Miracle-dz/UniFAR-FTUs huggingface dataset:
The immunosuppressant FK506 inhibits amino acid import in Saccharomyces cerevisiae

The immunosuppressants cyclosporin A, FK506, and rapamycin inhibit growth of unicellular eukaryotic microorganisms and also block activation of T lymphocytes from multicellular eukaryotes. In vitro, these compounds bind and inhibit two different types of peptidyl-prolyl cis-trans isomerases. Cyclosporin A binds cyclophilins, whereas FK506 and rapamycin bind FK506-binding proteins (FKBPs). Cyclophilins and FKBPs are ubiquitous, abundant, and targeted to multiple cellular compartments, and they may fold proteins in vivo. Previously, a 12-kDa cytoplasmic FKBP was shown to be only one of at least two FK506-sensitive targets in the yeast Saccharomyces cerevisiae. We find that a second FK506-sensitive target is required for amino acid import. Amino acid-auxotrophic yeast strains (trp1 his4 leu2) are FK506 sensitive, whereas prototrophic strains (TRP1 his4 leu2, trp1 HIS4 leu2, and trp1 his4 LEU2) are FK506 resistant. Amino acids added exogenously to the growth medium mitigate FK506 toxicity. FK506 induces GCN4 expression, which is normally induced by amino acid starvation. FK506 inhibits transport of tryptophan, histidine, and leucine into yeast cells. Lastly, several genes encoding proteins involved in amino acid import or biosynthesis confer FK506 resistance. These findings demonstrate that FK506 inhibits amino acid import in yeast cells, most likely by inhibiting amino acid transporters. Amino acid transporters are integral membrane proteins which import extracellular amino acids and constitute a protein family sharing 30 to 35% identity, including eight invariant prolines. Thus, the second FK506-sensitive target in yeast cells may be a proline isomerase that plays a role in folding amino acid transporters during transit through the secretory pathway.
Mechanisms of the anti-inflammatory effects of hydroxyethyl starch demonstrated in a flow-based model of neutrophil recruitment by endothelial cells*

Objective:To determine whether plasma volume expander hydroxyethyl starch (HES) may protect against reperfusion injury through an ability to reduce neutrophil recruitment. Design:An in vitro study using paired comparisons of adhesion of flowing neutrophils. Setting:A collaboration between clinical and basic science departments in a university hospital. Subjects:Neutrophils and cultured human umbilical vein endothelial cells (HUVEC). Interventions:Treatment with HES (average molecular weight of 200 kd and substitution of 0.62) at clinically relevant concentrations or with gelatin solution (average molecular weight of 30 kDa) of comparable viscosity. Measurements and Main Results:Glass capillaries were coated internally with either purified adhesion molecules or HUVEC, which were treated with tumor necrosis factor-&agr; in the presence or absence of HES. Neutrophils were perfused over these surfaces (with or without HES) and their recruitment quantified by video microscopy. Expression of adhesion molecules and of the chemokine interleukin-8 by HUVEC were analyzed by enzyme-linked immunosorbent assay and quantitation of messenger RNA. HES over a wide range of concentrations had no effect on selectin- or integrin-mediated adhesion of neutrophils. However, when HUVEC were cultured with 1.5% wt/vol HES, neutrophil capture induced by low-dose (1 unit/mL) tumor necrosis factor-&agr; and transendothelial migration induced by high-dose (100 units/mL) tumor necrosis factor-&agr; were significantly inhibited (p < .05, in each case). The effects were linked with reductions in expression of E-selectin and interleukin-8 by HUVEC at these respective tumor necrosis factor-&agr; concentrations (p < .05, in each case). Gelatin (2% wt/vol) had no significant effect in assays with HUVEC. Conclusions:Application of HES to HUVEC exerts an inhibitory effect on different stages of neutrophil recruitment, depending on the level of the inflammatory stimulus. These effects are associated with reduced adhesion molecule expression and chemokine production. In vivo, comparable effects might protect against complications associated with reperfusion injury.
Pneumococcal Nasopharyngeal Carriage following Reduced Doses of a 7-Valent Pneumococcal Conjugate Vaccine and a 23-Valent Pneumococcal Polysaccharide Vaccine Booster

