Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequence of Pseudomonas stutzeri 273 and Identification of the Exopolysaccharide EPS273 Biosynthesis Locus

Pseudomonas stutzeri 273 is a marine bacterium producing exopolysaccharide 273 (EPS273) with high anti-biofilm activity against P. aeruginosa PAO1. Here, the complete genome of P. stutzeri 273 was sequenced and the genome contained a circular 5.03 Mb chromosome. With extensive analysis of the genome, a genetic locus containing 18 genes was predicted to be involved in the biosynthesis of EPS273. In order to confirm this prediction, two adjacent genes (eps273-H and eps273-I) encoding glycosyltransferases and one gene (eps273-O) encoding tyrosine protein kinase within the genetic locus were deleted and biosynthesis of EPS273 was checked in parallel. The molecular weight profile of EPS purified from the mutant Δeps273-HI was obviously different from that purified from wild-type P. stutzeri 273, while the corresponding EPS was hardly detected from the mutant Δeps273-O, which indicated the involvement of the proposed 18-gene cluster in the biosynthesis of EPS273. Moreover, the mutant Δeps273-HI had the biofilm formed earlier compared with the wild type, and the mutant Δeps273-O almost completely lost the ability of biofilm formation. Therefore, EPS273 might facilitate the biofilm formation for its producing strain P. stutzeri 273 while inhibiting the biofilm formation of P. aeruginosa PAO1. This study can contribute to better understanding of the biosynthesis of EPS273 and disclose the biological function of EPS273 for its producing strain P. stutzeri 273.
Inferring reward prediction errors in patients with schizophrenia: a dynamic reward task for reinforcement learning

Abnormalities in the dopamine system have long been implicated in explanations of reinforcement learning and psychosis. The updated reward prediction error (RPE)—a discrepancy between the predicted and actual rewards—is thought to be encoded by dopaminergic neurons. Dysregulation of dopamine systems could alter the appraisal of stimuli and eventually lead to schizophrenia. Accordingly, the measurement of RPE provides a potential behavioral index for the evaluation of brain dopamine activity and psychotic symptoms. Here, we assess two features potentially crucial to the RPE process, namely belief formation and belief perseveration, via a probability learning task and reinforcement-learning modeling. Forty-five patients with schizophrenia [26 high-psychosis and 19 low-psychosis, based on their p1 and p3 scores in the positive-symptom subscales of the Positive and Negative Syndrome Scale (PANSS)] and 24 controls were tested in a feedback-based dynamic reward task for their RPE-related decision making. While task scores across the three groups were similar, matching law analysis revealed that the reward sensitivities of both psychosis groups were lower than that of controls. Trial-by-trial data were further fit with a reinforcement learning model using the Bayesian estimation approach. Model fitting results indicated that both psychosis groups tend to update their reward values more rapidly than controls. Moreover, among the three groups, high-psychosis patients had the lowest degree of choice perseveration. Lumping patients' data together, we also found that patients' perseveration appears to be negatively correlated (p = 0.09, trending toward significance) with their PANSS p1 + p3 scores. Our method provides an alternative for investigating reward-related learning and decision making in basic and clinical settings.
Towards Persistent Localization and Mapping with a Continuous Appearance-based Topology

Appearance-based localization can provide loop closure detection at vast scales regardless of accumulated metric error. However, the computation time and memory requirements of current appearance-based methods scale not only with the size of the environment but also with the operation time of the platform. Additionally, repeated visits to locations will develop multiple competing representations, which will reduce recall performance over time. These properties impose severe restrictions on long-term autonomy for mobile robots, as loop closure performance will inevitably degrade with increased operation time. In this paper we present a graphical extension to CAT-SLAM, a particle filter-based algorithm for appearance-based localization and mapping, to provide constant computation and memory requirements over time and minimal degradation of recall performance during repeated visits to locations. We demonstrate loop closure detection in a large urban environment with capped computation time and memory requirements and performance exceeding previous appearance-based methods by a factor of 2. We discuss the limitations of the algorithm with respect to environment size, appearance change over time and applications in topological planning and navigation for long-term robot operation.
On Oscillations in Discontinuous Galerkin Discretization Schemes for Steady State Problems

