Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Root Greening by Light and Auxin/Cytokinin Signaling in Arabidopsis[W]

Differentiation of plastids is tightly coordinated with plant development. This work shows that the development of chloroplasts in Arabidopsis roots is regulated in opposing directions by plant hormones auxin and cytokinin. Two types of transcription factors, HY5 and GLKs, are involved in this regulation; the former is a pivotal factor, and the latter is a potent activator for root greening. Tight coordination between plastid differentiation and plant development is best evidenced by the synchronized development of photosynthetic tissues and the biogenesis of chloroplasts. Here, we show that Arabidopsis thaliana roots demonstrate accelerated chlorophyll accumulation and chloroplast development when they are detached from shoots. However, this phenomenon is repressed by auxin treatment. Mutant analyses suggest that auxin transported from the shoot represses root greening via the function of INDOLE-3-ACETIC ACID14, AUXIN RESPONSE FACTOR7 (ARF7), and ARF19. Cytokinin signaling, on the contrary, is required for chlorophyll biosynthesis in roots. The regulation by auxin/cytokinin is dependent on the transcription factor LONG HYPOCOTYL5 (HY5), which is required for the expression of key chlorophyll biosynthesis genes in roots. The expression of yet another root greening transcription factor, GOLDEN2-LIKE2 (GLK2), was found to be regulated in opposing directions by auxin and cytokinin. Furthermore, both the hormone signaling and the GLK transcription factors modified the accumulation of HY5 in roots. Overexpression of GLKs in the hy5 mutant provided evidence that GLKs require HY5 to maximize their activities in root greening. We conclude that the combination of HY5 and GLKs, functioning downstream of light and auxin/cytokinin signaling pathways, is responsible for coordinated expression of the key genes in chloroplast biogenesis.
Distinct Antiviral Roles for Human 2′,5′-Oligoadenylate Synthetase Family Members against Dengue Virus Infection1

The 2′,5′-oligoadenylate synthetase (OAS) and its downstream effector RNase L play important roles in host defense against virus infection. Oas1b, one of the eight Oas1 genes in the mouse genome, has been identified as a murine flavivirus-resistance gene. Four genes, OAS1, OAS2, OAS3, and OAS-like (OASL), have been identified in the human OAS gene family, and 10 isoforms, including OAS1 (p42, p44, p46, p48, and p52), OAS2 (p69 and p71), OAS3 (p100), and OASL (p30 and p59) can be generated by alternative splicing. In this study, we determined the role of the human OAS/RNase L pathway in host defense against dengue virus (DEN) infection and assessed the antiviral potential of each isoform in the human OAS family. DEN replication was reduced by overexpression and enhanced by knockdown of RNase L expression, indicating a protective role for RNase L against DEN replication in human cells. The human OAS1 p42, OAS1 p46, and OAS3 p100, but not the other OAS isoforms, blocked DEN replication via an RNase L-dependent mechanism. Furthermore, the anti-DEN activities of these three OAS isoforms correlated with their ability to trigger RNase L activation in DEN-infected cells. Thus, OAS1 p42/p46 and OAS3 p100 are likely to contribute to host defense against DEN infection and play a role in determining the outcomes of DEN disease severity.
Importance of pH of Fixatives Used for Fixation of Histopathology Specimens – An UnRecognized Issue

Objective: Adequate fixation of the surgical specimens is very important to ensure optimal histopathology, immunohistochemistry and genetic tests results. To achieve these results, it is very important to use good fixatives with pH maintained at 7. We measured pH values of the histopathology specimens received from different parts of country to determine whether fixative being used is appropriate or not. Material and Methods: It was a descriptive cross sectional study carried out at Armed Forces Institute of Pathology, Rawalpindi, Independent Medical College and Mian Muhammad trust hospital Faisalabad on one thousand consecutive samples received for histopathology reporting. To assess the pH, fixative of the sample was taken out in the kidney tray and pH meter was dipped in it and value of pH noted. Results: The specimen pH was recorded. The mean value came out to 6.1 ranging from 1.3 8.8. The maximum number of readings fell between 6.1 -7.0 (n 530 cases). The second highest group was 5.16. 0 which comprised of 269 cases. About 366 specimens have pH less than 6 and 104 specimens above 7, whereas for ideal fixation, the ideal recommended pH is 7. Conclusion: Unfortunately, most of the specimens received did not have ideal pH. It is very important to educate medical and paramedical staff, who deal with the surgical specimens, about the importance of pH and also how to ensure proper fixation of the specimens. This will help in achieving ideal histopathology results.
Previously undiagnosed aortic stenosis revealed by auscultation in the hip fracture population – echocardiographic findings, management and outcome

