Miracle-dz/UniFAR-FTUs huggingface dataset:
The hydrological legacy of deforestation on global wetlands

Increased catchment erosion and nutrient loading are commonly recognized impacts of deforestation on global wetlands. In contrast, an increase in water availability in deforested catchments is well known in modern studies but is rarely considered when evaluating past human impacts. We used a Budyko water balance approach, a meta-analysis of global wetland response to deforestation, and paleoecological studies from Australasia to explore this issue. After complete deforestation, we demonstrated that water available to wetlands increases by up to 15% of annual precipitation. This can convert ephemeral swamps to permanent lakes or even create new wetlands. This effect is globally significant, with 9 to 12% of wetlands affected, including 20 to 40% of Ramsar wetlands, but is widely unrecognized because human impact studies rarely test for it. Ancient Australasian deforestations created wetlands where none previously existed. Impacts of deforestation on wetlands Deforestation worldwide may be causing an increase in the extent of wetlands. Using a combination of different approaches, Woodward et al. show that ancient and more recent deforestation has resulted in major changes in global wetland hydrology. For example, in Australia and New Zealand, deforestation has created new wetlands or increased the water level in existing wetlands. Recognition of this effect has implications for landscape management: Reforestation programs in wetland catchments may have unintended consequences for vulnerable wetlands. Science, this issue p. 844
Measuring Self-care in Chronic Heart Failure: A Review of the Psychometric Properties of Clinical Instruments

Background:Improved self-care skills and behaviors are an important outcome of patient education and counseling. Both researchers and health professionals need to utilize instruments that are reliable and valid at measuring this outcome to advance our understanding as to the efficacy of clinical practice directed toward improving self-care. Objective:The aim of this study was to identify instruments that measure chronic heart failure (CHF) self-care and demonstrate their psychometric properties. Methods:A search of Medline, Cumulative Index to Nursing and Allied Health Literature, Medline, PsycArticles, Psychology and Behavioral Sciences Collection, and PsycINFO databases elucidated studies published between January 1980 and February 2009 that measure CHF self-care. The clinical instruments selected were disease-specific measures of CHF self-care behaviors that are promoted in best practice guidelines. Only instruments that reported estimates of reliability and validity were included in this review. Psychometric properties of the instruments were evaluated according to practice guidelines. Results:The literature search identified 14 instruments published in peer-reviewed journals that measured constructs that predict or correlate to self-care rather than self-care itself. Only 2 disease-specific measures of self-care were identified (Self-care Heart Failure Index [SCHFI] and European Heart Failure Self-care Behavior Scale [EHFScBS]) that have undergone rigorous psychometric testing in CHF populations. Five aspects of validity had been demonstrated with EHFScBS, and 6 aspects of validity had been demonstrated with SCHFI. Two of 3 aspects of reliability have been demonstrated in both instruments. Conclusion:Only 2 reliable and valid tools have been developed to specifically measure CHF self-care. Further use of these instruments in the research arena may reduce gaps in our understanding of CHF self-care and further shape clinical practice directed at improving it.
Comprehensive analysis of the ubiquitinome during oncogene-induced senescence in human fibroblasts