ABSTRACT This study was conducted to evaluate the effect of a reduced-dose 7-valent pneumococcal conjugate vaccine (PCV) primary series followed by a 23-valent pneumococcal polysaccharide vaccine (23vPPS) booster on nasopharyngeal (NP) pneumococcal carriage. For this purpose, Fijian infants aged 6 weeks were randomized to receive 0, 1, 2, or 3 PCV doses. Within each group, half received 23vPPS at 12 months. NP swabs were taken at 6, 9, 12, and 17 months and were cultured for Streptococcus pneumoniae. Isolates were serotyped by multiplex PCR and a reverse line blot assay. There were no significant differences in PCV vaccine type (VT) carriage between the 3- and 2-dose groups at 12 months. NP VT carriage was significantly higher (P, <0.01) in the unvaccinated group than in the 3-dose group at the age of 9 months. There appeared to be a PCV dose effect in the cumulative proportion of infants carrying the VT, with less VT carriage occurring with more doses of PCV. Non-PCV serotype (NVT) carriage rates were similar for all PCV groups. When groups were pooled by receipt or nonreceipt of 23vPPS at 12 months, there were no differences in pneumococcal, VT, or NVT carriage rates between the 2 groups at the age of 17 months. In conclusion, there appeared to be a PCV dose effect on VT carriage, with less VT carriage occurring with more doses of PCV. By the age of 17 months, NVT carriage rates were similar for all groups. 23vPPS had no impact on carriage, despite the substantial boosts in antibody levels.
A new rule-based integrated decision making approach to container transshipment terminal selection

ABSTRACT The choice of the port or terminal to perform transshipment operations is a critical decision for container transportation companies (i.e. shipping line companies). This choice is not only affected by transshipment costs but also by the location, infrastructure, equipment, and technologies of the alternative terminals. In this study, a rule-based integrated multi-criteria group decision making approach is proposed in order to support such complex decision processes which involve substantial uncertainties and subjectivities. The proposed approach involves simple mathematics and provides a flexible modeling approach close to human reasoning that is able to consider uncertain information and relationships of arbitrary complexity. To prioritize the sub-criteria affecting the choice of the most appropriate terminal and to assess alternatives with respect to these sub-criteria, the Analytic Hierarchy Process (AHP) based on absolute measurement is used. Then, to determine the most appropriate terminal, a Fuzzy Rule-Based System is developed, which adopts the scores of criteria (i.e. the total scores of sub-criteria) obtained by AHP as input. In order to demonstrate the applicability and effectiveness of the proposed approach, an application is presented for the choice of the most appropriate container transshipment port in Turkey for a shipping line company.
The structural analysis of shark IgNAR antibodies reveals evolutionary principles of immunoglobulins

Significance Sharks are among the evolutionary oldest living organisms with an immune system that possesses a number of elements similar to ours, including antibodies. In this article, we present structural insights into one of the most ancient antibodies, shedding light on the molecular evolution of the immune system and the structural features of heavy chain-only antibodies. Sharks enrich urea in their blood to prevent osmotic loss of water in the marine environment. Urea, however, denatures proteins if they are not sufficiently stable. Indeed, we find that shark antibodies are particularly stable. We pinpointed specific features responsible for their high stability and found that transplanting them into a human antibody increased its secretion. Sharks and other cartilaginous fish are the phylogenetically oldest living organisms that rely on antibodies as part of their adaptive immune system. They produce the immunoglobulin new antigen receptor (IgNAR), a homodimeric heavy chain-only antibody, as a major part of their humoral adaptive immune response. Here, we report the atomic resolution structure of the IgNAR constant domains and a structural model of this heavy chain-only antibody. We find that despite low sequence conservation, the basic Ig fold of modern antibodies is already present in the evolutionary ancient shark IgNAR domains, highlighting key structural determinants of the ubiquitous Ig fold. In contrast, structural differences between human and shark antibody domains explain the high stability of several IgNAR domains and allowed us to engineer human antibodies for increased stability and secretion efficiency. We identified two constant domains, C1 and C3, that act as dimerization modules within IgNAR. Together with the individual domain structures and small-angle X-ray scattering, this allowed us to develop a structural model of the complete IgNAR molecule. Its constant region exhibits an elongated shape with flexibility and a characteristic kink in the middle. Despite the lack of a canonical hinge region, the variable domains are spaced appropriately wide for binding to multiple antigens. Thus, the shark IgNAR domains already display the well-known Ig fold, but apart from that, this heavy chain-only antibody employs unique ways for dimerization and positioning of functional modules.
Mutational Analysis of the Residue at Position 48 in the Salmonella enterica Serovar Typhimurium PhoQ Sensor Kinase