The 2001 Report of the National Confidential Enquiry into Perioperative Deaths recommended that an echocardiogram should be performed on patients with aortic stenosis prior to anaesthesia. In this study we present the patient details, management and outcome of the 272 hip fracture patients with a previously undiagnosed murmur and echocardiographically proven aortic stenosis admitted from 2001–2005 in our hospital. The patients with aortic stenosis were significantly older, and had significantly lower Abbreviated Mental Test Scores, than the control group of 3698 hip fracture patients without aortic stenosis. There were significant trends toward general anaesthesia over spinal anaesthesia, and use of invasive monitoring of blood pressure, as the severity of the aortic stenosis increased. There were no significant trends towards higher 30‐day or 1‐year mortality rates as the severity of the aortic stenosis increased. Resources for rapid pre‐operative echocardiograms should be made available for hip fracture patients as the results have significant implications for their subsequent anaesthetic management.
Breast cancer cell line MDA-231 stimulates osteoclastogenesis and bone resorption in human osteoclasts.

Breast cancers commonly cause osteolytic metastases in bone, a process that is dependent upon osteoclast-mediated bone resorption, but the mechanism responsible for tumor-mediated osteoclast activation has not yet been clarified. In the present study we utilized a well-known human breast cancer cell line (MDA-231) in order to assess its capability to influence osteoclastogenesis in human bone marrow cultures and bone resorption in fully differentiated osteoclasts. We demonstrated that conditioned medium (CM) harvested from MDA-231 increased the formation of multinucleated TRAP-positive cells in bone marrow cultures. Bone resorption activity of fully differentiated human osteoclasts and of osteoclast-like cell lines, from giant cell tumors of bone (GCT), was highly increased by the presence of MDA-231 CM. Moreover, while MDA-231 by themselves did not produce IL-6 tumor cell, CM increased the secretion of IL-6 by primary human osteoclasts and GCT cell lines compared to untreated controls. These data suggest that MDA-231 produce osteoclastic activating factor(s) that increase both osteoclast formation in bone marrow culture and bone resorption activity by mature cells. Moreover, breast cancer cells stimulate IL-6 secretion by osteoclasts that is one of the factors known to supports osteoclastogenesis.
Oversampling Method for Imbalanced Classification

Classification problem for imbalanced datasets is pervasive in a lot of data mining domains. Imbalanced classification has been a hot topic in the academic community. From data level to algorithm level, a lot of solutions have been proposed to tackle the problems resulted from imbalanced datasets. SMOTE is the most popular data-level method and a lot of derivations based on it are developed to alleviate the problem of class imbalance. Our investigation indicates that there are severe flaws in SMOTE. We propose a new oversampling method SNOCC that can compensate the defects of SMOTE. In SNOCC, we increase the number of seed samples and that renders the new samples not confine in the line segment between two seed samples in SMOTE. We employ a novel algorithm to find the nearest neighbors of samples, which is different to the previous ones. These two improvements make the new samples created by SNOCC naturally reproduce the distribution of original seed samples. Our experiment results show that SNOCC outperform SMOTE and CBSO (a SMOTE-based method).
Langerhans cells are not required for epidermal Vγ3 T cell homeostasis and function