Oncogene-induced senescence (OIS) is an important tumor suppression mechanism preventing uncontrolled proliferation in response to aberrant oncogenic signaling. The profound functional and morphological remodelling of the senescent cell involves extensive changes. In particular, alterations in protein ubiquitination during senescence have not been systematically analyzed previously. Here, we report the first global ubiquitination profile of primary human cells undergoing senescence. We employed a well-characterized in vitro model of OIS, primary human fibroblasts expressing oncogenic RAS. To compare the ubiquitinome of RAS-induced OIS and controls, ubiquitinated peptides were enriched by immune affinity purification and subjected to liquid chromatography tandem mass spectrometry (LC-MS/MS). We identified 4,472 ubiquitination sites, with 397 sites significantly changed (>3 standard deviations) in senescent cells. In addition, we performed mass spectrometry analysis of total proteins in OIS and control cells to account for parallel changes in both protein abundance and ubiquitin levels that did not affect the percentage of ubiquitination of a given protein. Pathway analysis revealed that the OIS-induced ubiquitinome alterations mainly affected 3 signaling networks: eIF2 signaling, eIF4/p70S6K signaling, and mTOR signaling. Interestingly, the majority of the changed ubiquitinated proteins in these pathways belong to the translation machinery. This includes several translation initiation factors (eIF2C2, eIF2B4, eIF3I, eIF3L, eIF4A1) and elongation factors (eEF1G, eEF1A) as well as 40S (RPS4X, RPS7, RPS11 and RPS20) and 60S ribosomal subunits (RPL10, RPL11, RPL18 and RPL35a). In addition, we observed enriched ubiquitination of aminoacyl-tRNA ligases (isoleucyl-, glutamine-, and tyrosine-tRNA ligase), which provide the amino acid-loaded tRNAs for protein synthesis. These results suggest that ubiquitination affects key components of the translation machinery to regulate protein synthesis during OIS. Our results thus point toward ubiquitination as a hitherto unappreciated regulatory mechanism during OIS.
Vacuum system design and research for the Super SOR

The Super SOR is a third-generation VUV and soft X-ray light source that is being designed at the University of Tokyo. Eight insertion devices (ID) including a 27-m long undulator will be installed in the ring. Since the ring has a very narrow acceptance for beam loss by collision with residual gases, the vacuum system is required to achieve operation pressure of 10/sup -9/ Pa range in order to guarantee a long beam lifetime. According to the designed lattice, the pump location and pressure distribution was examined by a simple calculation. Beam chambers should be equipped with high pumping speed, especially in arc sections. The chambers for arc sections and insertion devices have been designed. Some vacuum components were manufactured for trial and examined.
A comparison between space-time video descriptors

The description of space-time patches is a fundamental task in many applications such as video retrieval or classification. Each space-time patch can be described by using a set of orthogonal functions that represent a subspace, for example a sphere or a cylinder, within the patch. In this work, our aim is to investigate the differences between the spherical descriptors and the cylindrical descriptors. In order to compute the descriptors, the 3D spherical and cylindrical Zernike polynomials are employed. This is important because both the functions are based on the same family of polynomials, and only the symmetry is different. Our experimental results show that the cylindrical descriptor outperforms the spherical descriptor. However, the performances of the two descriptors are similar.
Transitional B Cell Fate Is Associated with Developmental Stage-Specific Regulation of Diacylglycerol and Calcium Signaling upon B Cell Receptor Engagement1

Functional peripheral mature follicular B (FoB) lymphocytes are thought to develop from immature transitional cells in a BCR-dependent manner. We have previously shown that BCR cross-linking in vitro results in death of early transitional (T1) B cells, whereas late transitional (T2) B cells survive and display phenotypic characteristics of mature FoB cells. We now demonstrate that diacylglycerol (DAG), a lipid second messenger implicated in cell survival and differentiation, is produced preferentially in T2 compared with T1 B cells upon BCR cross-linking. Consistently, inositol 1,4,5-triphosphate is also produced preferentially in T2 compared with T1 B cells. Unexpectedly, the initial calcium peak appears similar in both T1 and T2 B cells, whereas sustained calcium levels are higher in T1 B cells. Pretreatment with 2-aminoethoxydiphenylborate, an inhibitor of inositol 1,4,5-triphosphate receptor-mediated calcium release, and verapamil, an inhibitor of L-type calcium channels, preferentially affects T1 B cells, suggesting that distinct mechanisms regulate calcium mobilization in each of the two transitional B cell subsets. Finally, BCR-mediated DAG production is dependent upon Bruton’s tyrosine kinase and phospholipase C-γ2, enzymes required for the development of FoB from T2 B cells. These results suggest that calcium signaling in the absence of DAG-mediated signals may lead to T1 B cell tolerance, whereas the combined action of DAG and calcium signaling is necessary for survival and differentiation of T2 into mature FoB lymphocytes.
Number of interleukin‐4‐ and interferon‐γ‐secreting human T cells reactive with tetanus toxoid and the mycobacterial antigen PPD or phytohemagglutinin: distinct response profiles depending on the type of antigen used for activation

