Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolutionarily Conserved TOUGH Protein Is Required for Proper Development of Arabidopsis thalianaw⃞

In this study, we characterize the evolutionarily conserved TOUGH (TGH) protein as a novel regulator required for Arabidopsis thaliana development. We initially identified TGH as a yeast two-hybrid system interactor of the transcription initiation factor TATA-box binding protein 2. TGH has apparent orthologs in all eukaryotic model organisms with the exception of the budding yeast Saccharomyces cerevisiae. TGH contains domains with strong similarity to G-patch and SWAP domains, protein domains that are characteristic of RNA binding and processing proteins. Furthermore, TGH colocalizes with the splicing regulator SRp34 to subnuclear particles. We therefore propose that TGH plays a role in RNA binding or processing. Arabidopsis tgh mutants display developmental defects, including reduced plant height, polycotyly, and reduced vascularization. We found TGH expression to be increased in the amp1-1 mutant, which is similar to tgh mutants with respect to polycotyly and defects in vascular development. Interestingly, we observed a strong genetic interaction between TGH and AMP1 in that tgh-1 amp1-1 double mutants are extremely dwarfed and severely affected in plant development in general and vascular development in particular when compared with the single mutants.
Down-regulating ATDC inhibits the proliferation of esophageal carcinoma cells.

OBJECTIVE Our previous study showed that Ataxia-Telangiectasia Group D Complementing gene (ATDC) expression was correlated with tumor aggressiveness and poor prognosis in patients with esophageal squamous cell carcinoma (ESCC). However, the roles of ATDC on the esophageal carcinoma cells remain unclear. The present study aimed to explore the effects of ATDC gene silencing on the growth and proliferation of esophageal carcinoma cell lines EC109 and EC9706 in vivo and in vitro. MATERIALS AND METHODS The lentivirus-mediated siRNA targeting ATDC was constructed and transfected into EC109 and EC9706 cells. After the gene silencing effects were confirmed by Western blot analyses, the growth and proliferation were determined by MTT, palte clone and flow cytometry analyses. RESULTS The lentivirus-mediated siRNA markedly inhibited the expression of ATDC in both EC109 and EC9706 cells. MTT, plate colony formation and Xenograft assays illustrated that down-regulation of ATDC significantly repressed the growth of cells in vitro and in vivo. Furthermore, western blot assays revealed that ATDC down-regulation could decrease the expression of cyclinE in ESCC cell lines. CONCLUSIONS We demonstrated that down-regulation of ATDC could inhibit the growth and proliferation partly through regulation of cyclin E.
Co-design patterns for embedded network management

Designing and operating large-scale management systems has become extremely challenging due to the growing complexity of network technologies and networked service infrastructures. Both knowledge and functionality for performing management tasks are typically shared between service and management realms. However, current management practices do not adequately address this situation, and management functions are added only after services are deployed. In this paper, we introduce co-design patterns to embedded network management and show how they allow for a more structured design of recurring management tasks. Using a distributed fault management scenario we demonstrate how co-design patterns facilitate the interworking of service and management processes that share knowledge and functionality to handle faults collaboratively. We further show that applying co-design patterns results in significant improvement in the runtime performance of embedded management processes.
A New Approach to Flood Protection Design and Riparian Management

Conventional engineering methods of flood control design focus narrowly on the efficient conveyance of water, with little regard for environmental resource planning and natural geomorphic processes. Consequently, flood control projects are often environmentally disastrous, expensive to maintain, and even inadequate to control floods. In addition, maintenance programs to improve flood conveyance and enhance levee stability, such as clearing riparian vegetation in channels and on levees, undergo little – if any – technical scrutiny. Such programs are often prescriptive in nature, rather than based on actual performance standards. A new approach to planning channel modifications for flood damage reduction is presented that is multi-objective and incorporates proper consideration of hydrologic, geomorphic, and biologic factors that influence stream hydraulics.
Effects of hypercapnia on BP in hypoalbuminemic and Nagase analbuminemic rats.