This study tested the hypothesis that Vγ3 TCR‐bearing T cells are influenced by LCs. Vγ3 T cells and LCs are located in the epidermis of mice. Vγ3 T cells represent the main T cell population in the skin epithelium and play a crucial role in maintaining the skin integrity, whereas LCs are professional APCs. Although Vγ3 T cells and LCs form an interdigitating network in the epidermis, not much is known about their reciprocal influence and/or interdependence. We used two different LC‐deficient mouse models, in which LCs are constitutively or inducibly depleted, to investigate the role of LCs in maturation, homeostasis, and function of Vγ3 T cells. We show that Vγ3 T cell numbers are unaltered by LC deficiency, and Vγ3 T cells isolated from LC‐deficient mice are phenotypically and upon in vitro stimulation, functionally indistinguishable from Vγ3 T cells isolated from WT mice based on their cytotoxic potential and cytokine production. Additionally, in vivo skin‐wounding experiments show no major difference in response of Vγ3 T cells to wounding in the absence or presence of LCs. These observations indicate that Vγ3 T cells develop and function independently of LCs.
Vincristine and Dactinomycin in Infantile Myofibromatosis With a Review of Treatment Options

Although solitary presentations of infantile myofibromatosis tend toward spontaneous regression, multicentric forms fare worse. Previous case reports have depicted observation, surgical resection, and systemic therapies as treatment options. This paper reports well-tolerated, successful outcomes in a series of patients with high-risk infantile myofibromatosis in need of life-sustaining interventions treated with a combination of vincristine and dactinomycin. The clinical presentation, pathology, and radiographic findings are described.
Polarons, dressed molecules and itinerant ferromagnetism in ultracold Fermi gases

In this review, we discuss the properties of a few impurity atoms immersed in a gas of ultracold fermions—the so-called Fermi polaron problem. On one hand, this many-body system is appealing because it can be described almost exactly with simple diagrammatic and/or variational theoretical approaches. On the other, it provides a quantitatively reliable insight into the phase diagram of strongly interacting population-imbalanced quantum mixtures. In particular, we show that the polaron problem can be applied to the study of itinerant ferromagnetism, a long-standing problem in quantum mechanics.
Loss Rate Based Fountain Codes for Data Transfer

Fountain codes are becoming increasingly important for data transferring over dedicated high-speed long-distance network. However, the encoding and decoding complexity of traditional fountain codes such as LT and Raptor codes are still high. In this paper, a new fountain codes named LRF (Loss Rate Based Fountain) codes for data transfer is proposed. In order to improve the performance of encoding and decoding efficiency and decrease the number of redundant encoding symbols, an innovative degree distribution instead of robust soliton degree distribution in LT (Luby Transfer) codes is proposed. In LRF codes, the degree of encoding symbol is decided by loss rate property, and the window size is extended dynamic. Simulations result using LRF codes show that the proposed method has better performance in term of encoding ratio, degree ratio, encoding and decoding efficiency with respect to LT and Raptor codes.
Adaptive position anticipation in a support robot for overground gait training enhances transparency

Rehabilitation robots being developed nowadays rely on force and/or impedance control. This is guided by clinical evidence showing better performance if the patient is left with the capacity to influence the robot trajectory. The simplest, yet fundamental, mode of force control is when the robot has to be transparent, i.e. to apply no forces/torques on the patient. This mode is useful both in scenarios where the robot has to apply pinpointed support during some training phases and be transparent otherwise, and for any force controller in general, to avoid the reference forces to be polluted by the robot own dynamics. This contribution proposes a method to improve transparency on a support robot for overground training. The method consists in learning the patient's movement by using adaptive oscillators and then anticipate its future evolution in order to synchronize the robot movement. In experiments with human subjects walking in the gait support robot FLOAT, this method can decrease the undesired oscillations of the support force applied to the human user by up to 50%.
The adaptation of visual search strategy to expected information gain

An important question for HCI is to understand how and why visual search strategy is adapted to the demands imposed by the task of searching the results of a search engine. There is emerging evidence that a key part of the answer concerns the expected information gain of each of the set of available information gathering actions. We build on previous research to show that people are acutely sensitive to differences in the spacing and in the number of items returned by the search engine. These factors cause shifts in the efficiency of the available information gathering actions. We focus on an image browsing task, and show that, as a consequence of changes to the efficiency of available actions, people make small but significant changes to eye-movement strategy.
Comprehensive lower bounds on sequential prediction