The enzyme‐linked immunospot (ELISPOT) assay has been proven to be an efficient and sensitive method for the enumeration of single cells secreting antibodies or cytokines. Here we have used this method to determine the number of interleukin‐4 (IL‐4)‐ and interferon‐γ (IFN‐γ)‐producing cells in in vitro secondary responses to tetanus toxoid (TT) and the mycobacterial antigen (purified protein derivative; PPD) or the mitogen phytohemagglutinin (PHA). PHA‐induced IL‐4 and IFN‐γ secretion was well correlated suggesting polyclonal activation of cells. This was not the case with the specific antigens, where PPD preferentially induced IFN‐γ‐ and very few IL‐4‐producing cells, while TT‐induced both IL‐4 and IFN‐γ. These differences are probably a reflection of the types of immunity the two antigens induce, mycobacteria preferentially inducing a cell‐mediated T helper type 1 (Th 1) type of immunity, while immunity to tetanus is an antibody‐dependent, Th 2 type of response.
Bovine Osteochondral Tissues: A Questionable Model to Evaluate Mechanical Loading In Vitro

Articular cartilage exists within synovial joints to adsorb and distribute mechanical loads to the subchondral bone. Mechanical loading is one aspect of a wide range of microenvironmental stressors that contribute to the maintenance of articular cartilage. The aim of the current study was to characterize bovine osteochondral tissues and to assess their suitability to serve as a model for investigating the effects of mechanical loading on cartilage tissue in vitro using a custom-made reactor system. Osteochondral tissues were harvested from bovine knee joints and cultured up to 24 days in loaded and unloaded conditions. Notably, we found a considerable zone-specific heterogeneity between cartilage explants harvested from the same joint as evidenced by histology and gene expression levels. Results using the reactor system revealed that differences observed after mechanical loading varied within the range of the heterogeneity observed amongst the different cartilage explants. Thus, it may be difficult to obtain reliable and reproducible data in mechanical loading experiments from these tissues in vitro, especially in cases where small variations between the experimental groups are expected. This will likely lead to the reporting of false positives or negatives in studies investigating the effect of mechanical load on the function of cartilage tissue.
Effect of low-cost resistance training on lower-limb strength and balance in institutionalized seniors

ABSTRACT Background/Study Context: Given the rapid increase in the aging population worldwide, fall prevention is of utmost importance. It is essential to establish an efficient, simple, safe, and low-cost intervention method for reducing the risk of falls. This study examined the effect of 12 weeks of progressive elastic resistance training on lower-limb muscle strength and balance in seniors living in the Rumah Seri Kenangan, social welfare home in Cheras, Malaysia. Methods: A total of 51 subjects qualified to take part in this quasi-experimental study. They were assigned to either the resistance exercise group (n = 26) or control group (n = 25). The mean age of the 45 participants who completed the program was 70.7 (SD = 6.6). The exercise group met twice per week and performing one to three sets of 8 to 10 repetitions for each of nine lower-limb elastic resistance exercises. All exercises were conducted at low to moderate intensities in sitting or standing positions. The subjects were tested at baseline and 6 and 12 weeks into the program. Results: The results showed statistically significant improvements in lower-limb muscle strength as measured by five times sit-to-stand test (%Δ = 22.6) and dynamic balance quantified by the timed up-and-go test (%Δ = 18.7), four-square step test (%Δ = 14.67), and step test for the right (%Δ = 18.36) and left (%Δ = 18.80) legs. No significant changes were observed in static balance as measured using the tandem stand test (%Δ = 3.25), and one-leg stand test with eyes opened (%Δ = 9.58) and eyes closed (%Δ = −0.61) after completion of the program. Conclusion: The findings support the feasibility and efficacy of a simple and inexpensive resistance training program to improve lower-limb muscle strength and dynamic balance among the institutionalized older adults.
Combined Genomic and Proteomic Approaches Identify Gene Clusters Involved in Anaerobic 2-Methylnaphthalene Degradation in the Sulfate-Reducing Enrichment Culture N47

