Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the active site and thermostability regions of endoxylanase from Thermoanaerobacterium saccharolyticum B6A-RI

Deletion mutants were constructed from pZEP12, which contained the intact Thermoanaerobacterium saccharolyticum endoxylanase gene (xynA). Deletion of 1.75 kb from the N-terminal end of xynA resulted in a mutant enzyme that retained activity but lost thermostability. Deletion of 1.05 kb from the C terminus did not alter thermostability or activity. The deduced amino acid sequence of T. saccharolyticum B6A-RI endoxylanase XynA was aligned with five other family F beta-glycanases by using the PILEUP program of the Genetics Computer Group package. This multiple alignment of amino acid sequences revealed six highly conserved motifs which included the consensus sequence consisting of a hydrophobic amino acid, Ser or Thr, Glu, a hydrophobic amino acid, Asp, and a hydrophobic amino acid in the catalytic domain. Endoxylanase was inhibited by EDAC [1-(3-dimethylamino propenyl)-3-ethylcarbodiimide hydrochloride], suggesting that Asp and/or Glu was involved in catalysis. Three aspartic acids, two glutamic acids, and one histidine were conserved in all six enzymes aligned. Hydrophobic cluster analysis revealed that two Asp and one Glu occur in the same hydrophobic clusters in T. saccharolyticum B6A-RI endoxylanase and two other enzymes belonging to family F beta-glycanases and suggests their involvement in a catalytic triad. These two Asp and one Glu in XynA from T. saccharolyticum were targeted for analysis by site-specific mutagenesis. Substitution of Asp-537 and Asp-602 by Asn and Glu-600 by Gln completely destroyed endoxylanase activity. These results suggest that these three amino acids form a catalytic triad that functions in a general acid catalysis mechanism.
The effect of surgical margins on outcomes for low grade MPNSTs and atypical neurofibroma

While convention defines atypical neurofibroma as benign and low‐grade malignant peripheral nerve sheath tumors (MPNSTs) as malignant, sparse outcomes data exist for these tumors. This study reviews clinical outcomes of surgically resected low‐grade MPNST and atypical neurofibroma, focusing on the effect of surgical margins on outcome.
Medical and Developmental Histories Of Maltreated Children

This paper represents a first attempt at delineating and summarizing the issues in a child's medical and developmental history associated with the probability of suffering abuse. The sample consisted of 96 children between 5 and 10 years of age, 61 of whom had been maltreated and 35 of whom served as controls. There were 22 items about which the medical and developmental histories of the maltreated children revealed a significantly greater risk than those of the controls. A factor analysis revealed that 78% of the variance in these items can be represented by eight independent factors. None of these factors was dominant; rather, each accounted for a significant amount of the variation among the original items. The individual items tended to load on the four strongest factors in a coherent, interpretable manner: Factor 1 represented behavior problems; factor 2, neonatal issues and failure to thrive; factor 3, familial disruption, with the child suffering mental illness and/or head injury; and factor 4, a "difficult" temperament during the first year of life. We conclude there are numerous independent factors in the medical and developmental histories of maltreated children which should be considered by pediatricians involved in cases of child abuse and neglect.
Improved Coreceptor Usage Prediction and GenotypicMonitoring of R5-to-X4 Transition by Motif Analysis of HumanImmunodeficiency Virus Type 1 env V3 LoopSequences

