Miracle-dz/UniFAR-FTUs huggingface dataset:
ZmSnRK2.8 responds to ABA through the SnRK2-PP2C complex

Understanding the responses of maize to abscisic acid (ABA) dependent drought tolerance is an important topic for the biotechnological application of functional mechanisms of stress adaptation. Key components that control and modulate stress adaptive pathways include SnRK2 (sucrose non-fermenting 1-related protein kinases 2) proteins. Recent studies indicate that SnRK2 are plant specific kinases that together with ABA ligand PYR/PYL/RCAR proteins and type 2C group A protein phosphatases constitute the central core of abscisic acid perception and signal transduction. Here, we study drought responses in maize by analyzing the mechanism of ZmSnRK2.8 in ABA signaling to establish relevant analogies with other plant species. ZmSnRK2.8 is a very closely related protein to Arabidopsis OST1 (open stomata 1) kinase with nuclear and cytosolic subcellular localization able to auto-phosphorylate S182 or T183 amino acids on its activation loop suggesting that phosphorylation at these sites may be a general mechanism for SnRK2 activation. In addition, ZmSnRK2.8 is activated by ABA and interacts with PP2C phosphatases in a constitutive, ABA independent manner. Together, our data suggest a conserved mechanism of plant responses to ABA and drought stress in maize and point to the potential use of this kinase in improving programs of drought tolerance in crops.
Variational Inference with Mixture Model Approximation for Applications in Robotics

We propose to formulate the problem of representing a distribution of robot configurations (e.g. joint angles) as that of approximating a product of experts. Our approach uses variational inference, a popular method in Bayesian computation, which has several practical advantages over sampling-based techniques. To be able to represent complex and multimodal distributions of configurations, mixture models are used as approximate distribution. We show that the problem of approximating a distribution of robot configurations while satisfying multiple objectives arises in a wide range of problems in robotics, for which the properties of the proposed approach have relevant consequences. Several applications are discussed, including learning objectives from demonstration, planning, and warm-starting inverse kinematics problems. Simulated experiments are presented with a 7-DoF Panda arm and a 28-DoF Talos humanoid.
Reply.

Reply : We agree with Dr. Glasser that the intraocular penetration of topical fluorometholone is lower than that of other steroids. We performed a similar study in which we compared the effects of diclofenac and fluorometholone in preventing postoperative breakdown of the blood–aqueous barrier and cystoid macular edema. We also compared the abovementioned effects of diclofenac and betamethasone. We observed that diclofenac was more effective than the steroid and that betamethasone induced elevation in intraocular pressure in postoperative pseudophakic eyes. We based the design of the present study on these findings. The most essential reason for selecting fluorometholone as the control drug was its similarity in appearance to nepafenac; this enabled us to perform a double-masked scientific comparison. Placebos with no active antiinflammatory effects were not used for ethical reasons. Dr. Glasser also pointed out that dividing the financial disclosure statement between the abstract and the footnotemaymislead the readers.Whenwe submitted this paper for review, the financial disclosure statement was not divided between the abstract and the footnote. Having been published as such was not our intention, but we believe it to be the journal's guideline.dKensaku Miyake, MD, Ichiro Ota, MD, Goichiro Miyake, MD, Jiro Numaga, MD, PhD
10-Year Experience: Routine Assessment of Health Related Quality of Life in Head & Neck Cancer Patients

Clinical outcomes are daily used in head and neck oncology clinical practice. Clinical outcome assessments can be classified into categories according to who makes the report: clinician-reported outcome assessment (health professional); observer-reported outcome assessment (caregiver) and patient-reported outcome assessment (patient or proxies). We present our opinion and we share our experience concerning routine assessment of Health Related Quality of Life outcomes and its incorporation in head and neck cancer clinical practice. The critical factors for successful implementation we identified in a decade of experience were: the institutional approval and support, the inclusion of all first line caregivers, the standardization of team objectives and institutional proposes; team formation and training, promotion of defined workflow in daily clinical practice and the continuous monitoring and analysis. Ten years after, our team developed a much broader and inclusive understanding of Health Related Quality of Life importance in the course of the disease. Head and neck cancer patients consider the questionnaires administration as part of the clinical approach they know that someone, somewhere, will use these patient-centered outcomes to improve healthcare quality – this is also our main goal.
Cox Proportional Hazard Regression Analysis of Dengue Hemorrhagic Fever

