Miracle-dz/UniFAR-FTUs huggingface dataset:
A Synthetic 15-mer Peptide (PCK3145) Derived from Prostate Secretory Protein Can Reduce Tumor Growth, Experimental Skeletal Metastases, and Malignancy-Associated Hypercalcemia

In previous studies, we have shown that prostate secretory protein (PSP-94) can reduce prostate cancer growth in vivo. In the current study, we identified the amino acid sequence of PSP-94 that is required for eliciting this response. For these studies, we used rat prostate cancer Mat Ly Lu cells overexpressing parathyroid hormone-related protein (PTHrP), which is the main pathogenetic factor responsible for hypercalcemia of malignancy. Synthetic peptides corresponding to amino acids 7–21 (PCK721), 31–45 (PCK3145), and 76–94 (PCK7694) of PSP-94 were synthesized. Only PCK3145 showed a significant reduction in tumor cell proliferation. For in vivo studies, syngenic male Copenhagen rats were inoculated s.c. with Mat Ly Lu cells overexpressing PTHrP into the right flank or into the left ventricle via intracardiac injection, which results in experimental metastases to the lumbar vertebrae causing hind-limb paralysis. Animals were infused with different doses (1, 10, and 100 μg/kg/day) of peptides for 15 days, and the effect of these treatments on tumor volume, skeletal metastases, or development of hind-limb paralysis was determined. Treatment with PCK3145 resulted in a dose-dependent decrease in tumor volume and delay in the development of skeletal metastases. Bone histomorphometry showed that after intracardiac inoculation of tumor cells, the highest dose of PCK3145 (100 μg/kg/day) resulted in reducing skeletal tumor burden, which delayed the development of hind-limb paralysis. Treatment with PCK3145 led to reduction of plasma calcium and PTHrP levels and a significant decrease in PTHrP levels in the primary tumors and in vertebrae of experimental animals. These effects of PCK3145 were due to its ability to promote tumor cell apoptosis. Collectively, the results of these studies have demonstrated the ability of a small peptide derived from PSP-94 to reduce tumor volume and experimental skeletal metastases—results that will be highly beneficial in the continued development of this peptide as a novel therapeutic agent for patients with hormone refractory, late-stage prostate cancer.
Elkan's k-Means for Graphs

This paper extends k-means algorithms from the Euclidean domain to the domain of graphs. To recompute the centroids, we apply subgradient methods for solving the optimization-based formulation of the sample mean of graphs. To accelerate the k-means algorithm for graphs without trading computational time against solution quality, we avoid unnecessary graph distance calculations by exploiting the triangle inequality of the underlying distance metric following Elkan's k-means algorithm proposed in \cite{Elkan03}. In experiments we show that the accelerated k-means algorithm are faster than the standard k-means algorithm for graphs provided there is a cluster structure in the data.
Effect of gold thioglucose-induced obesity on adipose tissue weight and cellularity in male and female mice suckled in large and small litters: investigations into sex differences and site differences

1. Over- or undernutrition of newborn mice was caused by suckling in litters consisting initially of four or eighteen pups. After weaning, mice were fed ad lib. At 13 weeks some mice received gold thioglucose (GTG, 600 mg/kg, intraperitoneally) to induce hyperphagia, and all were killed at 39 weeks. 2. Mice suckled in small litters were heavier, with more body fat and protein. GTG treatment induced rapid weight gain and treated mice from large litters were heavier than untreated mice from small litters. However, the effect of litter size was not totally removed since GTG-treated small-litter mice were heavier than GTG-treated large-litter mice and had more fat, although body protein was not different. 3. Fat distribution between the depots was related to total body fatness and not to the treatment. 4. In male mice, preweaning undernutrition resulted in smaller fat depots containing smaller cells. GTG treatment of large-litter mice restored both to the levels found in small-litter mice: the depots of the latter mice were not significantly different after treatment. 5. In female mice, preweaning undernutrition resulted not only in smaller depots and cells but also fewer cells in all depots except mesenteric. GTG-treatment caused larger depots and cells in all mice with no difference in cell size whether mice were from large or small litters. The number of cells in the perirenal and mesenteric depots was greater in GTG-treated mice and was the same whether mice were from large or small litters. 6. We conclude that the level of preweaning nutrition does not affect the ability of adipose tissue to develop subsequently through hypertrophy or hyperplasia of the adipocytes or both, given a sufficient energy surplus consisting of normal pelleted feed, low in lipid.
Therapeutic Discovery RSK 2 Ser 227 at N-Terminal Kinase Domain Is a Potential Therapeutic Target for Multiple Myeloma

