Miracle-dz/UniFAR-FTUs huggingface dataset:
CpG‐DNA upregulates the major acute‐phase proteins SAA and SAP

The acute‐phase response is an immediate reaction of the host against invading microorganisms. We show here that oligodeoxynucleotides (ODNs) containing a CpG motif rapidly induce the major murine acute‐phase proteins in vivo, i.e. serum amyloid A (SAA) and serum amyloid P (SAP). Serum levels of these proteins are elevated within 12 h and peak at 24 h after the injection of CpG‐ODN or endotoxin. Liver cells produce the proteins with the same kinetics. Injection of interleukin 6 (IL‐6), IL‐1β and tumour necrosis factor α (TNF‐α) induces SAA and SAP in vivo, but the CpG‐ODN‐mediated induction does not depend on the presence of the TNF receptor p55, as the acute‐phase response in TNF receptor p55‐deficient mice does not differ from that of wild‐type mice. Aside from CpG‐ODN, bacterial genomic DNA also induces the acute‐phase response in LPS‐resistant C3H/Hej mice. The induction of the major acute‐phase proteins SAA and SAP is blocked by the simultaneous injection of CpG‐ODN together with d‐galactosamine ( d‐GalN). As d‐GalN sensitizes the host for the toxic effects of TNF‐α, a possible mechanism could be the prevention of synthesis of the major acute‐phase proteins SAA and SAP.
Characterization of Clinically Isolated Antibiotic-Resistant Salmonella Typhimurium Exposed to Subinhibitory Concentrations of Ceftriaxone and Ciprofloxacin

This study was designed mainly to assess the phenotypic properties of clinically isolated Salmonella Typhimurium exposed to ceftriaxone and ciprofloxacin. The antibiotic susceptibility, b-lactamase activity, efflux activity, bacterial motility, biofilm-forming ability, and gene expression were determined in S. Typhimurium ATCC 19585 and S. Typhimurium CCARM 8009 when exposed to subinhibitory concentrations of ceftriaxone and ciprofloxacin. S. Typhimurium CCARM 8009 was highly resistant to ampicillin, kanamycin, penicillin G, and streptomycin, showing minimum inhibitory concentration values of more than 512mg/ml, while S. Typhimurium ATCC 19585 showed resistance to erythromycin alone (64mg/ml). The highest b-lactamase activity was observed in S. Typhimurium CCARM 8009 when exposed to ceftriaxone (8.2mmol/min/ml), while the least b-lactamase activity was observed in S. Typhimurium ATCC 19585. Compared to S. Typhimurium CCARM 8009, the ethidium bromide (EtBr) accumulation was considerably increased in S. Typhimurium ATCC 19585 when treated with efflux pump inhibitors. S. Typhimurium ATCC 19585 and S. Typhimurium CCARM 8009 were highly susceptible to ciprofloxacin, erythromycin, levofloxacin, and sparfloxacin in the presence of phenylalanine-arginine-b-naphthylamide. The swimming motility of S. Typhimurium ATCC 19585 exposed to ceftriaxone was significantly reduced to 54% when compared to S. Typhimurium CCARM 8009 (93%). The numbers of attached S. Typhimurium CCARM 8009 cells were significantly increased by more than 1 log cfu/ ml when exposed to ceftriaxone and ciprofloxacin. The relative gene expression was stable in S. Typhimurium CCARM 8009 in the presence of ceftriaxone and ciprofloxacin compared to the absence of antibiotics. These results suggest that the antibiotic susceptibility of S. Typhimurium having different antibiotic resistance profiles varied depending on the presence of ceftriaxone and ciprofloxacin.
Glucose Control in the ICU

During the last 2 decades, the treatment of hyperglycemia in critically ill patients has become one of the most discussed topics in the intensive medicine field. The initial data suggesting significant benefit of normalization of blood glucose levels in critically ill patients using intensive intravenous insulin therapy have been challenged or even neglected by some later studies. At the moment, the need for glucose control in critically ill patients is generally accepted yet the target glucose values are still the subject of ongoing debates. In this review, we summarize the current data on the benefits and risks of tight glucose control in critically ill patients focusing on the novel technological approaches including continuous glucose monitoring and its combination with computer-based algorithms that might help to overcome some of the hurdles of tight glucose control. Since increased risk of hypoglycemia appears to be the major obstacle of tight glucose control, we try to put forward novel approaches that may help to achieve optimal glucose control with low risk of hypoglycemia. If such approaches can be implemented in real-world practice the entire concept of tight glucose control may need to be revisited.
Adapting a part-of-speech tagset to non-standard text: The case of STTS