STUDY OBJECTIVE To determine if animals with abnormally low albumin levels are more susceptible to the effects of hypercapnia on BP compared to normal animals. DESIGN Prospective, controlled laboratory experiment. SETTING University research laboratory. ANIMALS Eighteen male Sprague-Dawley rats: 6 rats 10 to 12 weeks old (young Sprague-Dawley [YSD]), 6 rats 6 to 9 months old (old Sprague-Dawley [OSD]), and 6 rats 10 to 12 weeks old (Nagase analbuminemic mutant Sprague-Dawley [NAR]). METHODS Under general anesthesia and paralysis, we varied the Paco(2) by changing the respiratory rate on mechanical ventilation. Mean arterial pressure (MAP) was monitored in a continuous fashion. We obtained arterial blood for blood gas and electrolyte analysis, and nitric oxide (NO) production. RESULTS OSD rats had reduced serum albumin, while NAR rats were analbuminemic. Although NAR animals had a decreased buffer capacity compared to age-matched control animals (0.010 vs 0.013, p < 0.05), the MAP decreased in an identical fashion in all three groups. NO production increased with hypercapnia but was similar in all three groups. However, NAR rats had consistently higher plasma strong ion gap (2.8 to 4.1 mEq/L greater) compared to either YSD or OSD rats (p < 0.01), and baseline strong ion difference (mean +/- SD) was significantly lower in NAR rats (28.7 +/- 2.1 mEq/L) compared to either YSD rats (33.0 +/- 5.1 mEq/L) or OSD rats (31.2 +/- 5.1 mEq/L) [p < 0.05]. CONCLUSIONS These findings suggest that analbuminemic or hypoalbuminemic rats are not more susceptible to hypercapnia-induced hemodynamic instability. Baseline values for apparent strong ion difference are lower in NA rats consistent with a reduced buffer base resulting from analbuminemia.
Downregulation of Sec23A Protein by miRNA-375 in Prostate Carcinoma

Prostate carcinoma (CaP) is a leading cause of cancer-related death in men. We have previously determined the microRNA (miRNA) profile of primary CaP in comparison with nontumor prostate tissue. miRNAs are small, noncoding RNAs that inhibit protein synthesis on a posttranscriptional level by binding to the 3′-untranslated region (3′-UTR) of their target genes. In primary CaP tissue, we have previously found by miRNA sequencing that miR-375 and miR-200c were upregulated 9.1- and 4.5-fold, respectively. A computational analysis predicted the 3′-UTR of the SEC23A gene as a potential target for both miR-375 and miR-200c. Here, we show that the 3′-UTR of SEC23A mRNA is indeed a target for miR-375 and miR-200c and that both miRNAs downregulate Sec23A protein expression when ectopically expressed in human 293T cells. In primary samples of CaP, we found a direct correlation between reduction of SEC23A mRNA and overexpression of miR-375 but not of miR-200c. The reduced levels of Sec23A protein were inversely correlated to the increased amount of miR-375 in the LNCaP and DU145 CaP cell lines when compared with normal prostate fibroblasts. In primary CaP, we also detected decreased amounts of Sec23A protein when compared with corresponding normal prostate tissue. Ectopically overexpressed Sec23A in LNCaP and DU145 CaP cells significantly reduced the growth properties, indicating that Sec23A might play a role in the induction or growth of prostate carcinoma. Sec23A overexpression reduced cell growth but did not induce apoptosis, whereas inhibition of Sec23A stimulated cell proliferation. Mol Cancer Res; 9(6); 791–800. ©2011 AACR.
Ectodomain shedding and ADAMs in development

Proteolytic enzymes belonging to the A Disintegin And Metalloproteinase (ADAM) family are able to cleave transmembrane proteins close to the cell surface, in a process referred to as ectodomain shedding. Substrates for ADAMs include growth factors, cytokines, chemokines and adhesion molecules, and, as such, many ADAM proteins play crucial roles in cell-cell adhesion, extracellular and intracellular signaling, cell differentiation and cell proliferation. In this Review, we summarize the fascinating roles of ADAMs in embryonic and adult tissue development in both vertebrates and invertebrates.
Developmental states of the collagen content, distribution and architecture in the pectoralis, iliotibialis lateralis and puboischiofemoralis muscles of male Red Cornish × New Hampshire and normal broilers