ABSTRACT Early in infection, human immunodeficiency virus type 1 (HIV-1) generally uses the CCR5 chemokine receptor (along with CD4) for cellular entry. In many HIV-1-infected individuals, viral genotypic changes arise that allow the virus to use CXCR4 (either in addition to CCR5 or alone) as an entry coreceptor. This switch has been associated with an acceleration of both CD3+ T-cell decline and progression to AIDS. While it is well known that the V3 loop of gp120 largely determines coreceptor usage and that positively charged residues in V3 play an important role, the process of genetic change in V3 leading to altered coreceptor usage is not well understood. Further, the methods for biological phenotyping of virus for research or clinical purposes are laborious, depend on sample availability, and present biosafety concerns, so reliable methods for sequence-based“ virtual phenotyping” are desirable. We introduce a simple bioinformatic method of scoring V3 amino acid sequences that reliably predicts CXCR4 usage (sensitivity, 84%; specificity, 96%). This score (as determined on the basis of position-specific scoring matrices [PSSM]) can be interpreted as revealing a propensity to use CXCR4 as follows: known R5 viruses had low scores, R5X4 viruses had intermediate scores, and X4 viruses had high scores. Application of the PSSM scoring method to reconstructed virus phylogenies of 11 longitudinally sampled individuals revealed that the development of X4 viruses was generally gradual and involved the accumulation of multiple amino acid changes in V3. We found that X4 viruses were lost in two ways: by the dying off of an established X4 lineage or by mutation back to low-scoring V3 loops.
Decentralized Administrative Law in the Organization for Economic Cooperation and Development

The article examines administrative law practices at the Organization for Economic Cooperation and Development (OECD) and is being published as part of an issue of Law & Contemporary Problems on global administrative law. While the OECD is neither a well-known nor well-studied international organization (I worked there from 1990-1992), a number of its activities influence domestic agency action far more than is generally realized. It also provides a wonderful example for the study of global administrative law for the simple reason that it is a hybrid organization. Through its many diverse activities, OECD shares aspects of primarily law-making international bodies such as the EU, primarily standard-setting bodies such as the World Health Organization, and primarily data gathering and research organizations such as the UN Conference on Trade and Development. Perhaps surprisingly, there is no uniform administrative law in the OECD. In managing this constellation of activities, the OECD has chosen largely to decentralize its administrative law down to its subject-specific directorates who develop administrative procedures on an ad hoc basis. Thus in studying administrative law at the OECD, one is effectively studying multiple administrative law systems under one roof. Because the OECD does not garner much attention from scholars or the public, The article commences with a description of the OECD, out the basics of the organization's origins, operations, and examples of its range of activities. Four case studies then examine the OECD's multiple roles and how these bear on the development of the organization's administrative law. The cases range from traditional treaty-making, to consensus development of standards, to quasi-judicial review of the actions of multinational enterprises. Each of these examples relies on different types of administrative mechanisms to address the core concerns of transparency, responsiveness and accountability. The final section explores whether administrative law safeguards should apply to OECD activities that, while not lawmaking themselves, exert important influence on domestic lawmaking and underscores why the OECD has adopted a decentralized model of administrative law.
Transformation From Hyperspectral Radiance Data to Data of Other Sensors Based on Spectral Superresolution

Hyperspectral radiance spectra are the sensor's response, through its spectral response functions (SRFs), to the at-sensor radiance field. As the SRFs vary with sensors, hyperspectral radiance data need to be transformed for cross-calibration with another sensor or data simulation of a future sensor. In fact, the hyperspectral radiance data are composed of average radiance in the sensor's passbands and bear a spectral smoothing effect. Current data transformation methods do not fully consider this spectral response effect in hyperspectral data, and it restricts the accuracy of the transformation and, hence, the accuracy of the cross-calibration and data simulation. The spectral response effect is modeled as a correlation-sampling process instead of convolution sampling to fit all the hyperspectral, multispectral, and panchromatic sensors. An iterative method is proposed to get a superresolution spectrum from the hyperspectral radiance spectrum according to the response model. Data of another sensor are simulated by responding to the superresolution spectrum. Validation experiments are performed using MODTRAN4-simulated spectrum, coincident Earth Observing-1 Hyperion and Advanced Land Imager (ALI) radiance data, and nearly coincident Hyperion and Landsat-7 Enhanced Thematic Mapper Plus data. For transformations from the MODTRAN4-simulated spectrum to the hyperspectral spectrum of different spectral resolutions, the proposed transformation method achieves the least root mean square relative error (RMSRE) compared with the linear interpolation, the cubic spline interpolation, and the deconvolution-sampling method. For transformation from the Hyperion data to the ALI multispectral and panchromatic data, the RMSRE is less than 9% and 4%, respectively.
Governing Knowledge Commons