The Stuttgart-Tübingen TagSet (STTS) is a de-facto standard for the part-of-speech tagging of German texts. Since its first publication in 1995, STTS has been used in a variety of annotation projects, some of which have adapted the tagset slightly for their specific needs. Recently, the focus of many projects has shifted from the analysis of newspaper text to that of non-standard varieties such as user-generated content, historical texts, and learner language. These text types contain linguistic phenomena that are missing from or are only suboptimally covered by STTS; in a community effort, German NLP researchers have therefore proposed additions to and modifications of the tagset that will handle these phenomena more appropriately. In addition, they have discussed alternative ways of tag assignment in terms of bipartite tags (stem, token) for historical texts and tripartite tags (lexicon, morphology, distribution) for learner texts. In this article, we report on this ongoing activity, addressing methodological issues and discussing selected phenomena and their treatment in the tagset adaptation process.
Matrix reconstruction with the local max norm

We introduce a new family of matrix norms, the "local max" norms, generalizing existing methods such as the max norm, the trace norm (nuclear norm), and the weighted or smoothed weighted trace norms, which have been extensively used in the literature as regularizers for matrix reconstruction problems. We show that this new family can be used to interpolate between the (weighted or unweighted) trace norm and the more conservative max norm. We test this interpolation on simulated data and on the large-scale Netflix and MovieLens ratings data, and find improved accuracy relative to the existing matrix norms. We also provide theoretical results showing learning guarantees for some of the new norms.
A local quantitative measure for community detection in networks

Recently, it has been proved that the resolution of methods based on optimising the modularity Q is limited. In order to improve this limit, a novel local quantitative measure called normalised modularity density NMD is proposed and optimised by simulated annealing technique. Both theoretical certifications on some schematic examples and numerical results on a suit of computer-generated and real-world networks show that optimising NMD can detect communities with different scales, especially small dense communities that optimising Q cannot detect, which provides meaningful evidence that optimising NMD can improve the resolution limit in optimising modularity Q.
Hydrophobic Fluorescent Probes Introduce Artifacts into Single Molecule Tracking Experiments Due to Non-Specific Binding

Single-molecule techniques are powerful tools to investigate the structure and dynamics of macromolecular complexes; however, data quality can suffer because of weak specific signal, background noise and dye bleaching and blinking. It is less well-known, but equally important, that non-specific binding of probe to substrates results in a large number of immobile fluorescent molecules, introducing significant artifacts in live cell experiments. Following from our previous work in which we investigated glass coating substrates and demonstrated that the main contribution to this non-specific probe adhesion comes from the dye, we carried out a systematic investigation of how different dye chemistries influence the behaviour of spectrally similar fluorescent probes. Single-molecule brightness, bleaching and probe mobility on the surface of live breast cancer cells cultured on a non-adhesive substrate were assessed for anti-EGFR affibody conjugates with 14 different dyes from 5 different manufacturers, belonging to 3 spectrally homogeneous bands (491 nm, 561 nm and 638 nm laser lines excitation). Our results indicate that, as well as influencing their photophysical properties, dye chemistry has a strong influence on the propensity of dye-protein conjugates to adhere non-specifically to the substrate. In particular, hydrophobicity has a strong influence on interactions with the substrate, with hydrophobic dyes showing much greater levels of binding. Crucially, high levels of non-specific substrate binding result in calculated diffusion coefficients significantly lower than the true values. We conclude that the physic-chemical properties of the dyes should be considered carefully when planning single-molecule experiments. Favourable dye characteristics such as photostability and brightness can be offset by the propensity of a conjugate for non-specific adhesion.
Stimulus Dependence of Barrel Cortex Directional Selectivity

