Miracle-dz/UniFAR-FTUs huggingface dataset:
Fingerprinting: Visualization and Automatic Analysis of Prisoner's Dilemma Strategies

Fingerprinting is a technique for generating a representation-independent functional signature for a game playing agent. Fingerprints can be used to compare agents across representations in an automatic fashion. The theory of fingerprints is developed for software agents that play the iterated prisoner's dilemma. Examples of the technique for computing fingerprints are given. This paper summarizes past results and introduces the following new results. Fingerprints of prisoner's dilemma strategies that are represented as finite-state machines must be rational functions. An example of a strategy that does not have a finite-state representation and which does not have a rational fingerprint function is given: the majority strategy. It is shown that the AllD- and AllC-based fingerprints can be derived from the tit-for-tat fingerprint by a simple substitution. Fingerprints for four new probe strategies are introduced, generalizing previous work in which tit-for-tat is the sole probe strategy. A trial comparison is made of evolved prisoner's dilemma strategies across three representations: finite-state machines, feedforward neural nets, and lookup tables. Fingerprinting demonstrates that all three representations sample the strategy space in a radically different manner, even though the neural net's and lookup table's parameters are alternate encodings of the same strategy space. This space of strategies is also a subset of those encoded by the finite-state representation. Shortcomings of the fingerprint technique are outlined, with illustrative examples, and possible paths to overcome these shortcomings are given.
Sorbate and benzoate in Turkish retail foodstuffs

From 2008 to 2011, surveys were conducted to determine the levels of benzoic and sorbic acids and their respective salts in 983 retail food samples which included sauces, vegetable and fruit preparations, flavoured syrups, food supplements, cereals, bakery products, jelly, synthetic cream, sprays, mustards, jam and preserves, molasses, chewing gum, confectionery, non-alcoholic beverages, tea, wine, vinegar, brine and beers. The analysis involved methanol extraction of the foodstuff and direct determination by HPLC with UV detection. Quality assurance was employed with each batch of samples. Accuracy was ensured through regular participation in proficiency tests. Over this four-year period, a total of 23 samples (2.3%), some syrups, tomato sauces and fruit contained individual or combined levels of sorbic and benzoic acids above regulatory limits. Unauthorised use of benzoic acid was also detected in a syrup sample, bakery products and fruit preserves.
Anatomical study of vestibulospinal neurons in lampreys

The present study was carried out to characterize anatomically the vestibulospinal (VS) system of lampreys. Cobalt‐lysine or Texas Red dextran amines were applied in vitro to the rostral spinal cord. Two distinct populations of VS neurons were labeled in the ventral nucleus of the area octavolateralis. The rostral group, comprising the intermediate octavomotor nucleus (ION), contained between 100 and 150 neurons, having somata of variable size and morphology. Intracellular injections of Lucifer Yellow in single neurons revealed ION VS neurons with dendrites extending in the ventrolateral alar plate as well as medially in the basal plate. The caudal group, comprising the posterior octavomotor nucleus (PON), contained approximately 65 neurons, most of which were unipolar with round or oval somata. To study the projections of VS axons, cobalt‐lysine was injected into the ION or PON regions in the brainstem. Axons from the ION projected to the ipsilateral spinal cord, whereas PON axons decussated within the basal plate giving out descending and ascending branches. The descending branch projected to the contralateral spinal cord. Injections of two fluorescent dextran‐amines, each restricted to one side of the spinal cord, did not double‐label VS cells in either octavomotor nuclei, indicating that the projections of each nucleus are restricted to one side. Injections of horseradish peroxidase further caudally in the spinal cord revealed that VS axons from the ION reached past the gill region. Our results indicate that the organization of the VS system of lampreys is similar to that observed in other vertebrates. J. Comp. Neurol. 407:512–526, 1999. © 1999 Wiley‐Liss, Inc.
The role of Ca2+‐dependent K+‐ channels at the rat corticostriatal synapses revealed by paired pulse stimulation

