Miracle-dz/UniFAR-FTUs huggingface dataset:
SNF1-related kinases allow plants to tolerate herbivory by allocating carbon to roots

Herbivore attack elicits costly defenses that are known to decrease plant fitness by using resources that are normally slated for growth and reproduction. Additionally, plants have evolved mechanisms for tolerating attack, which are not understood on a molecular level. Using 11C-photosynthate labeling as well as sugar and enzyme measurements, we found rapid changes in sink–source relations in the annual Nicotiana attenuata after simulated herbivore attacks, which increased the allocation of sugars to roots. This herbivore-induced response is regulated by the β-subunit of an SnRK1 (SNF1-related kinase) protein kinase, GAL83, transcripts of which are rapidly down-regulated in source leaves after herbivore attack and, when silenced, increase assimilate transport to roots. This C diversion response is activated by herbivore-specific elicitors and is independent of jasmonate signaling, which regulates most of the plant's defense responses. Herbivore attack during early stages of development increases root reserves, which, in turn, delays senescence and prolongs flowering. That attacked GAL83-silenced plants use their enhanced root reserves to prolong reproduction demonstrates that SnRK1 alters resource allocation so that plants better tolerate herbivory. This tolerance mechanism complements the likely defensive value of diverting resources to a less vulnerable location within the plant.
Dietary fiber intake and risk of colorectal cancer and incident and recurrent adenoma in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial.

BACKGROUND Dietary fiber has been associated with a reduced risk of colorectal cancer. However, it remains unclear at which stage in the carcinogenic pathway fiber may act or which food sources of dietary fiber may be most beneficial against colorectal cancer development. OBJECTIVE The objective was to prospectively evaluate the association between dietary fiber intake and the risk of incident and recurrent colorectal adenoma and incident colorectal cancer. DESIGN Study participants were identified from the intervention arm of the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial. Participants received flexible sigmoidoscopy at baseline and 3 or 5 y after. Dietary fiber intake was measured by using a self-reported dietary questionnaire. The colorectal cancer, incident adenoma, and recurrent adenoma analyses were based on 57,774, 16,980, and 1667 participants, respectively. Unconditional logistic regression was used to assess the risk of incident and recurrent adenoma, and Cox proportional hazards models were used to assess the risk of colorectal cancer across categories of dietary fiber intake, with adjustment for potential confounders. RESULTS Elevated total dietary fiber intake was associated with a significantly reduced risk of incident distal colorectal adenoma (ORhighest vs. lowest tertile of intake: 0.76; 95% CI: 0.63, 0.91; P-trend = 0.003) but not recurrent adenoma (P-trend = 0.67). Although the association was not statistically significant for colorectal cancer overall (HR: 0.85; 95% CI: 0.70, 1.03; P-trend = 0.10), a reduced risk of distal colon cancer was observed with increased total fiber intake (HR: 0.62; 95% CI: 0.41, 0.94; P-trend = 0.03). Protective associations were most notable for fiber originating from cereals or fruit. CONCLUSIONS This large, prospective study within a population-based screening trial suggests that individuals consuming the highest intakes of dietary fiber have reduced risks of incident colorectal adenoma and distal colon cancer and that this effect of dietary fiber, particularly from cereals and fruit, may begin early in colorectal carcinogenesis. This trial was registered at clinicaltrials.gov as NCT01696981.
Expression of a myosin regulatory light chain phosphorylation site mutant complements the cytokinesis and developmental defects of Dictyostelium RMLC null cells