High order discontinuous Galerkin discretization schemes are considered for steady state problems. We discuss the issue of oscillations arising when Newton's method is employed to obtain a steady state solution. It will be demonstrated that flux approximation near flux extrema may produce spurious oscillations propagating over the domain of computation. The control over the numerical flux in the problem allows one to obtain nonoscillating convergent solutions.
A new species of Chilotherium (Perissodactyla, Rhinocerotidae) from the Late Miocene of Qingyang, Gansu, China

An adult skull with articulated atlas and an adult mandible, collected by Emile Licent in 1920 from the Late Miocene of Qingyang (Gansu, China), is recognized as a new species Chilotherium licenti sp. nov. These specimens possess typical characters of the genus Chilotherium , such as the strongly expanded mandibular symphysis, the huge and dagger-shaped i2s with an upturned medial flange, strongly constricted protocones, well-developed crochet and crista, and weakly developed parastyle folds and paracone ribs. Chilotherium licenti is characterized by the near absence of lingual and buccal cingula, and the medifossette on P2 to M2 forming by well-developed crochet and crista. The derived characters of the new species indicate that it is the highly specialized taxon of the genus Chilotherium , corresponding to MN12–13 of the Turolian in Europe. Based on a phylogenetic analysis of rhinocerotids, C. licenti from the Late Miocene is the most derived species in the known species of the Chilotherium lineage.
Neuroleptic and benzodiazepine use in long-term care in urban and rural Alberta: characteristics and results of an education intervention to ensure appropriate use

Objectives: To examine the use of psychotropic drugs in 24 rural and urban long-term care (LTC) facilities, and compare the effect of an education intervention for LTC staff and family members on the use of psychotropic drugs in intervention versus control facilities. Methods: Interrupted time series with a non-equivalent no-treatment control group time series. Data on drug use were collected in 24 Western Canadian LTC facilities (10 urban, 14 rural) for three 2-month time periods before and after the intervention. Pharmacy records were used to collect data on drug, class of drug, dose, administration, and start/stop dates. Chart reviews provided demographics, pro re nata (prn) use, and indications for drug use. Subjects comprised 2443 residents living in the 24 LTC facilities during the 1-year study. An average of 796.33 residents (32.7%) received a psychotropic drug. An education intervention on psychotropic drug use in LTC was offered to intervention physicians, nursing staff, pharmacists and family members. Results: Approximately one-third of residents received a psychotropic drug during the study, often for considerable lengths of time. A minority of psychotropic drug prescriptions had a documented reason for their use, and 69.5% of the reasons would be inappropriate under Omnibus Budget Reconciliation Act (OBRA) legislation. Few psychotropic drug prescriptions were discontinued or reduced during the study. More urban LTC residents received neuroleptics and benzodiazepines than their rural counterparts (26.1% vs. 15.7%, and 18.0% vs. 7.6%, respectively). The education intervention did not result in any significant decline in the use of these drugs in intervention facilities. Conclusion: The results suggest substantial use of psychotropic drugs in LTC, although rural LTC residents received approximately half the number of psychotropic drugs compared with urban residents. A resource-intensive intervention did not significantly decrease the use of psychotropics. There is a need for better monitoring of psychotropic drugs in LTC, particularly given that voluntary educational efforts alone may be ineffective agents of change.
Rescue of axotomized retinal ganglion cells by BDNF gene electroporation in adult rats.

PURPOSE To determine whether the brain-derived neurotrophic factor (BDNF) gene can be transfected into retinal ganglion cells (RGCs) by electroporation and whether axotomized RGCs can be rescued after transfection by BDNF in adult rats. METHODS Mouse BDNF cDNA was injected intravitreally followed by in vivo electroporation in adult rats. The expression of BDNF in RGCs was confirmed by Western immunoblot analysis and immunohistochemistry. After introduction of BDNF cDNA, the survival of axotomized RGCs was estimated by the TdT-dUTP terminal nick-end labeling (TUNEL) method and measured by counting the number of RGCs that were labeled retrogradely by 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyamine percholorate (diI) applied to the superior colliculus (SC). RESULTS Eyes with injection of the BDNF gene followed by in vivo electroporation showed a significantly higher level of expression of BDNF in the RGC layer, a higher rescue ratio, and a lower number of TUNEL-positive cells than the control samples. CONCLUSIONS These findings demonstrate that electroporation is an effective method for the direct delivery of genes into RGCs, and that the BDNF gene transferred into RGCs by in vivo electroporation can protect axotomized RGCs against apoptosis.
Using artificial neural network for outflow estimation in an ungauged area