Potassium channels play an important role in modulating synaptic activity both at presynaptic and postsynaptic levels. We have shown before that presynaptically located KV and KIR channels modulate the strength of corticostriatal synapses in rat brain, but the role of other types of potassium channels at these synapses remains largely unknown. Here, we show that calcium‐dependent potassium channels BK‐type but not SK‐type channels are located presynaptically in corticostriatal synapses. We stimulated cortical neurons in rat brain slices and recorded postsynaptic excitatory potentials (EPSP) in medium spiny neurons (MSN) in dorsal neostriatum. By using a paired pulse protocol, we induced synaptic facilitation before applying either BK‐ or SK‐specific toxins. Thus, we found that blockage of BKCa with iberiotoxin (10 nM) reduces synaptic facilitation and increases the amplitude of the EPSP, while exposure to SK‐blocker apamin (100 nM) has no effect. Additionally, we induced train action potentials on striatal MSN by current injection before and after the exposure to KCa toxins. We found that the action potential becomes broader when the MSN is exposed to iberiotoxin, although it has no impact on frequency. In contrast, exposure to apamin results in loss of afterhyperpolarization phase and an increase of spike frequency. Therefore, we concluded that postsynaptic SK channels are involved in afterhyperpolarization and modulation of spike frequency while the BK channels are involved on the late repolarization phase of the action potential. Altogether, our results show that calcium‐dependent potassium channels modulate both input towards and output from the striatum.
Structural biology of gram‐positive bacterial adhesins

The structural biology of Gram‐positive cell surface adhesins is an emerging field of research, whereas Gram‐negative pilus assembly and anchoring have been extensively investigated and are well understood. Gram‐positive surface proteins known as MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) and individual proteins that assemble into long, hair‐like organelles known as pili have similar features at the primary sequence level as well as at the tertiary structural level. Some of these conserved features are essential for their transportation from the cytoplasm and for cell wall anchoring. More importantly, the MSCRAMMs and the individual pilins are assembled with building blocks that are variants of structural modules used for human immunoglobulins. MSCRAMMs target the host's extracellular matrix proteins, such as collagen, fibrinogen, and fibronectin, and they have received considerable attention from structural biologists in the last decade, who have primarily been interested in understanding their interactions with host tissue. The recent focus is on the newly discovered pili of Gram‐positive bacteria, and in this review, we highlight the advances in understanding of the individual pilus constituents and their associations and stress the similarities between the individual pilins and surface proteins.
Demonstration of improved transient response of inverters with steep slope strained Si NW TFETs by reduction of TAT with pulsed I-V and NW scaling

We present gate all around strained Si (sSi) nanowire array TFETs with high I<sub>ON</sub> (64μA/μm at V<sub>DD</sub>=1.0V). Pulsed I-V measurements provide small SS and record I<sub>60</sub> of 1×10<sup>-2</sup>μA/μm at 300K due to the suppression of trap assisted tunneling (TAT). Scaling the nanowires to 10 nm diameter greatly suppresses the impact of TAT and improves SS and I<sub>ON</sub>. Transient analysis of complementary TFET inverters demonstrates experimentally for the first time that device scaling and improved electrostatics yields to faster time response.
New approaches to developing lithium polymer batteries.

The electrochemical and physical-chemical properties of two families of lithium ion conducting membranes, i.e., the blends between high molecular weight poly(ethylene oxide) with a lithium salt commonly named "polymer electrolytes" and the gels of liquid solutions in a polymer matrix commonly named "gel electrolytes," are repoted and discussed. Particular attention is devoted to the newly developed approach of dispersing ceramic powders at the nanoscale particle dimension into the two types of membranes. This leads "nanocomposite" membranes having unique features, such as improved transport and interfacial properties in the case of the polymer electrolytes and enhanced liquid retention capability in the case of the gel electrolytes. Finally, the use of the gel electrolytes for the development of new-design, plastic-like, lithium-ion batteries is illustrated.
Ammonia-Induced Formation of an AmtB-GlnK Complex Is Not Sufficient for Nitrogenase Regulation in the Photosynthetic Bacterium Rhodobacter capsulatus

ABSTRACT A series of Rhodobacter capsulatus AmtB variants were created and assessed for effects on ammonia transport, formation of AmtB-GlnK complexes, and regulation of nitrogenase activity and NifH ADP-ribosylation. Confirming previous reports, H193 and H342 were essential for ammonia transport and the replacement of aspartate 185 with glutamate reduced ammonia transport. Several amino acid residues, F131, D334, and D335, predicted to be critical for AmtB activity, are shown here for the first time by mutational analysis to be essential for transport. Alterations of the C-terminal tail reduced methylamine transport, prevented AmtB-GlnK complex formation, and abolished nitrogenase switch-off and NifH ADP-ribosylation. On the other hand, D185E, with a reduced level of transport, was capable of forming an ammonium-induced complex with GlnK and regulating nitrogenase. This reinforces the notions that ammonia transport is not sufficient for nitrogenase regulation and that formation of an AmtB-GlnK complex is necessary for these processes. However, some transport-incompetent AmtB variants, i.e., F131A, H193A, and H342A, form ammonium-induced complexes with GlnK but fail to properly regulate nitrogenase. These results show that formation of an AmtB-GlnK complex is insufficient in itself for nitrogenase regulation and suggest that partial ammonia transport or occupation of the pore by ammonia is essential for this function.
[Effect of dexamethasone on expression of hypoxia inducible factor-1α and vascular endothelial growth factor in hypoxic mice].