Multiple myeloma is an entity of cytogenetically and genetically heterogenous plasma cell neoplasms. Despite recent improvement in the treatment outcome of multiple myeloma by novel molecular-targeted chemotherapeutics,multiplemyeloma remains incurable. The identification of a therapeutic targetmolecule in which various signaling for cell-survival converge is a core component for the development of new therapeutic strategies against multiple myeloma. RSK2 is an essential mediator of the ERK1/2 signaling pathway for cell survival and proliferation. In this study, we discovered that RSK2, which is located at the N-terminal kinase domain and is one site responsible for substrate phosphorylation, is activated through phosphorylation regardless of the type of cytogenetic abnormalities or upstream molecular signaling in all 12 multiple myeloma–derived cell lines examined and 6 of 9 patient-derived CD138-positive primary myeloma cells. The chemical inhibition of RSK2 by BI-D1870 or gene knockdown of RSK2 inhibits myeloma cell proliferation through apoptosis induction, and this anti-myeloma effect was accompanied by downregulation of c-MYC, cyclin D, p21, and MCL1. RSK2 inhibition resulting from BI-D1870 treatment restored lenalidomide-induced direct cytotoxicity of myeloma cells from interleukin-6–mediated cell protection, showed no cross-resistance to bortezomib, and exerted additive/synergistic antiproliferative effects in conjunction with the mTOR, histone deacetylase, and BH3-mimicking BCL2/BCLXL inhibitors. These results suggest that RSK2 is a potential therapeutic target not only for newly diagnosed but also for patients with later phase multiple myeloma who are resistant or refractory to currently available anti-myeloma therapies. Mol Cancer Ther; 11(12); 1–10. 2012 AACR.
Relationships between Sensory Evaluations, and Physical and Chemical Properties of Boiled Seeds in Black Soybean

57 Introduction Black soybeans cultivated in the Tanba region of Hyogo prefecture are characterized by extremely large seeds with suitability for boiled seeds processing (Hirota et al. 2005). “Tanbaguro” is now used as the collective name for landraces originating from the Tanba region. By pure-line isolation, “Hyoukei-kuro 3” was selected and has been widely cultivated as a dominant line in Hyogo prefecture. In the previous study (Hirota et al. 2012), we collected black soybean landraces originating from the Tanba region, and demonstrated that seed and/or filling characters varied among these landraces. In order to promote effective use of these genetic resources, it is important to establish a reliable and objective method of evaluation by physical and chemical research with many samples, replacing subjective sensory evaluations for the eating quality of boiled seeds, because sensory evaluations are susceptible to bias due to the panelists and the characteristics of particular trials. Food texture is one of the essential factors in the eating quality of boiled seeds. Hardness evaluation has been quantified using the breaking force of stress-rupture curve on a texture analyzer in potato (Furudate and Meguro 1997), muskmelon (Hirai et al. 2007), Japanese radish (Komiyama et al. 2009) and green soybean (Furutani et al. 2012). Additionally, the eating quality is strongly affected by other texture components, such as viscosity, as well as hardness. However, evaluation of the viscosity of boiled seeds has not yet been established, although several researchers have presented quantitative indexes of viscosity combining several parameters of stress-rupture curve on a texture analyzer in other foods. The solubility of pectic substances has been regarded as one of the factors that affect the hardness of samples in Japanese radish (Manabe 1980), muskmelon (Hirai et al. 2007) and soybean (Matsuoka and Shiokawa 1990). Additionally, it has been reported that the calcium content is correlated with the sensory hardness in several vegetables and beans (Kaneko et al. 1982, Makino et al. 1987, Odake et al. 1995). However, most of these studies investigated the change of products between different processing methods; there are few reports of studies that focused on varietal characteristics in soybean. In this study, we investigated the interrelations among sensory evaluations of hardness and viscosity, physical properties and chemical components, using several black soybean lines and varieties with various seed characteristics, and clarified the contribution of these properties to the texture of boiled seeds in black soybean. Relationships between Sensory Evaluations, and Physical and
Reduced Argininosuccinate Synthetase Is a Predictive Biomarker for the Development of Pulmonary Metastasis in Patients with Osteosarcoma