This research employs an artificial neural network with a variable mathematic structure that is capable of simulating a nonlinear structural system. A back-propagation neural network (BPN) is adopted to estimate outflow for an ungauged area by considering temporal distribution of rainfall-runoff and the spatial distribution of watershed environment. The nonlinear relationship among the physiographic factors, precipitation, and outflow of the specific watershed was established to estimate the outflow of the sub-watershed where no flow gauge has been settled. The model was tested at Bei-Shi watershed of Hou-Long River, Taiwan. Three typhoon occurrences were used for model calibration and verification that indicates the model validity and proves the model suitable for estimating the outflow of an ungauged area.
Revisiting Biomarkers of Total-Body and Partial-Body Exposure in a Baboon Model of Irradiation

In case of a mass casualty radiation event, there is a need to distinguish total-body irradiation (TBI) and partial-body irradiation (PBI) to concentrate overwhelmed medical resources to the individuals that would develop an acute radiation syndrome (ARS) and need hematologic support (i.e., mostly TBI victims). To improve the identification and medical care of TBI versus PBI individuals, reliable biomarkers of exposure could be very useful. To investigate this issue, pairs of baboons (n = 18) were exposed to different situations of TBI and PBI corresponding to an equivalent of either 5 Gy 60Co gamma irradiation (5 Gy TBI; 7.5 Gy left hemibody/2.5 right hemibody TBI; 5.55 Gy 90% PBI; 6.25 Gy 80% PBI; 10 Gy 50% PBI, 15 Gy 30% PBI) or 2.5 Gy (2.5 Gy TBI; 5 Gy 50% PBI). More than fifty parameters were evaluated before and after irradiation at several time points up to 200 days. A partial least square discriminant analysis showed a good distinction of TBI from PBI situations that were equivalent to 5 Gy. Furthermore, all the animals were pooled in two groups, TBI (n = 6) and PBI (n = 12), for comparison using a logistic regression and a non parametric statistical test. Nine plasmatic biochemical markers and most of hematological parameters turned out to discriminate between TBI and PBI animals during the prodromal phase and the manifest illness phase. The most significant biomarkers were aspartate aminotransferase, creatine kinase, lactico dehydrogenase, urea, Flt3-ligand, iron, C-reactive protein, absolute neutrophil count and neutrophil-to-lymphocyte ratio for the early period, and Flt3-ligand, iron, platelet count, hemoglobin, monocyte count, absolute neutrophil count and neutrophil-to-lymphocyte ratio for the ARS phase. These results suggest that heterogeneity could be distinguished within a range of 2.5 to 5 Gy TBI.
Biosynthesis of gold nanoparticles using chloroplasts

In this paper, a new method of one-pot biosynthesizing of gold nanoparticles (GNPs), using chloroplasts as reductants and stabilizers is reported. The as-prepared GNPs were characterized by ultraviolet visible spectroscopy, transmission electron microscopy, X-ray powder diffraction, and Fourier transform infrared spectroscopy (FTIR). The cytotoxicity of the GNPs was evaluated using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method against gastric mucous cell line GES-1 and gastric cancer cell line MGC-803. Rhodamine 6G as a Raman probe was used for investigating surface-enhanced Raman spectroscopy (SERS) enhancement of GNPs. The transmission electron microscopy results indicated that the GNPs were spherical in structure and almost 20 nm in diameter. Ultraviolet visible spectroscopy exhibited an absorption peak at 545 nm. The GNPs exhibited high crystallinity, with the (111) plane as the predominant orientation, clarified by X-ray powder diffraction. In addition, a potential mechanism was proposed to interpret the formation process of GNPs, mainly based on the analysis of FTIR results. The FTIR spectrum confirmed that the GNPs were carried with N–H groups. Toxicological assays of as-prepared GNPs revealed that the green GNPs were nontoxic. SERS analysis revealed that the GNPs without any treatment could substantially enhance the Raman signals of rhodamine 6G. The Raman enhancement factor was calculated to be nearly 1010 orders of magnitude. In conclusion, the GNPs with good biocompatibility and excellent SERS effect were successfully synthesized using chloroplasts. These biogenetic GNPs have great potential for ultrasensitive detection of biomarkers in vitro and in vivo based on SERS.
Sister chromatid separation and chromosome re‐duplication are regulated by different mechanisms in response to spindle damage