Survival analysis is a statistical procedure used to analyze data in the form of time of the incident until an event occurs. The purpose of the survival analysis is to estimate the probability of survival, recurrence, death or other events until a certain period of time. In this case, one of the regression method that can be used Cox Proportional Hazard (Cox PH) regression. Data used in this research is data of 70 patients Dengue Hemorrhagic Fever (DHF) in Makassar City Hospital. The results of analysis indicated that the factor that most affect the rate of healing DHF patients is platelet factor. The rate of recovery of patients with DHF with platelet counts below normal is 2,625 times the normal platelet count. Therefore, patients with dengue disease who have lower platelet counts tend to have a longer recovery rate than patients who have normal platelet counts.
I. Observations on the Fine Structure of the Yeast Cell

Vegetative cells of Saccharomyces cerevisiae were fixed with potassium permanganate followed by uranyl nitrate, embedded in methacrylate, and studied in electron micrographs of thin sections. Details of the structure of the cell wall, cytoplasmic membrane, nucleus, vacuole, and mitochondria are described. Cell membranes, about 70 to 80 A thick, have been resolved into two dense layers, 20 to 25 A thick, separated by a light layer of the same dimensions, which correspond in thickness and appearance to the components of the "uni t membrane" as described by Robertson (15). The cell wall is made up of zones of different electron opacity. Underlying the cell wall is the cytoplasmic membrane, a sinuous structure with numerous invaginations. The nucleoplasm, often of uneven electron opacity, is enclosed in a pair of unit membranes in which nuclear pores are apparent. The vacuole, limited by a single unit membrane, is usually irregular in outline and contains some dense material. Rod-shaped mitochondria, 0.4 to 0.6 g in length and 0.2 to 0.3 g in diameter, are smaller in size, but similar in structure to some of those described in plant and animal cells. Attempts to use osmium tetroxide as fixative were unsuccessful, a result similar to that obtained by other workers. I t is suggested that yeast cells are impermeable to osmium tetroxide, except when grown under specific conditions. The fine structure of the yeast cell was first studied in the electron microscope by Agar and Douglas (1). The cells were grown on a special presporulation medium and fixed in osmium tetroxide. These authors found, however, that cells grown on other media failed to fix satisfactorily in osmium tetroxide. We have confirmed this observation, but have found that cells grown on chemically defined media under aerobic conditions and suitable for metabolic studies can be satisfactorily prepared for electron microscopy by the fixation procedure described below. Membrane systems are particularly well preserved by this method. This communication is a part of a study of the oxidative metabolism in baker's yeast and describes the structure of the yeast cells used for such studies. An accompanying paper (17) describes some of the biochemical properties of isolated yeast particles and relates their morphology to cytoplasmic structures described herein. M A T E R I A L S A N D M E T H O D S Aerobically grown baker's yeast cells in their early stationary phase were obtained directly from the fermenters of Mauri Bros. & Thomson Ltd., Sydney. They were washed and used directly or transferred onto one of the two following media for further growth. On a small scale the cells were mainly grown
Project 1: Elucidating the role of carbon storage regulator A, csrA, in regulating the AcrAB-TolC efflux system in Salmonella enterica serovar Typhimurium andProject 2: Exploring the dynamics of Pseudomonas aeruginosa attachment to host cells during anti-adhesion therapy