"Knowledge commons" describes the institutionalized community governance of the sharing and, in some cases, creation, of information, science, knowledge, data, and other types of intellectual and cultural resources. It is the subject of enormous recent interest and enthusiasm with respect to policymaking about innovation, creative production, and intellectual property. Taking that enthusiasm as its starting point, Governing Knowledge Commons argues that policymaking should be based on evidence and a deeper understanding of what makes commons institutions work. It offers a systematic way to study knowledge commons, borrowing and building on Elinor Ostrom's Nobel Prize-winning research on natural resource commons. It proposes a framework for studying knowledge commons that is adapted to the unique attributes of knowledge and information, describing the framework in detail and explaining how to put it into context both with respect to commons research and with respect to innovation and information policy. Eleven detailed case studies apply and discuss the framework exploring knowledge commons across a wide variety of scientific and cultural domains.
New anti-inflammatory agents to reduce atherosclerosis

Abstract The concept that inflammation plays a major role in atherogenesis has become accepted in recent years (Hansson ). As a result, anti-inflammatory agents may become increasingly important in the treatment of atherogenesis, atherosclerosis, and possibly even acute coronary or ischemic syndromes. This presentation reviews two types of molecules associated with the diagnosis, development, or treatment of atherosclerosis: C-reactive protein (CRP), and cannabis.
Role of microtubuli in secretion of very‐low‐density lipoprotein in isolated rat hepatocytes: Early effects of thiol reagents

The secretion of very‐low‐density lipoprotein from hepatocytes proceeds through the microtubules. In this study, the role of glutathione in the maintenance of intact microtubules and the secretion of very‐low‐density lipoprotein has been investigated. When rat hepatocytes were incubated with reagents that deplete glutathione (e.g., diethylmaleate, α‐bromoisovalerylurea or allyl alcohol) or reacted directly with protein thiols (disulfiram), the secretion of very‐low‐density lipoprotein by the cells was inhibited and the microtubules were severely damaged as visualized by immunofluorescence staining. Both events occurred within 30 min; long before, an effect on the energy status of the cells became evident. The observed inhibition of the secretion therefore seems due to an effect of the toxicants on the microtubules. For α‐bromoisovalerylurea, diethylmaleic acid and allyl alcohol, it may be related to glutathione depletion; preincubation of the hepatocytes with N‐acetyl‐L‐cysteine reduced the decrease of glutathione by α‐bromoisovalerylurea and allyl alcohol (but not of diethylmaleic acid) and almost completely prevented the inhibition of very‐low‐density lipoprotein secretion and microtubule damage. Depletion of glutathione may result in modification of a small group of essential free protein thiols. Disulfiram did not deplete glutathione, and N‐acetyl‐L‐cysteine could not prevent the effects of disulfiram on microtubules. The binding to protein thiols of radiolabeled disulfiram, which binds to microtubules in vitro, was determined. At 0.2 mmol/L disulfiram, only 3% of total cellular protein thiols were conjugated, but secretion of very‐low‐density lipoprotein was already inhibited by 25%, and microtubules were severely affected. We propose that modification of a small fraction of cellular protein thiols results in the loss of microtubular ultrastructure and thereby leads to inhibition of very‐low‐density lipoprotein secretion. (HEPATOLOGY 1991;14:1259–1268.)
Human-Like Agents for Repeated Negotiation

Virtual agents have been used as tools in negotiation—from acting as mediators to manifesting as full-fledged conversational partners. Virtual agents are a powerful tool for teaching negotiation skills, but require an accurate model of human behavior to perform well both as partners and teachers. The work proposed here aims to expand the current horizon of virtual negotiating agents to utilize humanlike strategies. Further agents developed using this framework should be cognizant of the social factors influencing negotiation, including reputation effects and the implications of long-term repeated relationships. A roadmap of current efforts to develop agent platforms and future expansions is discussed.
APOE genotype‐dependent modulation of astrocyte chemokine CCL3 production