Pulmonary metastasis is the most significant prognostic determinant for osteosarcoma, but methods for its prediction and treatment have not been established. Using oligonucleotide microarrays, we compared the global gene expression of biopsy samples between seven osteosarcoma patients who developed pulmonary metastasis within 4 years after neoadjuvant chemotherapy and curative resection, and 12 patients who did not relapse. We identified argininosuccinate synthetase (ASS) as a gene differentially expressed with the highest statistical significance (Welch's t test, P = 2.2 × 10−5). Immunohistochemical analysis of an independent cohort of 62 osteosarcoma cases confirmed that reduced expression of ASS protein was significantly correlated with the development of pulmonary metastasis after surgery (log-rank test, P < 0.05). Cox regression analysis revealed that ASS was the sole significant predictive factor (P = 0.039; hazard ratio, 0.319; 95% confidence interval, 0.108-0.945). ASS is one of the enzymes required for the production of a nonessential amino acid, arginine. We showed that osteosarcoma cells lacking ASS expression were auxotrophic for arginine and underwent G0-G1 arrest in arginine-free medium, suggesting that an arginine deprivation therapy could be effective in patients with osteosarcoma. Recently, phase I and II clinical trials in patients with melanoma and hepatocellular carcinoma have shown the safety and efficacy of plasma arginine depletion by stabilized arginine deiminase. Our data indicate that in patients with osteosarcoma, reduced expression of ASS is not only a novel predictive biomarker for the development of metastasis, but also a potential target for pharmacologic intervention. Mol Cancer Ther; 9(3); 535–44
Expression of CDKN 1 A / p 21 and TGFBR 2 in breast cancer and their prognostic significance

Background: A new diagnostic and prognostic biomarker may be of value in cancer diseases. Our study aimed to evaluate the CDKN1A/p21 and TGFBR2 level measurable in a cohort of patients with breast cancer after mastectomy, and to confirm their suitability to serve as prognostic biomarkers of the cancer. Methods: The expression levels of CDKN1A/p21 and TGFBR2 were detected by reverse transcription-PCR (RT-PCR), western blot assay and immunohistochemical staining for 65 primary tumor samples and paired adjacent noncancerous breast tissues. Their relations to clinicopathologic parameters and to the prognosis of patients with breast cancer were analyzed. Results: We found the mRNA and protein expression levels of CDKN1A/p21 were significantly upregulated in breast cancer tissues compared with adjacent nontumorous breast tissues. Increased CDKN1A/p21 expression showed a significant correlation with larger tumor size (P=0.014), higher tumor dedifferentiation grade (P=0.021), lymph node metastasis (P=0.019) and a shorter disease-free survival (P=0.044). Contrarily, the expression levels of TGFBR2 mRNA and protein were significantly decreased in breast cancer tissues compared with adjacent nontumorous breast tissues. Underexpression of TGFBR2 in breast cancer was correlated with larger tumor size (P=0.034), lymph node metastasis (P=0.039) and a shorter disease-free survival (P=0.035). Statistical analysis suggested that there was no significant association between CDKN1A/p21 and TGFBR2 expression. Conclusions: in summary, our results suggested that high CDKN1A/p21 and low TGFBR2 expression was closely correlated with adverse pathological parameters and poor prognosis in breast cancer. Both CDKN1A/p21 and TGFBR2 are presented as possible candidates for breast cancer biomarkers.
Identification of Characteristic Fatty Acids to Quantify Triacylglycerols in Microalgae

