributing to increased oxidative stress, ICAM-1 levels, and cellular dysfunction. This provides a novel biochemical mechanism that elucidates the role of hyperketonemia in the excess cellular injury in T1D. New drugs targeting inhibition of NOX seems promising in preventing higher risk of complications associated with T1D.
A User-Oriented Approach to Music Information Retrieval

Search and retrieval of specific musical content (e.g. emotion, melody) has become an important aspect of system development but only little research is user-oriented. The success of music information retrieval technology primarily depends on both assessing and meeting the needs of its users. Potential users of music information retrieval systems, however, draw upon various ways of expressing themselves. But, who are the potential users of MIR systems and how would they describe music qualities? High-level concepts contribute to the definition of meaning in music. How can we measure meaning and emotion in music? How can we define the higher-order understanding of features of music that the average users share? Information on listenerA¢â‚¬â„¢s perception of qualities of music is needed to make automated access to music content attractive to system users. The emphasis of our investigation is on a user-oriented approach to the semantic description of music. We report the results of an experiment that explores how users perceive affects in music, and what structural descriptions of music best characterize their understanding of music expression. 79 potential users of music information retrieval systems rated different sets of adjectives, while they were listening to 160 pieces of real music. The subject group (79) was recruited amongst 774 participants in a large survey on the music background, habits and interests, preferred genres, taste and favourite titles of people who are willing to use interactive music systems. Moreover, the stimuli used reflected the musical taste of the average participant in the large survey (774). The study reveals that perceived qualities of music are affected by the profile of the user. Significant subject dependencies are found for age, music expertise, musicianship, broadness of taste and familiarity with classical music. Furthermore, interesting relationships are discovered between expressive and structural features. Analyses show that the targeted population most unanimously agrees on loudness and tempo, whilst less unanimity was found for timbre and articulation. Finally, our findings are tested and validated by means of a demo of a semantic music recommender system prototype that supports the querying of a music database by semantic descriptors for affect, structure and motion. The system, that recommends music from a relational database containing the quality ratings provided by the participants, illustrates the potential of a user-dependent and emotion-based retrieval of music.