ABSTRACT The PhoP/PhoQ two-component regulatory system of Salmonella enterica serovar Typhimurium plays an essential role in controlling virulence by mediating the adaptation to Mg2+ depletion. The pho-24 allele of phoQ harbors a single amino acid substitution (T48I) in the periplasmic domain of the PhoQ histidine kinase sensor. This mutation has been shown to increase net phosphorylation of the PhoP response regulator. We analyzed the effect on signaling by PhoP/PhoQ of various amino acid substitutions at this position (PhoQ-T48X [X = A, S, V, I, or L]). Mutations T48V, T48I, and T48L were found to affect signaling by PhoP/PhoQ both in vivo and in vitro. Mutations PhoQ-T48V and PhoQ-T48I increased both the expression of the mgtA::lacZ transcriptional fusion and the net phosphorylation of PhoP, conferring to cells a PhoP constitutively active phenotype. In contrast, mutation PhoQ-T48L barely responded to changes in the concentration of external Mg2+, in vivo and in vitro, conferring to cells a PhoP constitutively inactive phenotype. By analyzing in vitro the individual catalytic activities of the PhoQ-T48X sensors, we found that the PhoP constitutively active phenotype observed for the PhoQ-T48V and PhoQ-T48I proteins is solely due to decreased phosphatase activity. In contrast, the PhoP constitutively inactive phenotype observed for the PhoQ-T48L mutant resulted from both decreased autokinase activity and increased phosphatase activity. Our data are consistent with a model in which the residue at position 48 of PhoQ contributes to a conformational switch between kinase- and phosphatase-dominant states.
Essays in Applied Insurance Economics

The papers included in this thesis deal with a few aspects of insurance economics that have seldom been dealt with in the applied literature. In the first paper I apply for the first time the tools of the economics of crime to study the determinants of frauds, using data on Italian provinces. The contributions to the literature are manifold: -The price of insuring has a positive correlation with the propensity to defraud -Social norms constraint fraudulent behavior, but their strength is curtailed in economic downturns -I apply a simple extension of the Random Coefficient model, which allows for the presence of time invariant covariates and asymmetries in the impact of the regressors. The second paper assesses how the evolution of macro prudential regulation of insurance companies has been reflected in their equity price. I employ a standard event study methodology, deriving the definition of the “control” and “treatment” groups from what is implied by the regulatory framework. The main results are: -Markets care about the evolution of the legislation. Their perception has shifted from a first positive assessment of a possible implicit “too big to fail” subsidy to a more negative one related to its cost in terms of stricter capital requirement -The size of this phenomenon is positively related to leverage, size and on the geographical location of the insurance companies The third paper introduces a novel methodology to forecast non-life insurance premiums and profitability as function of macroeconomic variables, using the simultaneous equation framework traditionally employed macroeconometric models and a simple theoretical model of insurance pricing to derive a long term relationship between premiums, claims expenses and short term rates. The model is shown to provide a better forecast of premiums and profitability compared with the single equation specifications commonly used in applied analysis.
Do Past Extreme Returns Explain the Future Performance? MAX Effect Evidence from the Nordic Countries