Neurons throughout the rat vibrissa somatosensory pathway are sensitive to the angular direction of whisker movement. Could this sensitivity help rats discriminate stimuli? Here we use a simple computational model of cortical neurons to analyze the robustness of directional selectivity. In the model, directional preference emerges from tuning of synaptic conductance amplitude and latency, as in recent experimental findings. We find that directional selectivity during stimulation with random deflection sequences is strongly dependent on the mean deflection frequency: Selectivity is weakened at high frequencies even when each individual deflection evokes strong directional tuning. This variability of directional selectivity is due to generic properties of synaptic integration by the neuronal membrane, and is therefore likely to hold under very general physiological conditions. Our results suggest that directional selectivity depends on stimulus context. It may participate in tasks involving brief whisker contact, such as detection of object position, but is likely to be weakened in tasks involving sustained whisker exploration (e.g., texture discrimination).
A Numerical Method for the Inverse Stochastic Spectrum Problem

The inverse stochastic spectrum problem involves the construction of a stochastic matrix with a prescribed spectrum. The problem could be solved by first constructing a nonnegative matrix with the same prescribed spectrum. A differential equation aimed to bring forth the steepest descent flow in reducing the distance between isospectral matrices and nonnegative matrices, represented in terms of some general coordinates, is described. The flow is further characterized by an analytic singular value decomposition to maintain the numerical stability and to monitor the proximity to singularity. This flow approach can be used to design Markov chains with specified structure. Applications are demonstrated by numerical examples.
Cytokine Network Involvement in Subjects Exposed to Benzene

Benzene represents an ubiquitous pollutant both in the workplace and in the general environment. Health risk and stress posed by benzene have long been a concern because of the carcinogenic effects of the compound which was classified as a Group 1 carcinogen to humans and animals. There is a close correlation between leukemia, especially acute myeloid leukemia, and benzene exposure. In addition, exposure to benzene can cause harmful effects on immunological, neurological, and reproductive systems. Benzene can directly damage hematopoietic progenitor cells, which in turn could lead to apoptosis or may decrease responsiveness to cytokines and cellular adhesion molecules. Alternatively, benzene toxicity to stromal cells or mature blood cells could disrupt the regulation of hematopoiesis, including hematopoietic commitment, maturation, or mobilization, through the network of cytokines, chemokines, and adhesion molecules. Today there is mounting evidence that benzene may alter the gene expression, production, or processing of several cytokines in vitro and in vivo. The purpose of this review was to systematically analyze the published cases of cytokine effects on human benzene exposure, particularly hematotoxicity, and atopy, and on lungs.
Rock-fall hazards in the Yosemite Valley

This report with map shows the areas of highest rock-fall hazard in four selected parts of Yosemite Valley, California, defined by the National Park Service. Two specific levels of hazard are recognized and identified from rock falls ranging in size from individual boulders to moderatesized events with volumes of 100,000 m3. These different levels of hazard are associated with areas within the base of the talus (red line in Plate 1) and those normally beyond the base of the talus which we refer to as the rock-fall shadow (yellow line in Plate 1). Rock falls of even greater size, exceeding 100,000 m3, referred to as rock avalanches, are a potential hazard, but the extent of this hazard is not easily defined. Rock avalanches are considered to be much less likely to occur because of the relatively few prehistoric rock-fall avalanche deposits that have been recognized in the Yosemite Valley. With the configuration of the steep valley walls and the relatively narrow valley, it should be noted that there are no absolutely safe or zero probability areas from large rock avalanches. This study has shown in map form where rock-fall hazard exists and has given general indication of the expected frequency of these events; however, the study does not quantify the probability at any specific location, nor evaluate the risk to people or facilities to such events.
PHENOLOGICAL AND FITNESS RESPONSE TO WARMING 457