In yeast, anaphase entry depends on Pds1 proteolysis, while chromosome re‐duplication in the subsequent S‐phase involves degradation of mitotic cyclins such as Clb2. Sequential proteolysis of Pds1 and mitotic cyclins is mediated by the anaphase‐promoting complex (APC). Lagging chromosomes or spindle damage are detected by surveillance mechanisms (checkpoints) which block anaphase onset, cytokinesis and DNA re‐replication. Until now, the MAD and BUB genes implicated in this regulation were thought to function in a single pathway that blocks APC activity. We show that spindle damage blocks sister chromatid separation solely by inhibiting APCCdc20‐dependent Pds1 proteolysis and that this process requires Mad2. Blocking APCCdh1‐mediated Clb2 proteolysis and chromosome re‐duplication does not require Mad2 but a different protein, Bub2. Our data imply that Mad1, Mad2, Mad3 and Bub1 regulate APCCdc20, whereas Bub2 regulates APCCdh1.
Query Evaluation on Probabilistic Databases

We describe a system that supports arbitrarily complex SQL queries with ”uncertain” predicates. The query semantics is based on a probabilistic model and the results are ranked, much like in Information Retrieval. Our main focus is query evaluation. We describe an optimization algorithm that can compute eciently most queries. We show, however, that the data complexity of some queries is #P-complete, which implies that these queries do not admit any ecient evaluation methods. For these queries we describe both an approximation algorithm and a Monte-Carlo simulation algorithm.
Conceptualizing Auditability

Compliance has become a strategic concern for many companies and organizations. To prove actual compliance, the organization must disclose itself (be auditable). A plethora of advanced tools has been developed to support compliance management and auditing processes. However, not all organizations are the same. To apply these tools effectively and efficiently, the organization itself and the maturity of its management control should be considered as well. The goal of this exploratory paper is to define auditability on a general conceptual level. We introduce four levels of auditability, where each level adds to the self-knowledge and being-in-control of the organization.
Efficacy of Neurofeedback Treatment in ADHD: The Effects on Inattention, Impulsivity and Hyperactivity: A Meta-Analysis

Since the first reports of neurofeedback treatment in Attention Deficit Hyperactivity Disorder (ADHD) in 1976, many studies have investigated the effects of neurofeedback on different symptoms of ADHD such as inattention, impulsivity and hyperactivity. This technique is also used by many practitioners, but the question as to the evidence-based level of this treatment is still unclear. In this study selected research on neurofeedback treatment for ADHD was collected and a meta-analysis was performed. Both prospective controlled studies and studies employing a pre-and post-design found large effect sizes (ES) for neurofeedback on impulsivity and inattention and a medium ES for hyperactivity. Randomized studies demonstrated a lower ES for hyperactivity suggesting that hyperactivity is probably most sensitive to nonspecific treatment factors. Due to the inclusion of some very recent and sound methodological studies in this meta-analysis, potential confounding factors such as small studies, lack of randomization in previous studies and a lack of adequate control groups have been addressed, and the clinical effects of neurofeedback in the treatment of ADHD can be regarded as clinically meaningful. Three randomized studies have employed a semi-active control group which can be regarded as a credible sham control providing an equal level of cognitive training and client-therapist interaction. Therefore, in line with the AAPB and ISNR guidelines for rating clinical efficacy, we conclude that neurofeedback treatment for ADHD can be considered “Efficacious and Specific” (Level 5) with a large ES for inattention and impulsivity and a medium ES for hyperactivity.
Cognitive Enhancement or Cognitive Cost: Trait-Specific Outcomes of Brain Stimulation in the Case of Mathematics Anxiety