In a number of systems phosphorylation of the regulatory light chain (RMLC) of myosin regulates the activity of myosin. In smooth muscle and vertebrate nonmuscle systems RMLC phosphorylation is required for contractile activity. In Dictyostelium discoideum phosphorylation of the RMLC regulates both ATPase activity and motor function. We have determined the site of phosphorylation on the Dictyostelium RMLC and used site-directed mutagenesis to replace the phosphorylated serine with an alanine. The mutant light chain was then expressed in RMLC null Dictyostelium cells (mLCR-) from an actin promoter on an integrating vector. The mutant RMLC was expressed at high levels and associated with the myosin heavy chain. RMLC bearing a ser13ala substitution was not phosphorylated in vitro by purified myosin light chain kinase, nor could phosphate be detected on the mutant RMLC in vivo. The mutant myosin had reduced actin-activated ATPase activity, comparable to fully dephosphorylated myosin. Unexpectedly, expression of the mutant RMLC rescued the primary phenotypic defects of the mlcR- cells to the same extent as did expression of wild-type RMLC. These results suggest that while phosphorylation of the Dictyostelium RMLC appears to be tightly regulated in vivo, it is not essential for myosin-dependent cellular functions.
Event-driven Seismic Interferometry with Ambient Seismic Noise

By cross-correlating recordings of ambient seismic noise, one can retrieve the subsurface reflection response. The quality of the retrieved reflections would depend on the qualities of the ambient noise. In a previous study, we cross-correlated ambient-noise data recorded in a desert area in North Africa and showed that we retrieved reflections. This was done assuming that body-wave noise continuously illuminates the recording array. But this is not necessarily true - noise which carries body-wave information can be present only at certain times. We now use only parts of the recorded noise during the correlation process. These parts contain identifiable body-wave events. We show that the results, retrieved only from the noise containing the events, exhibit clearer reflection arrivals.
Outcomes With Fidaxomicin Therapy in Clostridium difficile Infection

Background and Goals: Fidaxomicin is a new antibiotic used to treat Clostridium difficile infection (CDI). Given limited clinical experience with fidaxomicin, we assessed outcomes in a diverse cohort of patients with CDI treated with fidaxomicin. Study: All CDI cases treated with fidaxomicin at 3 referral centers over a 4-year period were included. Response was defined as resolution of diarrhea and recurrence was defined by recurrence of CDI within 8 weeks of the end of treatment. Results: Overall, 81 patients (median age 55.9 y; 53% female; 26% with inflammatory bowel disease) were included. Response occurred in 90%. Responders had fewer prior CDI episodes [median 1 (range, 0 to 8)] than nonresponders [median 2.5 (range, 1 to 8)], P=0.01. Response after a first CDI episode was 100%, 96% after 1 prior episode, and 82% after 2 or more, P=0.02. Recurrence occurred in 19%. Patients without recurrence had fewer prior episodes of CDI [median 1 (range, 0 to 6)] than patients who recurred [median 2 (range, 1 to 8)], P=0.005. Recurrence after a first episode was 0%, 23% after 1 prior episode, and 29% after 2 or more, P=0.005. All patients with inflammatory bowel disease responded either with improvement of symptoms or a negative C. difficile test; 19% recurred. Conclusions: All patients with a first CDI episode treated with fidaxomicin responded with no recurrences. Patients with prior CDI episodes were less likely to respond (especially with more than 1 prior episode) and more likely to recur, suggesting a greater clinical benefit of fidaxomicin earlier in the course of CDI.
Prenatal Exposure to Organophosphates, Paraoxonase 1, and Cognitive Development in Childhood