Significant changes in plant phenology have been observed in response to increases in mean global temperatures. There are concerns that accelerated phenologies can negatively impact plant populations. However, the fitness consequence of changes in phenology in response to elevated temperature is not well understood, particularly under field conditions. We address this issue by exposing a set of recombinant inbred lines of Arabidopsis thaliana to a simulated global warming treatment in the field. We find that plants exposed to elevated temperatures flower earlier, as predicted by photothermal models. However, contrary to life-history trade-off expectations, they also flower at a larger vegetative size, suggesting that warming probably causes acceleration in vegetative development. Although warming increases mean fitness (fruit production) by ca. 25%, there is a significant genotype-by-environment interaction. Changes in fitness rank indicate that imminent climate change can cause populations to be maladapted in their new environment, if adaptive evolution is limited. Thus, changes in the genetic composition of populations are likely, depending on the species’ generation time and the speed of temperature change. Interestingly, genotypes that show stronger phenological responses have higher fitness under elevated temperatures, suggesting that phenological sensitivity might be a good indicator of success under elevated temperature at the genotypic level as well as at the species level.
Allopolyploid speciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization.

Thirty-six percent of the wild potato (Solanum L. section Petota Dumort.) species are polyploid, and about half of the polyploids are tetraploid species (2n = 4x = 48). Determination of the type of polyploidy and development of the genome concept for members of section Petota traditionally has been based on the analysis of chromosome pairing in species and their hybrids and, most recently, DNA sequence phylogenetics. Based on these data, the genome designation AABB was proposed for Mexican tetraploid species of series Longipedicellata Buk. We investigated this hypothesis with genomic in situ hybridization (GISH) for both representatives of the series, S. stoloniferum Schltdl. and S. hjertingii Hawkes. GISH analysis supports an AABB genome constitution for these species, with S. verrucosum Schltdl. (or its progenitor) supported as the A genome donor and another North or Central American diploid species (S. cardiophyllum Lindl., S. ehrenbergii (Bitter) Rydb. , or S. jamesii Torrey) as the B genome donor. GISH analysis of chromosome pairing of S. stoloniferum also confirms the strict allopolyploid nature of this species. In addition, fluorescence in situ hybridization data suggest that 45S rDNA regions of the two genomes of S. stoloniferum were changed during coevolution of A and B genomes of this allotetraploid species.
Six-year follow-up of a preventive intervention for parentally bereaved youths: a randomized controlled trial.

OBJECTIVE To evaluate the efficacy of the Family Bereavement Program (FBP) to prevent mental health problems in parentally bereaved youths and their parents 6 years later. DESIGN Randomized controlled trial. SETTING Arizona State University Prevention Research Center from November 2002 to July 2005. PARTICIPANTS Two hundred eighteen bereaved youths (89.34% of 244 enrolled in the trial 6 years earlier) and 113 spousally bereaved parents. INTERVENTIONS The FBP includes 12 group sessions for caregivers and youths; the literature control (LC) condition includes bereavement books for youths and caregivers. MAIN OUTCOME MEASURES Comparisons of youths in the FBP and LC on a measure of mental disorder diagnosis, 5 measures of mental health problems, and 4 measures of competent functioning; and comparisons of spousally bereaved parents on 2 measures of mental health problems. RESULTS Youths in the FBP as compared with those in the LC had significantly lower externalizing problems as reported by caregivers and youths (adjusted mean, -0.06 vs 0.13, respectively; P = .02) and on teacher reports of externalizing problems (adjusted mean, 52.69 vs 56.27, respectively; P = .001) and internalizing problems (adjusted mean, 47.29 vs 56.27, respectively; P = .002), and they had higher self-esteem (adjusted mean, 33.93 vs 31.91, respectively; P = .005). Parents in the FBP had lower depression scores than those in the LC (adjusted mean, 5.48 vs 7.83, respectively; P = .04). A significant moderated program effect indicated that for youths with lower baseline problems, the rate of diagnosed mental disorder was lower for those in the FBP than in the LC. CONCLUSION This study demonstrates efficacy of the FBP to reduce mental health problems of bereaved youths and their parents 6 years later. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01008189.
When to say when: can excessive drinking explain silicon uptake in diatoms?