Project 1: In MDR isolates of Enterobacteriaceae, except Escherichia coli and Shigella spp. , RamA, locally regulated by RamR, activates the transcription of the tripartite efflux pump, AcrAB-TolC. TraDIS sequencing of Salmonella enterica serovar Typhimurium SL1344 generated gene-deletion mutants, which were interrogated with pMW82-pramA, encoding a green fluorescent protein (GFP) fused to the ramA promoter sequence. Disruption of the csrA gene in SL1344 resulted in a significant increase in the fluorescence of pMW82-pramA, therefore it was hypothesised that CsrA is involved in the regulation of RamA and the generation of antimicrobial resistance by upregulation of AcrAB-TolC. The aims of this study were to create and characterise a csrA::aph mutant in SL1344. Project 2: There is an urgent need for alternative therapeutics to treat bacterial infections and limit the transmission of resistance. The attachment of bacteria to host cells is considered a prerequisite for bacteria to establish and propagate infection and anti-attachment therapies are well-documented; however, clinical treatments are currently unavailable. Mathematical modelling is a useful tool to model the efficacy of anti-virulence therapies in silico, particularly in combination with standard antibiotics, although, computer simulations based on theoretical values may limit the specificity of dosing regimens. The aims of this study were to generate experimental data in support of in silico modelling for anti-virulence therapy.
THE LYSIS OF GROUP A HEMOLYTIC STREPTOCOCCI BY EX- TRACELLULAR ENZYMES OF STREPTOMYCES ALBUS I. PRODUCTION AND FRACTIONATION OF "l'JJa~ LYTIC ENZYMES BY MACLYN McCARTY, M.D

The lysis of bacteria by Streptomyces has been studied in detail by Welsch, using a strain designated as Streptomyces albu, G, and he has given the name actinomycetin to the soluble preparations from this organism which are capable of lysing heat-killed Gram-negative organisms and many species of living Gram-positive organisms. Welsch has prepared an extensive monograph concerned with his investigations (2). Maxted (3) applied the techniques of lysis with Streptomyces albus preparations to the practical problem of grouping hemolytic streptococci, and showed that lysates containing the group-specific polysaccharide could be prepared rapidly as a routine laboratory procedure. The value of this procedure has been confirmed in other laboratories (4, 5). The fact that Streptomyces albus elaborates a soluble, extracellular enzyme system which can dissolve hemolytic streptococci suggests that this material may provide a potential tool for the study of cellular components of group A streptococci. The need for gentle, more biological methods of extracting the cellular components of streptococci is emphasized by the nature of the procedures that are now required for obtaining certain of the antigenic constituents in soluble form. The type-specific M protein, for example, is best prepared by heating cells at 100°C. and pH 2 (6). While this procedure has proved useful in the study of M protein, it has no general applicability for the investigation of other cellular constituents. Prior to the use of Streptomyces albus enzymes for the release of the group-specific carbohydrate, the application of enzymatic techniques to the extraction of hemolytic streptococci has been limited to the preparation of certain antigens, as exemplified by the release of T antigen from group A cells with the aid of trypsin (7).
A N T I G E N I C RELATIONSHIPS BETWEEN I M M U N E GL()BUIANS AND CERTAIN RELATED PARAPROTEINS IN MAN* By EDWARD C. FRANKLIN,{: M.D., AND DENIS R. STANWORTH,§ ProD