Background: Prenatal exposure to organophosphate pesticides has been shown to negatively affect child neurobehavioral development. Paraoxonase 1 (PON1) is a key enzyme in the metabolism of organophosphates. Objective: We examined the relationship between biomarkers of organophosphate exposure, PON1, and cognitive development at ages 12 and 24 months and 6–9 years. Methods: The Mount Sinai Children’s Environmental Health Study enrolled a multiethnic prenatal population in New York City between 1998 and 2002 (n = 404). Third-trimester maternal urine samples were collected and analyzed for organophosphate metabolites (n = 360). Prenatal maternal blood was analyzed for PON1 activity and genotype. Children returned for neurodevelopment assessments ages 12 months (n = 200), 24 months (n = 276), and 6–9 (n = 169) years of age. Results: Prenatal total dialkylphosphate metabolite level was associated with a decrement in mental development at 12 months among blacks and Hispanics. These associations appeared to be enhanced among children of mothers who carried the PON1 Q192R QR/RR genotype. In later childhood, increasing prenatal total dialkyl- and dimethylphosphate metabolites were associated with decrements in perceptual reasoning in the maternal PON1 Q192R QQ genotype, which imparts slow catalytic activity for chlorpyrifos oxon, with a monotonic trend consistent with greater decrements with increasing prenatal exposure. Conclusion: Our findings suggest that prenatal exposure to organophosphates is negatively associated with cognitive development, particularly perceptual reasoning, with evidence of effects beginning at 12 months and continuing through early childhood. PON1 may be an important susceptibility factor for these deleterious effects.
Kinesthesia: The role of muscle receptors

The kinesthetic sense, the sense of position and movement of our limbs, has been the subject of speculation for more than 400 years. The present‐day view is that it is signaled principally by muscle spindles, with a subsidiary role played by skin and joint receptors. The problem with muscle spindles as position sensors is that they are able to generate impulses in response to muscle length changes as well as from fusimotor activity. The central nervous system must be able to distinguish between activity from the two sources. Recent observations on position sense after fatigue and during load‐bearing suggest that an additional source of kinesthetic information comes from a centrally generated sensation, the sense of effort. This has consequences for kinesthesia in the presence of the force of gravity. A contribution from central feedback mechanisms to the sense of effort is relevant to certain clinical conditions. Muscle Nerve, 2006
A Kullback-Leibler View of Maximum Entropy and Maximum Log-Probability Methods

Entropy methods enable a convenient general approach to providing a probability distribution with partial information. The minimum cross-entropy principle selects the distribution that minimizes the Kullback–Leibler divergence subject to the given constraints. This general principle encompasses a wide variety of distributions, and generalizes other methods that have been proposed independently. There remains, however, some confusion about the breadth of entropy methods in the literature. In particular, the asymmetry of the Kullback–Leibler divergence provides two important special cases when the target distribution is uniform: the maximum entropy method and the maximum log-probability method. This paper compares the performance of both methods under a variety of conditions. We also examine a generalized maximum log-probability method as a further demonstration of the generality of the entropy approach.
Protein Purification by Fusion with an Environmentally Responsive Elastin‐Like Polypeptide: Effect of Polypeptide Length on the Purification of Thioredoxin

Elastin‐like polypeptides (ELPs) undergo a reversible, soluble‐to‐insoluble phase transition in aqueous solution upon heating through a characteristic transition temperature (Tt). Incorporating a terminal ELP expression tag into the gene of a protein of interest allows ELP fusion proteins to be purified from cell lysate by cycles of environmentally triggered aggregation, separation from solution by centrifugation, and resolubilization in buffer. In this study, we examine the effect of ELP length on the expression and purification of a thioredoxin‐ELP fusion protein and show that reducing the size of the ELP tag from 36 to 9 kDa increases the expression yield of thioredoxin by 4‐fold, to a level comparable to that of free thioredoxin expressed without an ELP tag, while still allowing efficient purification. However, truncation of the ELP tag also results in a more complex transition behavior than is observed with larger tags. For both the 36 kDa and the 9 kDa ELP tag fused to thioredoxin, dynamic light scattering showed that large aggregates with hydrodynamic radii of ∼2 μm form as the temperature is raised to above the Tt. These aggregates persist at all temperatures above the Tt for the thioredoxin fusion with the 36 kDa ELP tag. With the 9 kDa tag, however, smaller particles with hydrodynamic radii of ∼12 nm begin to form at the expense of the larger, micron‐size aggregates as the temperature is further raised above the Tt. Because only large aggregates can be effectively retrieved by centrifugation, efficient purification of fusion proteins with short ELP tags requires selection of solution conditions that favor the formation of the micron‐size aggregates. Despite this additional complexity, our results show that the ELP tag can be successfully truncated to enhance the yield of a target protein without compromising its purification.
A high isolation CMFB downconversion micromixer