1. Developmental states of the collagen content, distribution and architecture in the pectoralis (PT), iliotibialis lateralis (ITL) and puboischiofemoralis (PIF) muscles of male Red Cornish × New Hampshire (RN, 80 d, body weight 2·9 kg) and normal (3·1 kg) broilers were evaluated. 2. In PT muscle the total amount of collagen was significantly greater in RN broilers (3·33 mg/g) than in normal ones (1·71 mg/g). This higher collagen content in RN broilers was based mainly on the closer mesh sizes of endomysial honeycomb. The collagen structures in the perimysia also differed between broiler types, when more collagen fibres were observed in RN broilers. 3. ITL muscle contained total collagen of 4·10 to 5·00 mg/g. Types I and III collagens were distributed on the perimysia at higher percentages in RN broilers (31·6%, 37·2%) than normal (15·6%, 30·8%), respectively. The thick bands of tough collagen fibres characteristic of ITL muscle perimysium in cockerels had not yet developed in these broilers. 4. Total collagen was 4·63 to 6·29 mg/g in PIF material with fascia. In PIF muscle the perimysial collagen fibres had not yet attained their full growth but consisted of densely packed fibrils. PIF muscle was characterised by the earlier maturing collagen structure. 5. These results show that a perimysial collagen structure in broilers is still in an undeveloped state. It is supposed that tenderness of broiler meat is attributed mainly to characteristics of the collagen distribution, in which the majority of types I and III collagens is distributed on the closer mesh of endomysial honeycomb.
Genotyping Yersinia pestis in Historical Plague: Evidence for Long-Term Persistence of Y. pestis in Europe from the 14th to the 17th Century

Ancient DNA (aDNA) recovered from plague victims of the second plague pandemic (14th to 17th century), excavated from two different burial sites in Germany, and spanning a time period of more than 300 years, was characterized using single nucleotide polymorphism (SNP) analysis. Of 30 tested skeletons 8 were positive for Yersinia pestis-specific nucleic acid, as determined by qPCR targeting the pla gene. In one individual (MP-19-II), the pla copy number in DNA extracted from tooth pulp was as high as 700 gene copies/μl, indicating severe generalized infection. All positive individuals were identical in all 16 SNP positions, separating phylogenetic branches within nodes N07_N10 (14 SNPs), N07_N08 (SNP s19) and N06_N07 (s545), and were highly similar to previously investigated plague victims from other European countries. Thus, beside the assumed continuous reintroduction of Y. pestis from central Asia in multiple waves during the second pandemic, long-term persistence of Y. pestis in Europe in a yet unknown reservoir host has also to be considered.
Effects of the integrin-linked kinase inhibitor QLT0267 on squamous cell carcinoma of the head and neck.

OBJECTIVE To study the expression of integrin-linked kinase (ILK) in human squamous cell carcinoma of the head and neck (SCCHN) tumor specimens and cell lines and the efficacy of the novel small molecule QLT0267. DESIGN Immunohistochemical analysis of 17 SCCHN tumor tissue specimens and 3 normal tongue tissue specimens for ILK expression and in vitro analysis of the effectiveness of QLT0267 on SCCHN cells. SETTING Academic medical center. MAIN OUTCOME MEASURES Expression levels of ILK in SCCHN tumor specimens and cell lines and the efficacy of QLT0267 in inhibiting cell growth and inducing apoptosis in SCCHN cell lines. RESULTS Most SCCHN tumor specimens stained for ILK, whereas none of the 3 normal tongue tissue specimens stained for ILK. Integrin-linked kinase was expressed in all 6 SCCHN cell lines tested. In 4 pairs of normal and SCCHN tumor specimens, ILK expression and activity were higher in most tumor samples tested. A kinase assay showed that QLT0267 inhibited the ILK activity of 2 SCCHN cell lines (TU167 and MDA1986). Modified tetrazolium salt 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, DNA fragmentation ladder, and TUNEL (terminal deoxynucleotidyl transferase-mediated biotin-deoxyuridine triphosphate nick-end()labeling) assays showed that QLT0267 inhibited cell growth and induced apoptosis in these 2 cell lines. A dose-dependent decrease in Akt phosphorylation was observed for these 2 cell lines on treatment with QLT0267. CONCLUSIONS Integrin-linked kinase is overexpressed in SCCHN tumor specimens. Targeting ILK with the small-molecule ILK inhibitor QLT0267 inhibits cell growth and induces apoptosis in SCCHN cell lines by reducing ILK activity and Akt phosphorylation. Integrin-linked kinase may be an attractive target for molecular therapy with which to enhance treatment of SCCHN.
Oocyte Polarization Is Coupled to the Chromosomal Bouquet, a Conserved Polarized Nuclear Configuration in Meiosis