I t is now generally accepted that the serum antibodies in man and several other species are associated with a group of structurally and functionally closely related proteins known collectively as the "immune globulins" (1, 2). In man these consist of the two major molecular size types of y-globulins, i.e., 7S and 19S y-globulins, as well as the B2a-globulin recently isolated by Heremans and coworkers (3). I t now appears probable that the 19S y-globulin is identical to the ~2M-globulin defined by immunoelectrophoresis (2). Certain proliferative states of the plasmocytic and lymphocytic cell systems are associated with the production of a group of closely related paraproteins. These include the 3'and/~-myeloma proteins associated with multiple myeloma and a group of high molecular weight macroglobulins found in macroglobulinemia of Waldenstr6m. In addition, the antigenically related Bcnce Jones proteins of smaller molecular size are frequently seen in the urine in both conditions (1, 2). While each of these proteins possesses a certain degree of unique antigenic specificity, their serological cross-reactivity can be readily demonstrated (3-5). However, studies to elucidate the nature of this cross-reactivity have been hampered by the structural complexity of these proteins. The recent finding that human 7S y-globulins can be reproducibly degraded to smaller units which differ from each other in antigenic properties by the method described by Porter (6) offers a possible approach to a clearer definition of the antigenic relationships between these proteins (7). In the present report experiments are described comparing the antigenic properties of these proteins to the two major antigenicatly distinct fragments of 7S y-globulin. The results indicate that all of these proteins cross-react with 7S y-globulin and each other by virtue of certain determinant groups associated with those fragments of 7S y-globulin that carry the antibody-combining
Metode deteksi untuk pengujian respon ketahanan beberapa genotipe cabai terhadap infeksi chilli veinal mottle potyvirus (ChiVMV)

ENDANG OPRIANA. Detection Methods for Evaluastion of Response of Chillipepper Genotypes to chilli veinal mottle potyvirus (ChiVMV) Infection Survey SRI HENDRASTUTI HIDAYAT and SRIANI SUJIPRIHATI. Chilli veinal mottle potyvirus (ChiVMV) are considered one of the major constraints to chilli production In Indonesia. Preliminary surveys in several provinces in 2005 indicated that ChiVMV were causing disease incidence up to 100%. The use of resistance varieties has become the major focus for controlling ChiVMV. To support breeding activities in developing chillipepper varieties resistace to ChiVMV, rapid and accurate detection method is required. The research was conducted involving three activities: 1) survey to chillipepper growing area to collect field isolates of ChiVMV; 2) evaluation of detection method for ChiVMV, i.e: ELISA, DIBA, and RT-PCR; 3) evaluation of chillipepper genotypes for resistence to ChiVMV. It was evidenced from the survey that ChiVMV infection has spread widely in chillipepper growing area. Thirteen isolates of ChiVMV were collected and 5 of them showing different symptom types were selected for further studies. Three detection methods tested using 5 different ChiVMV isolates showed variability results in term of their sensitifity. I-ELISA was able to detect ChiVMV at the level of 1: 10.000 (b/w) of leaf extraction; whereas DIBA has less sensitifity with detection level of 1 : 1.000 of leaf extract. However, DIBA requires less amount of antiserum and shorter detection time than I-ELISA. Specific DNA fragment of ChiVMV i.e. 800 bp in size was successfully amplified using RTPCR. Evaluation of genotypes showed that IPB C1, PBC 521, IPB C10 with highly resistance response and IPB C8, IPB C17, IPB C 14 and Keriting Sumatera with resistence response might be useful for further breeding activities to develop ChiVMV resistance varieties. It was further proved that IPB C99 showed high signal in DIBA when inoculated with the most virulent ChiVMV isolates (CKB) and less virulent isolates (BL) while IPB C521 showed very weak signal in inoculated leaves in DIBA when inoculated with the most virulent ChiVMV isolates (CKB). Its proved that plant response to virus infection definately related to plant genotipes and virulence level of pathogen.
Pulse-shape effects in qubit dynamics demonstrated on an IBM quantum computer

We present a study of the coherent interaction of a qubit with a pulse-shaped external field of a constant carrier frequency. We explore, theoretically and experimentally, the transition line profile -- the dependence of the transition probability on the detuning -- for five different pulse shapes: rectangular, Gaussian, hyperbolic-secant, squared hyperbolic-secant and exponential. The theoretical description for all cases but sech$^2$ is based on the analytical solutions to the Schr\"odinger equation or accurate approximations available in the literature. For the sech$^2$ pulse we derive an analytical expression for the transition probability using the Rosen-Zener conjecture, which proves very accurate. The same conjecture turns out to provide a very accurate approximation for the Gaussian and exponential pulses too. The experimental results are obtained with one of IBMQ's quantum processors. An excellent agreement between theory and experiment is observed, demonstrating some pulse-shape-dependent fine features of the transition probability profile. The mean absolute error -- a measure of the accuracy of the fit -- features an improvement by a factor of 4 to 8 for the analytic models compared to the commonly used Lorentzian fits. Moreover, the uncertainty of the qubit's resonance frequency is reduced by a factor of 4 for the analytic models compared to the Lorentzian fits. These results demonstrate both the accuracy of the analytic modelling of quantum dynamics and the excellent coherent properties of IBMQ's qubit.
Combination Radiation Therapy and Oncolytic Vaccinia Virus Therapy in Preclinical Models of Glioma