The surge in noninvasive brain stimulation studies investigating cognitive enhancement has neglected the effect of interindividual differences, such as traits, on stimulation outcomes. Using the case of mathematics anxiety in a sample of healthy human participants in a placebo-controlled, double-blind, crossover experiment, we show that identical transcranial direct current stimulation (tDCS) exerts opposite behavioral and physiological effects depending on individual trait levels. Mathematics anxiety is the negative emotional response elicited by numerical tasks, impairing mathematical achievement. tDCS was applied to the dorsolateral prefrontal cortex, a frequent target for modulating emotional regulation. It improved reaction times on simple arithmetic decisions and decreased cortisol concentrations (a biomarker of stress) in high mathematics anxiety individuals. In contrast, tDCS impaired reaction times for low mathematics anxiety individuals and prevented a decrease in cortisol concentration compared with sham stimulation. Both groups showed a tDCS-induced side effect—impaired executive control in a flanker task—a cognitive function subserved by the stimulated region. These behavioral and physiological double dissociations have implications for brain stimulation research by highlighting the role of individual traits in experimental findings. Brain stimulation clearly does not produce uniform benefits, even applied in the same configuration during the same tasks, but may interact with traits to produce markedly opposed outcomes.
Tight Control of Trehalose Content Is Required for Efficient Heat-induced Cell Elongation in Candida albicans*

Background: Heat-induced morphogenetic switch is Hsp90- and PKA-dependent. Results: The G protein-coupled receptor Gpr1, upstream of PKA, regulates trehalose levels in glucose-grown cells. Conclusion: The link between the PKA pathway and Hsp90-mediated regulation of heat-induced morphogenesis is trehalose. Significance: Tight control of trehalose levels is required for morphogenesis in Candida albicans. The ability to form hyphae in the human pathogenic fungus Candida albicans is a prerequisite for virulence. It contributes to tissue infection, biofilm formation, as well as escape from phagocytes. Cell elongation triggered by human body temperature involves the essential heat shock protein Hsp90, which negatively governs a filamentation program dependent upon the Ras-protein kinase A (PKA) pathway. Tight regulation of Hsp90 function is required to ensure fast appropriate response and maintenance of a wide range of regulatory and signaling proteins. Client protein activation by Hsp90 relies on a conformational change of the chaperone, whose ATPase activity is competitively inhibited by geldanamycin. We demonstrate a novel regulatory mechanism of heat- and Hsp90-dependent induced morphogenesis, whereby the nonreducing disaccharide trehalose acts as a negative regulator of Hsp90 release. By means of a mutant strain deleted for Gpr1, the G protein-coupled receptor upstream of PKA, we demonstrate that elevated trehalose content in that strain, resulting from misregulation of enzymatic activities involved in trehalose metabolism, disrupts the filamentation program in response to heat. Addition of geldanamycin does not result in hyphal extensions at 30 °C in the gpr1Δ/gpr1Δ mutant as it does in wild type cells. In addition, validamycin, a specific inhibitor of trehalase, the trehalose-degrading enzyme, inhibits cell elongation in response to heat and geldanamycin. These results place Gpr1 as a regulator of trehalose metabolism in C. albicans and illustrate that trehalose modulates Hsp90-dependent activation of client proteins and signaling pathways leading to filamentation in the human fungal pathogen.
NORMAL PRESSURE HYDROCEPHALUS

Doctors find the management of normal pressure hydrocephalus (NPH) difficult because their diagnosis is often uncertain and the treatment with shunt surgery carries a significant risk. With the aim of bringing to the attention of clinicians the useful, but largely anecdotal information available regarding this problem, this chapter will address the following: epidemiology, reasons why the diagnosis is difficult, differential diagnosis, features of the history, examination, neuropsychological assessment, radiologic evaluation, and special tests that may help clinicians with management. The review will also address how to measure surgical outcome, surgical complications, and choice of shunt. Lastly, it will discuss associations with idiopathic NPH that might have bearing on the etiology. This chapter presents a practical approach to the management of patients with NPH. Continuum Lifelong Learning Neurol 2007;13(2):144-164.