ABSTRACT The highly enriched deltaproteobacterial culture N47 anaerobically oxidizes the polycyclic aromatic hydrocarbons naphthalene and 2-methylnaphthalene, with sulfate as the electron acceptor. Combined genome sequencing and liquid chromatography-tandem mass spectrometry-based shotgun proteome analyses were performed to identify genes and proteins involved in anaerobic aromatic catabolism. Proteome analysis of 2-methylnaphthalene-grown N47 cells resulted in the identification of putative enzymes catalyzing the anaerobic conversion of 2-methylnaphthalene to 2-naphthoyl coenzyme A (2-naphthoyl-CoA), as well as the reductive ring cleavage of 2-naphthoyl-CoA, leading to the formation of acetyl-CoA and CO2. The glycyl radical-catalyzed fumarate addition to the methyl group of 2-methylnaphthalene is catalyzed by naphthyl-2-methyl-succinate synthase (Nms), composed of α-, β-, and γ-subunits that are encoded by the genes nmsABC. Located upstream of nmsABC is nmsD, encoding the Nms-activating enzyme, which harbors the characteristic [Fe4S4] cluster sequence motifs of S-adenosylmethionine radical enzymes. The bns gene cluster, coding for enzymes involved in beta-oxidation reactions converting naphthyl-2-methyl-succinate to 2-naphthoyl-CoA, was found four intervening open reading frames further downstream. This cluster consists of eight genes (bnsABCDEFGH) corresponding to 8.1 kb, which are closely related to genes for enzymes involved in anaerobic toluene degradation within the denitrifiers “Aromatoleum aromaticum” EbN1, Azoarcus sp. strain T, and Thauera aromatica. Another contiguous DNA sequence harbors the gene for 2-naphthoyl-CoA reductase (ncr) and 16 additional genes that were found to be expressed in 2-methylnaphthalene-grown cells. These genes code for enzymes that were supposed to catalyze the dearomatization and ring cleavage reactions converting 2-naphthoyl-CoA to acetyl-CoA and CO2. Comparative sequence analysis of the four encoding subunits (ncrABCD) showed the gene product to have the closest similarity to the Azoarcus type of benzoyl-CoA reductase. The present work provides the first insight into the genetic basis of anaerobic 2-methylnaphthalene metabolism and delivers implications for understanding contaminant degradation.
Molecular architecture of mammalian nitric oxide synthases

Significance In mammals, NO produced by NOS acts as a signaling molecule in the nervous and cardiovascular systems and as a cytotoxin in the immune system’s response to infection. Although structures of smaller portions of NOS have been solved, the structures of the entire NOS homodimer have remained elusive. In this study, we use single-particle EM to directly visualize the 3D structures, domain organization, and conformations accessed by all three mammalian NOSs. The observed conformational changes provide insight into the mechanisms through which calmodulin binding results in efficient NO formation. NOSs are homodimeric multidomain enzymes responsible for producing NO. In mammals, NO acts as an intercellular messenger in a variety of signaling reactions, as well as a cytotoxin in the innate immune response. Mammals possess three NOS isoforms— inducible, endothelial, and neuronal NOS—that are composed of an N-terminal oxidase domain and a C-terminal reductase domain. Calmodulin (CaM) activates NO synthesis by binding to the helical region connecting these two domains. Although crystal structures of isolated domains have been reported, no structure is available for full-length NOS. We used high-throughput single-particle EM to obtain the structures and higher-order domain organization of all three NOS holoenzymes. The structures of inducible, endothelial, and neuronal NOS with and without CaM bound are similar, consisting of a dimerized oxidase domain flanked by two separated reductase domains. NOS isoforms adopt many conformations enabled by three flexible linkers. These conformations represent snapshots of the continuous electron transfer pathway from the reductase domain to the oxidase domain, which reveal that only a single reductase domain participates in electron transfer at a time, and that CaM activates NOS by constraining rotational motions and by directly binding to the oxidase domain. Direct visualization of these large conformational changes induced during electron transfer provides significant insight into the molecular underpinnings governing NO formation.
Extraction and Recognition of Nonlinear Interval-Type Features Using Symbolic KDA Algorithm with Application to Face Recognition