Diatoms are the single most important drivers of the oceanic silicon biogeochemical cycle. Due to their considerable promise in nanotechnology, there is tremendous interest in understanding the mechanism by which they produce their intricately and ornately decorated silica‐based cell wall. Although specific proteins have been implicated in some of the key steps of silicification, the exact mechanisms are poorly understood.
Application of serum anti-Müllerian hormone levels in selecting patients with polycystic ovary syndrome for in vitro maturation treatment

Objective The purpose of this study was to identify useful clinical factors for the identification of patients with polycystic ovary syndrome (PCOS) who would benefit from in vitro maturation (IVM) treatment without exhibiting compromised pregnancy outcomes. Methods A retrospective cohort study was performed of 186 consecutive patients with PCOS who underwent human chorionic gonadotropin-primed IVM treatment between March 2010 and March 2014. Only the first IVM cycle of each patient was included in this study. A retrospective case-control study was subsequently conducted to compare pregnancy outcomes between IVM and conventional in vitro fertilization (IVF) cycles. Results Through logistic regression analyses, we arrived at the novel finding that serum anti-Müllerian hormone (AMH) levels and the number of fertilized oocytes in IVM were independent predictive factors for live birth with unstandardized coefficients of 0.078 (95% confidence interval [CI], 1.005–1.164; p=0.037) and 0.113 (95% CI, 1.038–1.208; p=0.003), respectively. Furthermore, these two parameters were able to discriminate patients who experienced live births from non-pregnant IVM patients using cut-off levels of 8.5 ng/mL and five fertilized oocytes, respectively. A subsequent retrospective case-control study of patients with PCOS who had serum AMH levels ≥8.5 ng/mL showed that IVM had pregnancy outcomes comparable to conventional IVF, and that no cases of ovarian hyperstimulation syndrome were observed. Conclusion Serum AMH levels are a useful factor for predicting pregnancy outcomes in PCOS patients before the beginning of an IVM cycle. IVM may be an alternative to conventional IVF for PCOS patients if the patients are properly selected according to predictive factors such as serum AMH levels.
Preventing Olanzapine-Induced Weight Gain Using Betahistine: A Study in a Rat Model with Chronic Olanzapine Treatment

Olanzapine is the one of first line antipsychotic drug for schizophrenia and other serious mental illness. However, it is associated with troublesome metabolic side-effects, particularly body weight gain and obesity. The antagonistic affinity to histamine H1 receptors (H1R) of antipsychotic drugs has been identified as one of the main contributors to weight gain/obesity side-effects. Our previous study showed that a short term (2 weeks) combination treatment of betahistine (an H1R agonist and H3R antagonist) and olanzapine (O+B) reduced (−45%) body weight gain induced by olanzapine in drug-naïve rats. A key issue is that clinical patients suffering with schizophrenia, bipolar disease and other mental disorders often face chronic, even life-time, antipsychotic treatment, in which they have often had previous antipsychotic exposure. Therefore, we investigated the effects of chronic O+B co-treatment in controlling body weight in female rats with chronic and repeated exposure of olanzapine. The results showed that co-administration of olanzapine (3 mg/kg, t.i.d.) and betahistine (9.6 mg/kg, t.i.d.) significantly reduced (−51.4%) weight gain induced by olanzapine. Co-treatment of O+B also led to a decrease in feeding efficiency, liver and fat mass. Consistently, the olanzapine-only treatment increased hypothalamic H1R protein levels, as well as hypothalamic pAMPKα, AMPKα and NPY protein levels, while reducing the hypothalamic POMC, and UCP1 and PGC-1α protein levels in brown adipose tissue (BAT). The olanzapine induced changes in hypothalamic H1R, pAMPKα, BAT UCP1 and PGC-1α could be reversed by co-treatment of O+B. These results supported further clinical trials to test the effectiveness of co-treatment of O+B for controlling weight gain/obesity side-effects in schizophrenia with chronic antipsychotic treatment.
Patent Protection and Innovation Over 150 Years

The paper seeks to understand the impact of the patent system on innovation by examining shifts in the strength of patent protection across sixty countries and a 150-year period. An examination of 177 policy changes reveals that strengthening patent protection appears to have few positive effects on patent applications by entities in the country undertaking the policy change, whether filings in Great Britain or the nation making the policy change are considered. Cross-sectional analyses suggest that the impact of patent protection-enhancing shifts were greater in nations with weaker initial protection and greater economic development, consistent with economic theory. I address concerns about the endogeneity of these changes by employing an instrumental variable approach.