The source of symmetry breaking in vertebrate oocytes is unknown. Animal—vegetal oocyte polarity is established by the Balbiani body (Bb), a conserved structure found in all animals examined that contains an aggregate of specific mRNAs, proteins, and organelles. The Bb specifies the oocyte vegetal pole, which is key to forming the embryonic body axes as well as the germline in most vertebrates. How Bb formation is regulated and how its asymmetric position is established are unknown. Using quantitative image analysis, we trace oocyte symmetry breaking in zebrafish to a nuclear asymmetry at the onset of meiosis called the chromosomal bouquet. The bouquet is a universal feature of meiosis where all telomeres cluster to one pole on the nuclear envelope, facilitating chromosomal pairing and meiotic recombination. We show that Bb precursor components first localize with the centrosome to the cytoplasm adjacent to the telomere cluster of the bouquet. They then aggregate around the centrosome in a specialized nuclear cleft that we identified, assembling the early Bb. We show that the bouquet nuclear events and the cytoplasmic Bb precursor localization are mechanistically coordinated by microtubules. Thus the animal—vegetal axis of the oocyte is aligned to the nuclear axis of the bouquet. We further show that the symmetry breaking events lay upstream to the only known regulator of Bb formation, the Bucky ball protein. Our findings link two universal features of oogenesis, the Bb and the chromosomal bouquet, to oocyte polarization. We propose that a meiotic—vegetal center couples meiosis and oocyte patterning. Our findings reveal a novel mode of cellular polarization in meiotic cells whereby cellular and nuclear polarity are aligned. We further reveal that in zygotene nests, intercellular cytoplasmic bridges remain between oocytes and that the position of the cytoplasmic bridge coincides with the location of the centrosome meiotic—vegetal organizing center. These results suggest that centrosome positioning is set by the last mitotic oogonial division plane. Thus, oocytes are polarized in two steps: first, mitotic divisions preset the centrosome with no obvious polarization yet, then the meiotic—vegetal center forms at zygotene bouquet stages, when symmetry is, in effect, broken.
Bone Histology of Phytosaur, Aetosaur, and Other Archosauriform Osteoderms (Eureptilia, Archosauromorpha)

As in other archosauriforms, phytosaurs and aetosaurs are characterized by the presence of well‐developed osteoderms. Here we provide a comparative study on the microstructure of phytosaur (five taxa) and aetosaur (thirteen taxa) osteoderms. For outgroup comparison, we sampled osteoderms of the sister taxon to Aetosauria, Revueltosaurus callenderi, and the doswelliid Jaxtasuchus salomoni. Phytosaur, aetosaur, and Jaxtasuchus osteoderms are composed of a diploe structure, whereas the Revueltosaurus osteoderm microanatomy is more compact. The external cortex of phytosaurs, Revueltosaurus and Jaxtasuchus osteoderms is mainly composed of parallel‐fibered bone. In aetosaurs, the external cortex mainly consists of lamellar bone, with lines of resorption within the primary bone indicating successive cycles of bone erosion and deposition. The basal cortex in all the specimens is composed of parallel‐fibered bone, with the cancellous internal core being more strongly developed in aetosaurs than in phytosaurs. Woven or fibro‐lamellar bone was recorded in both phytosaurian and aetosaurian taxa, as well as in Jaxtasuchus. Structural fibers, which at least partly suggest metaplastic origin, were only recorded in the internal core of two phytosaurs and in the basal cortex of one aetosaur. Osteoderm thickness and cancellous to compact bone ratios appear to be subject to ontogenetic change. Minimum growth mark counts in osteoderms sampled indicate that some aetosaurs and phytosaurs lived for at least two decades. Bone microstructures are more uniform in phytosaur osteoderms and show a higher level of disparity among aetosaur osteoderms, and at least in the latter, histological features are potentially apomorphic for species/genus level. Anat Rec, 297:240–260, 2014. © 2013 Wiley Periodicals, Inc.
The Importance of the Proximal Saphenous Nerve Block for Foot and Ankle Surgery