BACKGROUND It has been proved that hypoxia is closely related to oncogenesis and development of tumor. The aim of this study is to observe the effect of dexamethasone on expression of hypoxia inducible factor 1α (HIF-1α) and vascular endothelial growth factor (VEGF) in lung tissues of hypoxic mice, and to investigate the relationship between hypoxia and angiogenesis and mechanism of dexamethasone. METHODS The Kunming mice were randomly divided into control group and three experimental groups (3-day hypoxia group, 6-day hypoxia group, and hypoxia+dexamethasone group). HIF-1α and VEGF protein expression was detected in lung tissues of mice by immunohistochemistry. RESULTS Expression of HIF-1α and VEGF significantly increased in hypoxia group compared with control group (P < 0.05). Compared with hypoxia group, expression of HIF-1α and VEGF decreased dramatically in hypoxia+dexamethasone group (P < 0.05). A positive correlation was found between the expression of HIF-1α and VEGF (r=0.730, P=0.007). CONCLUSIONS Hypoxia can increase the expression of VEGF and HIF-1α in lung tissues of mice. Dexamethasone can inhibit the expression of VEGF and HIF-1α of hypoxic mice and it may have anti-angiogenetic effect.
The Poxvirus A35 Protein Is an Immunoregulator

ABSTRACT It was shown previously that the highly conserved vaccinia virus A35 gene is an important virulence factor in respiratory infection of mice. We show here that A35 is also required for full virulence by the intraperitoneal route of infection. A virus mutant in which the A35 gene has been removed replicated normally and elicited improved antibody, gamma interferon-secreting cell, and cytotoxic T-lymphocyte responses compared to wild-type virus, suggesting that A35 increases poxvirus virulence by immunomodulation. The enhanced immune response correlated with an improved control of viral titers in target organs after the development of the specific immune response. Finally, the A35 deletion mutant virus also provided protection from lethal challenge (1,000 50% lethal doses) equal to that of the wild-type virus. Together, these data suggest that A35 deletion viruses will make safer and more efficacious vaccines for poxviruses. In addition, the A35 deletion viruses will serve as improved platform vectors for other infectious diseases and cancer and will be superior vaccine choices for postexposure poxvirus vaccination, as they also provide improved kinetics of the immune response.
Incidence and Risk Factors of Long-term Opioid Use in Elderly Trauma Patients

Objective: Evaluate the incidence and risk factors of opioid use 1 year after injury in elderly trauma patients. Background: The current epidemic of prescription opioid misuse and overdose observed in North America generally concerns young patients. Little is known on long-term opioid use among the elderly trauma population. Methods: In a retrospective observational multicenter cohort study conducted on registry data, all patients 65 years and older admitted (hospital stay >2 days) for injury in 57 adult trauma centers in the province of Quebec (Canada) between 2004 and 2014 were included. We searched for filled opioid prescriptions in the year preceding the injury, up to 3 months and 1 year after the injury. Results: In all, 39,833 patients were selected for analysis. Mean age was 79.3 years (±7.7), 69% were women, and 87% of the sample was opioid-naive. After the injury, 38% of the patients filled an opioid prescription within 3 months and 10.9% [95% confidence interval (CI) 10.6%–11.2%] filled an opioid prescription 1 year after trauma: 6.8% (95% CI 6.5%–7.1%) were opioid-naïve and 37.6% (95% CI 36.3%–38.9%) were opioid non-naive patients. Controlling for confounders, patients who filled 2 or more opioid prescriptions before the injury and those who filled an opioid prescription within 3 months after the injury were, respectively, 11.4 and 3 times more likely to use opioids 1 year after the injury compared with those who did not fill opioid prescriptions. Conclusions: These results highlight that elderly trauma patients are at risk of long-term opioid use, especially if they had preinjury or early postinjury opioid consumption.
SecA2-dependent secretion of autolytic enzymes promotes Listeria monocytogenes pathogenesis