Apolipoprotein E (apoE) is well known as a regulator of cholesterol homeostasis, and is increasingly recognized to play a prominent role in the modulation of innate immune response, including cell‐to‐cell communication and migration. Alzheimer's disease (AD) is a slowly progressive neurodegenerative disorder characterized by neuroinflammation that appears to be an important component of the pathophysiology of the disease. Astrocytes are the majority cell type in brain, exerting significant influence over a range of central nervous system activities, including microglial‐mediated neuroinflammatory responses. As the resident innate immune effector cells of the brain, microglia respond to soluble chemical signals released from tissue during injury and disease by mobilizing to lesion sites, clearing toxic molecules, and releasing chemical signals of their own. While microglial‐mediated neuroinflammation in the AD brain remains an area of intense investigation, the mechanisms underlying reinforcement and regulation of these aberrant microglial responses by astrocytes are largely unstudied. Moreover, although inheritance of APOE ɛ4 represents the greatest genetic risk factor for sporadic AD, the mechanism by which apoE isoforms differentially influence AD pathophysiology is unknown. Here we show that APOE ɛ4 genotype specifically modulates astrocyte secretion of potent microglial chemotactic agents, including CCL3, thus providing evidence that APOE modulation of central nervous system (CNS) innate immune response is mediated through astrocytes. GLIA 2015;63:51–65
Abusing ETFs

Using data from a large German brokerage, we find that individuals investing in passive exchange-traded funds (ETFs) do not improve their portfolio performance, even before transaction costs. Further analysis suggests that this is because of poor ETF timing as well as poor ETF selection (relative to the choice of low-cost, well-diversified ETFs). An exploration of investor heterogeneity shows that though investors who trade more have worse ETF timing, no groups of investors benefit by using ETFs, and no groups will lose by investing in low-cost, well-diversified ETFs.
EMLA cream for renal extracorporeal shock wave lithotripsy in ambulatory patients.

The effectiveness of a Eutectic Mixture of Local Anaesthetics (EMLA cream) for pain control during renal extracorporeal shock wave lithotripsy (ESWL) was evaluated in a group of 20 patients who had not been able to tolerate a previous session without intravenous (i.v.) analgesia. EMLA cream (10 g) was applied on the skin over the area (64-100 cm2) where the shock waves were to be focussed. A second generation lithotriptor Siemens Lithostar was used. The following measurements were made: the shock wave (kV) maximum voltage, the number of successful stone fragmentations (SSF), the visual analogue scale score (0-10) for pain (VAS), and the tolerance scale score (1-4) for the tolerance for the procedure. Significantly higher voltage (17.9 +/- 0.6 kV vs. 16.2 +/- 0.8 kV), lower VAS scores (5.9 +/- 1.1 vs. 8.7 +/- 1.3), lower TS score (2.3 +/- 0.6 vs. 3.6 +/- 0.6) and a higher number of SSF (18 vs. 5) were found in those patients for whom EMLA cream was used. Intravenous analgesia was not needed in nine patients. Nine patients received fentanyl 0.05 mg, one 0.10 mg and another 0.15 mg. These favourable results were attributed both to the sequence of gradual voltage increments used and to the cutaneous analgesia produced by EMLA cream.
Moment method analysis of dispersion in SRR-type FSS loaded rectangular waveguides using spectral domain green’s functions and RWG basis functions

This work has extended a previously devised moment-method treatment of sidewall loaded rectangular waveguides with periodic metallizations (FSS) imprinted on the dielectric surfaces. Arbitrarily shaped inclusions can now be treated with RWG basis functions. The SRR-type inclusions have been chosen for illustration here. The extended numerical code has been able to demonstrate the characteristic attributes of such SRR- FSS loaded waveguides, particularly the existence of bandgaps and backward propagating modes within a narrow passband below the ordinary modal cutoff frequency. The dispersion graphs generated by this code also checks well with those obtained by CST simulations.
Investigating the nature of the INTEGRAL gamma-ray bursts and sub-threshold triggers with Swift follow-up