Figure 2.8. Exposure to IR does not reduce ΔF4LΔJ2R VACV yield in U-87 MG cels. Subconfluent U87 cels were irradiated with 5 Grays (Gy) or 8 Gy IR or mock-irradiated. Cels were infected with ΔF4LΔJ2R VACV at 24 h.p.ir. at an MOI of 0.03 pfu/cel. Cels were harvested at the indicated time points and titred on BSC40 cels. Points ploted represent mean titres +/S.E. M. from three independent experiments. Virus yield at 96 h.p.ir. was not reduced in irradiated cels compared to non-irradiated (t-test, p>0.05). 0 24 48 72 96 0.01 0.1 1 10 100
Implementation of the Critical Wave Groups Method with Computational Fluid Dynamics and Neural Networks

Accurate and efficient prediction of extreme ship responses continues to be a challenging problem in ship hydrodynamics. Probabilistic frameworks in conjunction with computationally efficient numerical hydrodynamic tools have been developed that allow researchers and designers to better understand extremes. However, the ability of these hydrodynamic tools to represent the physics quantitatively during extreme events is limited. Previous research successfully implemented the critical wave groups (CWG) probabilistic method with computational fluid dynamics (CFD). Although the CWG method allows for less simulation time than a Monte Carlo approach, the large quantity of simulations required is cost prohibitive. The objective of the present paper is to reduce the computational cost of implementing CWG with CFD, through the construction of long short-term memory (LSTM) neural networks. After training the models with a limited quantity of simulations, the models can provide a larger quantity of predictions to calculate the probability. The new framework is demonstrated with a 2-D midship section of the Office of Naval Research Tumblehome (ONRT) hull in Sea State 7 and beam seas at zero speed. The new framework is able to produce predictions that are representative of a purely CFD-driven CWG framework, with two orders of magnitude of computational cost savings.
Acidic Pericellular Ph: Effects On Proteolysis And Gene Expression As Determined In 3d Models Of Breast Carcinoma

ACIDIC PERICELLULAR PH: EFFECTS ON PROTEOLYSIS AND GENE EXPRESSION AS DETERMINED IN 3D MODELS OF BREAST CARCINOMA by Jennifer M. Rothberg August 2013 Advisor: Bonnie F. Sloane, Ph.D. Major: Cancer Biology (Pharmacology) Degree: Doctor of Philosophy Among the non-cellular microenvironmental factors that contribute to malignancy of solid tumors is an acidic peritumoral pH. The first objective was to determine if an acidic extracellular pH observed in vivo (i.e., pHe 6.8) affects the activity of proteases, such as cathepsin B, that contribute to degradation of collagen IV by tumor cells when grown in biologically relevant three-dimensional cultures. At pHe 6.8 there were increases in pericellular active cysteine cathepsins and in degradation of DQ-collagen IV, which was partially blocked by a cathepsin B inhibitor. Imaging probes for active cysteine cathepsins localized to tumors in vivo. The amount of bound probe decreased in tumors in bicarbonate-treated mice, a treatment previously shown to increase peritumoral pHe and reduce local invasion of the tumors. Our results are consistent with the acid-mediated invasion hypothesis and with a role for cathepsin B in promoting degradation of a basement membrane protein substrate, i.e. type IV collagen, in an acidic peritumoral environment. The second objective was to use a microarray approach to identify significantly altered genes that may be of