CMOS deep N-well technology can eliminate body effects of NMOS transistors and improve LO-IF and LO-RF isolation in a Gilbert micromixer. A 37 dB LO-IF and 38 dB LO-RF isolation downconversion micromixer with 19 dB conversion gain, IP1/sub dB/ = -19.5 dBm and IIP/sub 3/ = -12.5 dBm when RF = 2.4 GHz and LO = 2.25 GHz is demonstrated in this paper by using 0.18 /spl mu/m deep N-well CMOS technology. The input return loss and output return loss are better than 15 dB for frequencies up to 6 GHz. On the other hand, a downconversion micromixer without deep n-well has almost identical power performance but achieves only 20 dB LO-IF isolation and 21 dB LO-RF isolation even if two kinds of mixers are fabricated in adjacent areas of the same wafer. The downconversion micromixer used here has intrinsically single-to-differential input stage and active differential PMOS loads to increase IF differential gain while CMFB is used to stabilize bias points. An IF differential amplifier converts differential output into a single-ended output. Finally, an off-chip rat-race coupler provides balanced LO signals to facilitate isolation measurement.
Synthesis of Glycine Betaine from Exogenous Choline in the Moderately Halophilic Bacterium Halomonas elongata

ABSTRACT The role of choline in osmoprotection in the moderate halophileHalomonas elongata has been examined. Transport and conversion of choline to betaine began immediately after addition of choline to the growth medium. Intracellular accumulation of betaine synthesized from choline was salt dependent up to 2.5 M NaCl. Oxidation of choline was enhanced at 2.0 M NaCl in the presence or absence of externally provided betaine. This indicates that the NaCl concentration in the growth medium has major effects on the choline-betaine pathway of H. elongata.
Over-expression of ST3Gal-I promotes mammary tumorigenesis

Changes in glycosylation are common in malignancy, and as almost all surface proteins are glycosylated, this can dramatically affect the behavior of tumor cells. In breast carcinomas, the O-linked glycans are frequently truncated, often as a result of premature sialylation. The sialyltransferase ST3Gal-I adds sialic acid to the galactose residue of core 1 (Galβ1,3GalNAc) O-glycans and this enzyme is over-expressed in breast cancer resulting in the expression of sialylated core 1 glycans. In order to study the role of ST3Gal-I in mammary tumor development, we developed transgenic mice that over-express the sialyltransferase under the control of the human membrane-bound mucin 1 promoter. These mice were then crossed with PyMT mice that spontaneously develop mammary tumors. As expected, ST3Gal-I transgenic mice showed increased activity and expression of the enzyme in the pregnant and lactating mammary glands, the stomach, lungs and intestine. Although no obvious defects were observed in the fully developed mammary gland, when these mice were crossed with PyMT mice, a highly significant decrease in tumor latency was observed compared to the PyMT mice on an identical background. These results indicate that ST3Gal-I is acting as a tumor promoter in this model of breast cancer. This, we believe, is the first demonstration that over-expression of a glycosyltransferase involved in mucin-type O-linked glycosylation can promote tumorigenesis.
The Observational Consequences of Merging Clusters of Galaxies