The fatty acid profiles of lipids from microalgae are unique. Polyunsaturated fatty acids are generally enriched in polar lipids, whereas saturated and monounsaturated fatty acids constitute the majority of fatty acids in triacylglycerols (TAG). Each species has characteristic fatty acids, and their content is positively or negatively correlated with TAGs. The marine oleaginous diatom Phaeodactylum tricornutum was used as the paradigm to determine the quantitative relationship between TAG and characteristic fatty acid content. Fatty acid profiles and TAG content of Phaeodactylum tricornutum were determined in a time course. C16:0/C16:1 and eicosapentaenoic acid (EPA, C20:5n3) were identified as characteristic fatty acids in TAGs and polar lipids, respectively. The percentage of those characteristic fatty acids in total fatty acids had a significant linear relationship with TAG content, and thus, the correlation coefficient presenting r2 were 0.96, 0.94, and 0.97, respectively. The fatty acid-based method for TAG quantification could also be applied to other microalgae such as Nannochloropsis oceanica in which the r2 of C16:0 and EPA were 0.94 and 0.97, respectively, and in Chlorella pyrenoidosa r2-values for C18:1 and C18:3 with TAG content were 0.91 and 0.99, repectively. This characteristic fatty acid-based method provided a distinct way to quantify TAGs in microalgae, by which TAGs could be measured precisely by immediate transesterification from wet biomass rather than using conventional methods. This procedure simplified the operation and required smaller samples than conventional methods.
Heart Disease : A Population-Based Case-Control Study Low Serum Insulin-Like Growth Factor I Is Associated With Increased Risk of Ischemic

Heart Disease : A Population-Based Case-Control Study Low Serum Insulin-Like Growth Factor I Is Associated With Increased Risk of Ischemic Print ISSN: 0009-7322. Online ISSN: 1524-4539 Copyright © 2002 American Heart Association, Inc. All rights reserved. is published by the American Heart Association, 7272 Greenville Avenue, Dallas, TX 75231 Circulation doi: 10.1161/01.CIR. 0000027563.44593. CC 2002;106:939-944; originally published online August 5, 2002; Circulation. http://circ.ahajournals. org/content/106/8/939 World Wide Web at: The online version of this article, along with updated information and services, is located on the
Perceptuo-Motor Interactions during Prehension Movements

Adaptive behavior relies on the integration of perceptual and motor processes. In this study, we aimed at characterizing the cerebral processes underlying perceptuo-motor interactions evoked during prehension movements in healthy humans, as measured by means of functional magnetic resonance imaging. We manipulated the viewing conditions (binocular or monocular) during planning of a prehension movement, while parametrically varying the slant of the grasped object. This design manipulates the relative relevance and availability of different depth cues necessary for accurate planning of the prehension movement, biasing visual information processing toward either the dorsal visual stream (binocular vision) or the ventral visual stream (monocular vision). Two critical nodes of the dorsomedial visuomotor stream [V6A (anterior visual area 6) and PMd (dorsal premotor cortex)] increased their activity with increasing object slant, regardless of viewing conditions. In contrast, areas in both the dorsolateral visuomotor stream [anterior intraparietal area (AIP) and ventral premotor cortex (PMv)] and in the ventral visual stream [lateral-occipital tactile-visual area (LOtv)] showed differential slant-related responses, with activity increasing when monocular viewing conditions and increasing slant required the processing of pictorial depth cues. These conditions also increased the functional coupling of AIP with both LOtv and PMv. These findings support the view that the dorsomedial stream is automatically involved in processing visuospatial parameters for grasping, regardless of viewing conditions or object characteristics. In contrast, the dorsolateral stream appears to adapt motor behavior to the current conditions by integrating perceptual information processed in the ventral stream into the prehension plan.
Finding subtle motifs by branching from sample strings

UNLABELLED Many motif finding algorithms apply local search techniques to a set of seeds. For example, GibbsDNA (Lawrence et al. 1993, Science, 262, 208-214) applies Gibbs sampling to random seeds, and MEME (Bailey and Elkan, 1994, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (ISMB-94), 28-36) applies the EM algorithm to selected sample strings, i.e. substrings of the sample. In the case of subtle motifs, recent benchmarking efforts show that both random seeds and selected sample strings may never get close to the globally optimal motif. We propose a new approach which searches motif space by branching from sample strings, and implement this idea in both pattern-based and profile-based settings. Our PatternBranching and ProfileBranching algorithms achieve favorable results relative to other motif finding algorithms. AVAILABILITY http://www-cse.ucsd. edu/groups/bioinformatics/software.html
Properties of the solar neighbor WISE J072003.20-084651.2