We explore the potential of the INTErnational Gamma-Ray Astrophysics Laboratory (INTEGRAL) to improve our understanding of the low-fluence regime for explosive transients, such as Gamma-ray Bursts (GRBs). We probe the nature of the so-called 'WEAK' INTEGRAL triggers, when the gamma-ray instruments record intensity spikes that are below the usual STRONG significance thresholds. In a targeted Swift follow-up campaign, we observed 15 WEAK triggers. We find six of these can be classified as GRBs. This includes GRB 150305A, a GRB discovered from our campaign alone. We also identified a source coincident with one trigger, IGRW 151019, as a candidate active galactic nucleus. We show that real events such as GRBs exist within the INTEGRAL Burst Alert System (IBAS) WEAK trigger population. A comparison of the fluence distributions of the full INTEGRAL IBAS and Swift-BAT GRB samples showed that the two are similar. We also find correlations between the prompt gamma-ray and X-ray properties of the two samples, supporting previous investigations. We find that both satellites reach similar, low fluence levels regularly, although Swift is more sensitive to short, low-fluence GRBs.
The Measurement of Boredom

There are two commonly used measures of boredom: the Boredom Proneness Scale (BPS) and the Boredom Susceptibility Scale (ZBS). Although both were designed to measure the propensity to experience boredom (i.e., trait boredom), there are reasons to think they may not measure the same construct. The present research sought to evaluate this proposition in several stages. Specifically, relationships between the BPS, ZBS, and important causal (Study 1, N = 837), correlational (Study 2, N = 233), and outcome variables (Study 3, N = 137) were examined in university students. Taken together, results support the notion that the BPS and ZBS do not measure the same construct. Specifically, higher BPS scores were associated with higher levels of neuroticism, experiential avoidance, attentional and nonplanning impulsivity, anxiety, depression, dysphoria, and emotional eating. Conversely, higher ZBS scores were associated with higher levels of motor impulsivity, sensitivity to reward, gambling, and alcohol use and lower levels of neuroticism, experiential avoidance, and sensitivity to punishment.
Lower-Extremity Amputation: A 6-Year Follow-up Study in Brazil

Purpose. To evaluate the 6-year mortality in 50 patients following lower-limb amputation. Methods. The cumulative survival rate of 50 (28 men, 22 women) amputees aged 54 to 94 years (mean, 67.3; median, 73.5) was retrospectively studied from 1993 to 1998. Indications for above- or below-knee amputation were trauma (n=2), vasculitis (n=2), and critical ischaemia of the lower limbs (n=46). Leg amputation was performed after anamnesis, physical examination, and angiography. All patients were followed up for 6 years by phone or domiciliary visit. A death certificate was verified when a patient was lost to follow-up. Statistical analysis was expressed by the actuarial survival curve. Results. Of 50 amputees, 36 died in the 6 years following leg amputation: 22 in the first year, 3 in the second year, 5 in the third year, 2 in the fourth year, 2 in the fifth year, 2 in the sixth year; 14 remained alive after 6 years. Conclusion. Patients who underwent lower-limb amputation had a high 6-year mortality. Most deaths occurred in the first year.
Human herpesvirus type 8 infections among solid organ transplant recipients

Abstract: Human herpes virus 8 (HHV‐8) is known to be associated with Kaposi's sarcoma (KS), primary effusion lymphoma (PEL) and a form of Castleman's disease. Recently, it has also been shown to be associated with acute bone marrow failure in transplant patients. While, the full spectrum of clinical manifestations due to HHV‐8 is yet to be defined in transplant recipients, it is known to cause post‐transplant KS as a result of primary as well as secondary infection. This review will discuss the possible role of HHV‐8 as a cause of disease in solid organ transplant recipients by focussing on important issues, including the biology of the virus, epidemiology, clinical manifestations, laboratory diagnosis and treatment, followed by a discussion of issues of relevance to the pediatric transplant recipient.