We study the problem of sequential prediction of real-valued sequences under the squared error loss function. While refraining from any statistical and structural assumptions on the underlying sequence, we introduce a competitive approach to this problem and compare the performance of a sequential algorithm with respect to the large and continuous class of parametric predictors. We define the performance difference between a sequential algorithm and the best parametric predictor as “regret”, and introduce a guaranteed worst-case lower bounds to this relative performance measure. In particular, we prove that for any sequential algorithm, there always exists a sequence for which this regret is lower bounded by zero. We then extend this result by showing that the prediction problem can be transformed into a parameter estimation problem if the class of parametric predictors satisfy a certain property, and provide a comprehensive lower bound to this case.
Hormone therapy and skeletal muscle strength: a meta-analysis.

BACKGROUND Our objective was to perform a systematic review and meta-analysis of the research literature that compared muscle strength in postmenopausal women who were and were not on estrogen-based hormone therapy (HT). METHODS Twenty-three relevant studies were found. Effect sizes (ESs) were calculated as the standardized mean difference, and meta-analyses were completed using a random effects model. RESULTS HT was found to result in a small beneficial effect on muscle strength in postmenopausal women (overall ES = 0.23; p = .003) that equated to an approximately 5% greater strength for women on HT. Among the 23 studies, various muscle groups were assessed for strength, and those that benefitted the most were the thumb adductors (ES = 1.14; p < .001). Ten studies that compared muscle strength in rodents that were and were not estradiol deficient were also analyzed. The ES for absolute strength was moderate but not statistically significant (ES = 0.44; p = .12), whereas estradiol had a large effect on strength normalized to muscle size (ES = 0.66; p = .03). CONCLUSION Overall, estrogen-based treatments were found to beneficially affect strength.
The surprising magnetic topology of τ Sco: fossil remnant or dynamo output?

We report the discovery of a medium-strength (~0.5 kG) magnetic field on the young, massive star ? Sco (B0.2V), which becomes the third-hottest magnetic star known. Circularly polarized Zeeman signatures are clearly detected in observations collected mostly with the ESPaDOnS spectropolarimeter, recently installed on the 3.6-m Canada-France-Hawaii Telescope; temporal variability is also clearly established in the polarimetry, and can be unambiguously attributed to rotational modulation with a period close to 41 d. Archival ultraviolet (UV) spectra confirm that this modulation repeats over time-scales of decades, and refine the rotation period to 41.033 +/- 0.002 d. Despite the slow rotation rate of ? Sco, we none the less succeed in reconstructing the large-scale structure of its magnetic topology. We find that the magnetic structure is unusually complex for a hot star, with significant power in spherical-harmonic modes of degree up to 5. The surface topology is dominated by a potential field, although a moderate toroidal component is probably present. We fail to detect intrinsic temporal variability of the magnetic structure over the 1.5-yr period of our spectropolarimetric observations (in agreement with the stable temporal variations of the UV spectra), and infer that any differential surface rotation must be very small. The topology of the extended magnetic field that we derive from the photospheric magnetic maps is also more complex than a global dipole, and features in particular a significantly warped torus of closed magnetic loops encircling the star (tilted at about 90° to the rotation axis), with additional, smaller, networks of closed-field lines. This topology appears to be consistent with the exceptional X-ray properties of ? Sco and also provides a natural explanation of the variability observed in wind-formed UV lines. Although we cannot completely rule out the possibility that the field is produced through dynamo processes of an exotic kind, we conclude that its magnetic field is most probably a fossil remnant from the star formation stage. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii. E-mail: donati@ast.obs-mip.fr (J-FD); idh@star.ucl. ac.uk (IDH); mmj@st-andrews.ac.uk (MMJ); petit@ast.obs-mip.fr (PP); claude.catala@obspm.fr (CC); jlandstr@uwo.ca (JDL); jean-claude.bouret@oamp.fr (J-CB); evelyne.alecian@obspm.fr (EA); jrb3@st-andrews.ac.uk (JRB); forveill@cfht.hawaii. edu (TF); fpaletou@ast.obs-mip.fr (FP); manset@cfht.hawaii. edu (NM)
Dynamic Expression of Proteoglycans during Skeletal Muscle Development