Context. The severe crowding towards the Galactic plane suggests that the census of nearby stars in that direction may be incomplete. Recently, Scholz reported a new M9 object at an estimated distance d ≃ 7 pc (WISE J072003.20−084651.2; hereafter WISE J0720) at Galactic latitude b = 2.3°. Aims. Our goals are to determine the physical characteristics of WISE J0720, its kinematic properties, and to address the question of whether it is a binary object, as was suggested in the discovery paper. Methods. Optical and infrared spectroscopy from the Southern African Large Telescope and Magellan, respectively, and spectral energy distribution fitting were used to determine the spectral type of WISE J0720. The measured radial velocity, proper motion, and parallax yielded its Galactic velocities. We also investigated if WISE J0720 may show X-ray activity based on archival data. Results. Our spectra are consistent with spectral type L0±1. We find no evidence for binarity, apart from a minor 2σ level difference in the radial velocities taken at two different epochs. The spatial velocity of WISE J0720 does not connect it to any known moving group; instead, it places the object with high probability in the old thin disk or in the thick disk. The spectral energy distribution fit hints at excess in the 12 μm and 22 μm WISE bands which may be due to a redder companion, but the same excess is visible in other late-type objects, and it more likely implies a shortcoming of the models (e.g., problems with the effective wavelengths of the filters for these extremely cool objects, etc.) rather than a disk or redder companion. The optical spectrum shows some Hα emission, indicative of stellar activity. Archival X-ray observations yield no detection. Conclusions. WISE J0720 is a new member of the solar neighborhood, the third nearest L dwarf. Our data do not support the hypothesis of its binary nature.
Leucine elicits myotube hypertrophy and enhances maximal contractile force in tissue engineered skeletal muscle in vitro

The amino acid leucine is thought to be important for skeletal muscle growth by virtue of its ability to acutely activate mTORC1 and enhance muscle protein synthesis, yet little data exist regarding its impact on skeletal muscle size and its ability to produce force. We utilized a tissue engineering approach in order to test whether supplementing culture medium with leucine could enhance mTORC1 signaling, myotube growth, and muscle function. Phosphorylation of the mTORC1 target proteins 4EBP‐1 and rpS6 and myotube hypertrophy appeared to occur in a dose dependent manner, with 5 and 20 mM of leucine inducing similar effects, which were greater than those seen with 1 mM. Maximal contractile force was also elevated with leucine supplementation; however, although this did not appear to be enhanced with increasing leucine doses, this effect was completely ablated by co‐incubation with the mTOR inhibitor rapamycin, showing that the augmented force production in the presence of leucine was mTOR sensitive. Finally, by using electrical stimulation to induce chronic (24 hr) contraction of engineered skeletal muscle constructs, we were able to show that the effects of leucine and muscle contraction are additive, since the two stimuli had cumulative effects on maximal contractile force production. These results extend our current knowledge of the efficacy of leucine as an anabolic nutritional aid showing for the first time that leucine supplementation may augment skeletal muscle functional capacity, and furthermore validates the use of engineered skeletal muscle for highly‐controlled investigations into nutritional regulation of muscle physiology.
THE EFFECT OF STUDENT’S DIGITAL LITERACY AND SELF-EFFICACY ON STUDENTS LEARNING INDEPENDENCE WITH LEARNING MOTIVATION AS AN INTERVENING VARIABLE

This study aims to determine the effect of student digital literacy and self-efficacy on student learning independence in economic subjects through learning motivation as an intervening variable in South Jakarta State High School. This study is to determine the direct and indirect effects. Research using quantitative methods with data collection methods using questionnaires. The total population is 180 students from the sample used in class XI economics. The results of this research analysis are that there is a direct influence of student digital literacy variables on learning independence, there is a direct influence of self-efficacy variables on learning independence, there is a direct influence of learning motivation variables on learning independence, there is a direct influence of digital literacy variables on learning motivation, there is a direct influence of self-efficacy variables on learning motivation, there is an indirect influence of digital literacy variables on learning independence through learning motivation, good digital literacy can find information from various sources through the internet, so learning motivation will increase when it can get information easily which will have an impact on the independence of students in finding material and doing assignments independently. There is an indirect influence of self-efficacy variables on learning independence through learning motivation, Students who are able to increase their confidence in their ability to complete a particular task by having the desire and desire to succeed will encourage the emergence of learning independence in students.