Pathogenic bacteria secrete proteins that promote invasion of host tissues and resistance to immune responses. However, secretion mechanisms that contribute to the enormous morbidity and mortality of Gram-positive bacteria are largely undefined. An auxiliary protein secretion system (SecA2) has recently emerged in Listeria monocytogenes and eight other Gram-positive pathogens. Here, a proteomics approach identified seventeen SecA2-dependent secreted and surface proteins of L. monocytogenes, the two most abundant of which [the p60 and N-acetylmuramidase (NamA) autolysins] hydrolyze bacterial peptidoglycan (PGN) and contribute to host colonization. SecA2-deficient (ΔSecA2) bacteria were rapidly cleared after systemic infection of murine hosts, and in cultured cells showed reduced cell-cell spread. p60 or NamA deficiencies (Δp60 and ΔNamA) caused intermediate reductions in bacterial virulence in vivo, yet showed no defect for infection of cultured cells. Restoration of virulence in Δp60 bacteria required full-length p60 with an intact catalytic domain, suggesting that PGN hydrolysis by p60 is crucial for L. monocytogenes virulence. Coordinated PGN hydrolysis by p60 and NamA activities is predicted to generate a muramyl glycopeptide, glucosaminylmuramyl dipeptide (GMDP), which is known to modify host inflammatory responses. Thus, SecA2-dependent secretion may promote release of muramyl peptides that subvert host pattern recognition.
Vitamin D3 supplementation during weight loss: a double-blind randomized controlled trial.

BACKGROUND Vitamin D deficiency is associated with obesity; whether repletion supports weight loss and changes obesity-related biomarkers is unknown. OBJECTIVE We compared 12 mo of vitamin D3 supplementation with placebo on weight, body composition, insulin, and C-reactive protein (CRP) in postmenopausal women in a weight-loss intervention. DESIGN A total of 218 overweight/obese women (50-75 y of age) with serum 25-hydroxyvitamin D [25(OH)D] ≥10 ng/mL but <32 ng/mL were randomly assigned to weight loss + 2000 IU oral vitamin D3/d or weight loss + daily placebo. The weight-loss intervention included a reduced-calorie diet (10% weight loss goal) and 225 min/wk of moderate-to-vigorous aerobic activity. Mean 12-mo changes in weight, body composition, serum insulin, CRP, and 25(OH)D were compared between groups (intent-to-treat) by using generalized estimating equations. RESULTS A total of 86% of participants completed the 12-mo measurements. The mean (95% CI) change in 25(OH)D was 13.6 (11.6, 15.4) ng/mL in the vitamin D3 arm compared with -1.3 (-2.6, -0.3) ng/mL in the placebo arm (P < 0.0001). Changes in weight [-7.1 (-8.7, -5.7) compared with -7.4 (-8.1, -5.4) kg], body mass index (in kg/m(2): both -2.8), waist circumference [-4.9 (-6.7, -2.9) compared with -4.5 (-5.6, -2.6) cm], percentage body fat [-4.1 (-4.9, -2.9) compared with -3.5 (-4.5, -2.5)], trunk fat [-4.1 (-4.7, -3.0) compared with -3.7 (-4.3, -2.9) kg], insulin [-2.5 (-3.4, -1.7) compared with -2.4 (-3.3, -1.4) μU/mL], and CRP [-0.9 (-1.2, -0.6) compared with -0.79 (-0.9, -0.4) mg/L] [corrected] were similar between groups (all P > 0.05). Compared with women who achieved 25(OH)D <32 ng/mL, women randomly assigned to vitamin D who became replete (ie, 25(OH)D ≥32 ng/mL) lost more weight [-8.8 (-11.1, -6.9) compared with -5.6 (-7.2, -5.0) kg; P = 0.05], waist circumference [-6.6 (-9.3, -4.3) compared with -2.5 (-4.6, -2.0) cm; P = 0.02], and percentage body fat [-4.7 (-6.1, -3.5) compared with -2.6 (-3.9, -2.2); P = 0.04]. Among women with complete pill counts (97% adherence), the mean decrease in CRP was 1.18 mg/mL (46%) in the vitamin D arm compared with 0.46 mg/mL (25%) in the placebo arm (P = 0.03). CONCLUSIONS Vitamin D3 supplementation during weight loss did not increase weight loss or associated factors compared with placebo; however, women who became replete experienced greater improvements. This trial was registered at clinicaltrials.gov as NCT01240213.
The inability of human immunodeficiency virus to infect chimpanzee monocytes can be overcome by serial viral passage in vivo