Proteoglycans are glycoconjugates composed of a core protein and covalcntly attached glycosaminoglycans. Skeletal muscle produces a number of different types of proteogiycans, and, importantly, the types of proteogiycans made by skeletal muscle vary during muscle development. At early stages of muscle development, large chondroiim sulfate proteogiycans of the PG-M/versican type are produced both in culture and in vivo. Localization both by autoradiography of radiolabeled material and by imrnunohistochemistry indicates that the chondroitin sulfate proteogiycans are deposited in a peri cellular region around the muscle cells. Although biosynthesis of these molecules is not detected in mature skeielal muscle, their synthesis is re-initiated during regeneration, which suggests a requirement for these molecules in some early aspect of muscle development. Al later stages of muscle development, small dermatan sulfate proteogiycans are synthesized. One of the ::iajor types of dermatan sulfate proteogiycans in skeletal muscle is decorin, which can bind to collagen and affect fibril formation. Decorin is initially localized in the fibrous connective tissue areas of skeletal muscle, but eventually, at later stages of muscle development, is also found in proximity to the myotubes. Hcparan sulfate proteogiycans are also present in skeletal muscle, and among these are molecules of the syndecan, glypican, and perlecan types. Heparan sulfate proteogiycans are significant because of their involvement in signal transduction of growth factors such as fibroblast growth factor. Evidence indicates that hcparan sulfate proteogiycans play a role in the stimulation of myoblast proliferation by fibroblast growth factor. The exact roles played by other proteogiycans in muscle development are unclear at present. However, proteogiycans have the ability to affect cell adhesion and migration, processes which are important in muscle development. Because of this, it is likely that the changing patterns of proteoglycan biosynthesis during muscle development arc part of and, indeed, influence the orchestrated cellular interactions which are essential for proper muscle formation.
Predictive Biomarkers and Personalized Medicine Biomarkers for Cetuximab-Based Neoadjuvant Radiochemotherapy in Locally Advanced Rectal Cancer

Purpose: Phase II trials in locally advanced rectal cancer have shown that cetuximab-based neoadjuvant radiochemotherapy is feasible but without an improvement in complete pathologic response rates. Our goal was to identify patients who would benefit from cetuximab-based neoadjuvant chemoradiation measuring gene expression levels of proteins involved in tumor growth [endothelial growth factor receptor (EGFR)], angiogenesis [VEGF, VEGF receptors 1 and 2 (VEGFR1, VEGFR2)], DNA repair [excision repair cross-complementing 1 (ERCC1)], and drug metabolism [thymidylate synthetase (TS)]. We also determined mutation status of KRAS and BRAF. Experimental Design: This study was carried out on 130 patients with locally advanced rectal cancer who were enrolled in 4 different phase II clinical trials, using cetuximab-based chemoradiation. Tumor tissues were obtained before neoadjuvant and at surgical therapy. After microdissection, intratumoral gene expression levels and KRAS/BRAF mutation status were analyzed. Results: A significant decrease of TS, VEGFR1, and VEGFR2 gene expression was seen following neoadjuvant therapy (P < 0.03). High pretreatment VEGF gene expression levels were associated with nonresponse (P 1⁄4 0.070). KRAS mutations were found in 42% and mutant KRAS (KRAS mt) was significantly associated with pathologic nonresponse (P 1⁄4 0.037). In patients with wild-type KRAS (KRAS wt), low EGFR was significantly associated with higher nonresponse and VEGF mRNA expressions were associated with complete pathologic response (P 1⁄4 0.012; P 1⁄4 0.06). KRAS transversion (KRAS tv) was associated with tumor regression: nonresponse was more common in patients with KRAS tv than with KRAS wt (P 1⁄4 0.007). BRAF V600E mutations were not detected in any of the patients. Conclusion: This study suggests that pretreatment intratumoral EGFR andVEGFmRNA expression levels as well as KRAS mutation status are predictive markers of pathologic response to neoadjuvant cetuximabbased chemoradiation in locally advanced rectal cancer. Clin Cancer Res; 17(10); 3469–77. 2011 AACR.