To the Editor: W e read with interest the excellent report by López et al. on ankle block for forefoot surgery. The authors focused on the role of saphenous nerve block (SNB) for forefoot surgery and concluded that SNB is unnecessary in most patients because its sensory coverage extends only to the midfoot. This publication is timely, as ankle and foot surgery is a common procedure for which nerve blocks are used for anesthesia and/or analgesia, yet little clinical data are available on the utility of SNB. We wanted to compare our observation of the importance of a more proximal SNB for major ankle and foot surgery and report analgesic efficacy of the adductor canal block (SNB) for postoperative analgesia in 2 patients where a working popliteal sciatic nerve block alone or in combination with saphenous block at the level of the ankle was inadequate.
Bp-AR-Based Human Joint angle estimation using Multi-Channel sEMG

Human motion estimation by surface electromyogram (sEMG) is one of the most important human intention recognition methods for active rehabilitation training. This paper proposes a back propagation (BP) neural network and autoregressive (AR) model based real-time sEMG-joint angle estimation method. To reduce the time delay, a moving Butterworth filtering method is designed to filter the lower limb multi-channel sEMG signals. Then correlation analysis between sEMG signals and joint angles is made to reduce redundant channels. A first-order BP neural network is used to build the mapping relationship between multi-channel sEMG signals and joint angles, then the approximated angle by BP model is adjusted by the AR de-noising model, which describes the angle variation features of the given training mode to improve the accuracy and continuity. To validate this method, five able-bodied subjects participated in cycling exercise experiment, and the angle estimation results show that this method presents a good performance on real-time computation, accuracy and continuity.
Ontology Based Automatic Image Annotation Using Multi-class SVM

Image annotation is usually formed as a multiclass classification problem. Traditional methods learn the co-occurrence of keywords and images while they ignore the correlation between keywords, which turned out to be one of the reasons causing poor experiment results. In this paper, we propose an automatic image annotation approach by using multiclass SVM with ontology to achieve a higher accuracy. In our paper, we choose semantic dictionary Word Net in which hierarchy defined words are derived from the text ontology to calculate the correlations between keywords. Specifically, we use Bags of Visual Words model to present the image visual feature and apply a mixed kernel in multiclass SVM. Finally, we combine the probability outputs to get the final results. Compared to other state-of-the-art multiclass classification methods, our approach tested in typical Corel dataset maintain a high level of accuracy in classification.
Probabilistic Graphical Models Specified by Probabilistic Logic Programs: Semantics and Complexity

We look at probabilistic logic programs as a specification language for probabilistic models, and study their interpretation and complexity. Acyclic programs specify Bayesian networks, and, depending on constraints on logical atoms, their inferential complexity reaches complexity classes #P, #NP, and even #EXP. We also investigate (cyclic) stratified probabilistic logic programs, showing that they have the same complexity as acyclic probabilistic logic programs, and that they can be depicted using chain graphs.
Spatiotemporal Sampling and Interpolation for Dense Video Camera Arrays ∗

We explore the application of dense camera arrays to view interpolation across space and time for dynamic scenes. Large video camera arrays are typically synchronized, but we show that staggering camera triggers provides a much richer set of samples on which to base the interpolation. We do not increase the total number of samples—we merely distribute them more effectively in time. We use optical flow to interpolate new views. Within this framework, we find that the dense space-time sampling provided by staggered timing improves the robustness of the interpolation. We present an novel optical flow method that combines a plane plus parallax framework with knowledge of camera spatial and temporal offsets to generate flow fields for virtual images at new space-time locations. We present results interpolating video from a 96-camera light field using this method. CR Categories: I.4. 8 [Image Processing and Computer Vision]: Scene Analysis—Time-varying imagery; I.4. 9 [Image Processing and Computer Vision]: Applications
Analysis of resonant transmission characteristics of two sub-wavelength apertures with a ridge located in parallel

There have been numerous studies for the problem of electromagnetic coupling through electrically small holes or apertures in microwave areas and optics. Bethe was first treated this problem using the aperture polarizability concept and it was found that the transmittance normalized to the area scales as (a/λ)4 where a is the hole radius and λ is the wavelength [1]. This problem was generalized by Harrington introducing radiation terms in the equivalent circuit and he suggested an easy way of improving the poor transmittance by satisfying resonance condition [2]. The resonance condition can be realized by loading the small aperture with a capacitive lumped element or a capacitive structure. Recently, Yeo et. al. have analyzed an electrically small circular aperture with a ridge for resonant transmission and have shown the convergence of the transmitted power of an electrically small aperture to the transmission cross section [3].