We present an observational analysis of the numerical simulations of galaxy custer mergers. We identify several observational signatures of recent merger activity and quantitatively assess the uncertainty introduced into cluster mass estimates when invoking the commonly held assumptions of hydrostatic equilibrium, virial equilibrium, spherical symmetry, and isothermality. We find that mergers result in multiple X-ray peaks, long-lived elongation of the X-ray emission, as well as isophotal twisting and centroid shifting to a degree consistent with recent observations. We also find an enlargement of the X-ray core relative to the dark matter core. Mergers result in nonisothermal clusters exhibiting observable inhomogeneities in the emission-weighted X-ray temperature of several keV on linear scales of less than 0.5 Mpc. The resulting gasdynamics are extremely complex, and we present an example of what might be observed by a high resolution X-ray spectograph. We further speculate that the gas dynamics, via shocks, bulk flows, and turbulence, play an important role in the evolution of cluster galaxies and associated radio sources, particularly wide-angle tailed (WAT) sources and radio halos. We find that X-ray based cluster mass estimates made under equilibrium assumptions can be uncertain by 50% or more in the first 2 Gyrs after a merger and by up to 25% after 2 Gyrs depending on the details of the analysis and projection effects. Uncertainties can be considerably larger if the temperature is not well constrained. Similar uncertainties are observed in the X-ray derived baryon mass fractions. Virial mass estimates are typically overestimated because the observed one-dimensional velocity dispersion can be severely contaminated by the infall velocity of the subcluster.
Towards a Cubical Type Theory without an Interval

Following the cubical set model of type theory which validates the univalence axiom, cubical type theories have been developed that interpret the identity type using an interval pretype. These theories start from a geometric view of equality. A proof of equality is encoded as a term in a context extended by the interval pretype. Our goal is to develop a cubical theory where the identity type is defined recursively over the type structure, and the geometry arises from these definitions. In this theory, cubes are present explicitly, e.g., a line is a telescope with 3 elements: two endpoints and the connecting equality. This is in line with Bernardy and Moulin's earlier work on internal parametricity. In this paper we present a naive syntax for internal parametricity and by replacing the parametric interpretation of the universe, we extend it to univalence. However, we do not know how to compute in this theory. As a second step, we present a version of the theory for parametricity with named dimensions which has an operational semantics. Extending this syntax to univalence is left as further work.
severity of nonalcoholic fatty liver disease is associated with ncreased cardiovascular risk in a large cohort of non-obese sian subjects i

Backgrounds: Nonalcoholic fatty liver disease (NAFLD) has been linked to cardiovascular disease (CVD) but it is largely unknown if such a relationship between NAFLD and CVD risk relates to severity of liver disease or if it is independent. We aimed to study the severity of NAFLD in a well characterized non-obese population and to compare this to prevalence of CVD risk factors and Framingham risk score. Methods: This study included 30,172 subjects. Based on the presence or absence of steatosis on ultrasound and serum alanine aminotransferase (ALT), subjects were divided into controls, an increased serum ALT group without steatosis and a group with presumed nonalcoholic fatty liver disease (NAFLD), which included a steatosis alone group and a group with presumed nonalcoholic steatohepatitis (NASH) with steatosis and an elevated ALT. ramingham risk score epatic steatosis Results: The odds ratio for 10-year risk by total Framingham risk scores ≥10% was 5.3 times higher in NASH groups. The prevalence of diabetes, hypertension, elevated CRP and metabolic syndrome were all increased up to 15-fold over controls, independent of age, BMI, smoking and exercise habits. Overall CVD risk was significantly greater in NASH than in either steatosis or raised ALT alone. Conclusion: Young, non-obese subjects with NAFLD are at significantly increased CVD risk, especially those with NASH. As well as specific therapy for liver disease, a diagnosis of NAFLD should lead to targeted risk assessment and risk factor modification. © 2008 Elsevier Ireland Ltd. All rights reserved.
Projective Non-Negative Matrix Factorization with Applications to Facial Image Processing

We propose a new variant of Non-negative Matrix Factorization (NMF), including its model and two optimization rules. Our method is based on positively constrained projections and is related to the conventional SVD or PCA decomposition. The new model can potentially be applied to image compression and feature extraction problems. Of the latter, we consider processing of facial images, where each image consists of several parts and for each part the observations with different lighting mainly distribute along a straight line through the origin. No regularization terms are required in the objective functions and both suggested optimization rules can easily be implemented by matrix manipulations. The experiments show that the derived base vectors are spatially more localized than those of NMF. In turn, the better part-based representations improve the recognition rate of semantic classes such as the gender or existence of mustache in the facial images.