We present symbolic kernel discriminant analysis (symbolic KDA) for face recognition in the framework of symbolic data analysis. Classical KDA extracts features, which are single-valued in nature to represent face images. These single-valued variables may not be able to capture variation of each feature in all the images of same subject; this leads to loss of information. The symbolic KDA algorithm extracts most discriminating nonlinear interval-type features which optimally discriminate among the classes represented in the training set. The proposed method has been successfully tested for face recognition using two databases, ORL database and Yale face database. The effectiveness of the proposed method is shown in terms of comparative performance against popular face recognition methods such as kernel Eigenface method and kernel Fisherface method. Experimental results show that symbolic KDA yields improved recognition rate.
Identification of the active-site lysine residues of two biosynthetic 3-dehydroquinases.

The lysine residues involved in Schiff-base formation at the active sites of both the 3-dehydroquinase component of the pentafunctional arom enzyme of Neurospora crassa and of the monofunctional 3-dehydroquinase of Escherichia coli were labelled by treatment with 3-dehydroquinate in the presence of NaB3H4. Radioactive peptides were isolated by h.p.l.c. following digestion with CNBr (and in one case after further digestion with trypsin). The sequence established for the N. crassa peptide was ALQHGDVVKLVVGAR, and that for the E. coli peptide was QSFDADIPKIA. An amended nucleotide sequence for the E. coli gene (aroD) that encode 3-dehydroquinase is also presented, along with a revised alignment of the deduced amino acid sequences for the biosynthetic enzymes.
An Adaptive Failure Detection Method with Controllable QoS for Distributed Storage System

According to the situation that different application asks for different requirement of storage node's performance, an adaptive failure detection method with controllable QoS for distributed storage system is proposed. The delay characteristic of heartbeat message is summarized. The relational expressions of neighbor heartbeat message's arrival time in the different network state are established. The QoS parameters formulas of different network state are proposed. The controllability of QoS parameters is analyzed. The algorithm of the method is designed. The experimental results show that the method realizes the balance control between detection speed and detection accuracy by setting safe remaining time with a certain value, and has adaptability that it can have a high detection speed but fewer mistakes.
Object Recognition with Videos Student : Liu Bingbin ( 3035085748 ) Supervisor : Dr

Object recognition is an interesting task in computer vision with a wide range of real world applications. While object recognition in still images has achieved impressive performance, object recognition in videos is yet to be explored. Due to motion blur and other complexities, still image methods directly applied to videos frames usually cannot yield satisfying results, which calls for the need to better study and incorporate temporal information in videos. In this project, the baseline framework is chosen to be T-CNN [1], which leverages video’s temporal and contextual information by post-processing techniques such as motion-guided propagation and tracking. However, temporal information is only incorporated after stillimage detection results are obtained, and some of the post-processing processes are time consuming. This project therefore attempts to address these two issues by utilizing temporal information at the feature and proposal level, as well as improving the post-processing efficiency. The objective is to increase the mean Average Precision under the setting of ImageNet VID task [2].
Mesoscopic and Macroscopic Models for Mesenchymal Motion

In this paper mesoscopic (individual based) and macroscopic (population based) models for mesenchymal motion of cells in fibre networks are developed. Mesenchymal motion is a form of cellular movement that occurs in three-dimensions through tissues formed from fibre networks, for example the invasion of tumor metastases through collagen networks. The movement of cells is guided by the directionality of the network and in addition, the network is degraded by proteases. The main results of this paper are derivations of mesoscopic and macroscopic models for mesenchymal motion in a timely varying network tissue. The mesoscopic model is based on a transport equation for correlated random walk and the macroscopic model has the form of a drift-diffusion equation where the mean drift velocity is given by the mean orientation of the tissue and the diffusion tensor is given by the variance-covariance matrix of the tissue orientations. The transport equation as well as the drift-diffusion limit are coupled to a differential equation that describes the tissue changes explicitly, where we distinguish the cases of directed and undirected tissues. As a result the drift velocity and the diffusion tensor are timely varying. We discuss relations to existing models and possible applications.