Studies of lentivirus infection in ruminants, nonhuman primates, and humans suggest that virus infection of macrophages plays a central role in the disease process. To investigate whether human immunodeficiency virus type 1 (HIV-1) can infect chimpanzee macrophages, we recovered monocytes from peripheral blood mononuclear cells of HIV-1-negative animals and inoculated these and control human monocytes with a panel of four human-passaged monocytotropic virus strains and one chimpanzee-passaged isolate. HIV-1 infected human monocytes synthesized proviral DNA, viral mRNA, p24 antigen, and progeny virions. In contrast, except for the chimpanzee-passaged HIV-1 isolate, chimpanzee monocytes failed to support HIV-1 replication when cultured under both identical and a variety of other conditions. Proviral DNA was demonstrated only at background levels in these cell cultures by polymerase chain reaction for gag- and env-related sequences. Interestingly, the chimpanzee-passaged HIV-1 isolate did not replicate in human monocytes; viral p24 antigens and progeny virions were not detected. The same monocytotropic panel of HIV-1 strains replicated in both human and chimpanzee CD4+ T lymphoblasts treated with phytohemagglutinin and interleukin-2. The failure of HIV-1 to infect chimpanzee monocytes, which can be overcome by serial in vivo viral passage, occurs through a block early in the viral life cycle.
In utero diethylstilbestrol (DES) exposure alters Hox gene expression in the developing mullerian system

Diethylstilbestrol (DES) was widely used to treat pregnant women through 1971. The reproductive tracts of their female offspring exposed to DES in utero are characterized by anatomic abnormalities. Here we show that DES administered to mice in utero produces changes in the expression pattern of several Hox genes that are involved in patterning of the reproductive tract. DES produces posterior shifts in Hox gene expression and ho‐meotic anterior transformations of the reproductive tract. In human uterine or cervical cell cultures, DES induces HOXA9 or HOXA10 gene expression, respectively, to levels approximately twofold that induced by estradiol. The DES‐induced expression is not inhibited by cyclohexamide. Estrogens are novel morphogens that directly regulate the expression pattern of posterior Hox genes in a manner analogous to retinoic acid regulation of anterior Hox genes. Alterations in HOX gene expression are a molecular mechanism by which DES affects reproductive tract development. Changes in Hox gene expression are a potential marker for the effects of in utero drug use that may become apparent only at late stages of development. —Block, K. , Kardana, A. , Igarashi, P., Taylor, H. S. In utero diethylstilbestrol (DES) exposure alters Hox gene expression in the developing mullerian system. FASEB J. 14, 1101–1108 (2000)
Critical Assessment of Analytical Techniques in the Search for Biomarkers on Mars: A Mummified Microbial Mat from Antarctica as a Best-Case Scenario

Abstract The search for biomarkers of present or past life is one of the major challenges for in situ planetary exploration. Multiple constraints limit the performance and sensitivity of remote in situ instrumentation. In addition, the structure, chemical, and mineralogical composition of the sample may complicate the analysis and interpretation of the results. The aim of this work is to highlight the main constraints, performance, and complementarity of several techniques that have already been implemented or are planned to be implemented on Mars for detection of organic and molecular biomarkers on a best-case sample scenario. We analyzed a 1000-year-old desiccated and mummified microbial mat from Antarctica by Raman and IR (infrared) spectroscopies (near- and mid-IR), thermogravimetry (TG), differential thermal analysis, mass spectrometry (MS), and immunological detection with a life detector chip. In spite of the high organic content (ca. 20% wt/wt) of the sample, the Raman spectra only showed the characteristic spectral peaks of the remaining beta-carotene biomarker and faint peaks of phyllosilicates over a strong fluorescence background. IR spectra complemented the mineralogical information from Raman spectra and showed the main molecular vibrations of the humic acid functional groups. The TG-MS system showed the release of several volatile compounds attributed to biopolymers. An antibody microarray for detecting cyanobacteria (CYANOCHIP) detected biomarkers from Chroococcales, Nostocales, and Oscillatoriales orders. The results highlight limitations of each technique and suggest the necessity of complementary approaches in the search for biomarkers because some analytical techniques might be impaired by sample composition, presentation, or processing. Key Words: Planetary exploration—Life detection—Microbial mat—Life detector chip—Thermogravimetry—Raman spectroscopy—NIR—DRIFTS. Astrobiology 17, 984–996.