I examine MAX effect, i.e. negative relation between high maximum daily returns in the past month and returns in the next month, in the Nordics. Bali et. al. (2011) first find the MAX effect in U.S.A. I examine the MAX effect in the Nordics because of lack of evidence in the Nordics and the Aboulamer et. al (2016) recent contradictory finding in Canada. I confirm the previous results about MAX effect. I find negative cross-sectional relation between high maximum returns in past month and returns in the next month after controlling for variables: beta, size, book-to-market ratio, momentum, short term reversal and illiquidity. My results are also robust for idiosyncratic volatility puzzle i.e. negative relation between high idiosyncratic volatility and returns introduced by Ang et. al (2009), in fact the idiosyncratic volatility puzzle seems to overturn to positive effect after controlling MAX. The effect is consistent with investors preference for lottery-like stocks which lead to over-demand, higher prices and lower expected returns for high MAX stocks. Bachelor’s Thesis Aalto University School of Business Department of Finance Anton Kokljuschkin 05.12. 2016
Efferent neurons and suspected interneurons in motor cortex of the awake rabbit: axonal properties, sensory receptive fields, and subthreshold synaptic inputs.

1. Properties of antidromically identified efferent neurons within the cortical representation of the vibrissae, sinus hairs, and philtrum were examined in motor cortex of fully awake adult rabbits. Efferent neurons were tested for both receptive field and axonal properties and included callosal (CC) neurons (n = 31), ipsilateral corticocortical (C-IC) neurons (n = 34) that project to primary somatosensory cortex (S-1), and corticofugal neurons of layer 5 (CF-5) (n = 33) and layer 6 (CF-6) (n = 32) that project to and/or beyond the thalamus. Appropriate collision tests demonstrated that substantial numbers of corticocortical efferent neurons project an axon to both the corpus callosum and to ipsilateral S-1. 2. Suspected interneurons (SINs, n = 37) were also studied. These neurons were not activated antidromically from any stimulus site but did respond synaptically to electrical stimulation of the ventrolateral (VL) thalamus and/or S-1 with a burst of three or more spikes at frequencies from 600 to > 900 Hz. All of these neurons also responded synaptically to stimulation of the corpus callosum. The action potentials of these neurons were much shorter in duration (mean = 0.48 ms), than those of efferent neurons (mean = 0.90 ms). 3. CF-5 neurons differed from CC, C-IC, and CF-6 neurons in their spontaneous firing rates, axonal properties, and receptive field properties. Whereas CF-5 neurons had a mean spontaneous firing rate of 4.1 spikes/s, CC, C-IC, and CF-6 neurons all had mean values of < 1 spike/s. Axonal conduction velocities of CF-5 neurons were much higher (mean = 12.76 m/s) than either CC (1.47 m/s), C-IC (0.97 m/s), or CF-6 (mean = 1.96 m/s) neurons. A decrease in antidromic latency (the "supernormal" period) followed a single prior impulse in most CC, C-IC, and CF-6 neurons but was minimal or absent in CF-5 neurons. Although all but two CF-5 neurons responded to peripheral sensory stimulation, many CC (35%), C-IC (59%), or CF-6 (66%) neurons did not. CC, CF-5, and CF-6 neurons that did not respond to sensory stimulation had significantly lower axonal conduction velocities and spontaneous firing rates than those that responded to such stimulation. 4. Sensory receptive fields of neurons in motor cortex were considerably larger than those observed in S-1 but were similar in size to those seen in secondary somatosensory cortex (S-2). (ABSTRACT TRUNCATED AT 400 WORDS)
Serum free IGF-I during a hyperinsulinemic clamp following 3 days of administration of IGF-I vs. saline.

In a randomized crossover study in eight healthy subjects, we compared the effect of 3 days of continuous subcutaneous administration of insulin-like growth factor I (IGF-I; 10 micrograms.kg-1.h-1) and saline on fasting serum levels of free IGF-I, total (extractable) IGF-I, and IGF-binding protein (IGFBP)-1 and -3. On the 3rd day a hyperinsulinemic (euglycemic and hypoglycemic) clamp was performed. When preclamp (baseline) levels were compared after 3 days, IGF-I administration had increased total IGF-I from 225 +/- 21 (means +/- SE) to 1,003 +/- 46 micrograms/l (P < 0.0001), free IGF-I from 0.5 +/- 0.2 to 10.4 +/- 1.7 micrograms/l (P < 0.001), IGFBP-3 from 2,908 +/- 148 to 3,591 +/- 179 micrograms/l (P < 0.01), and IGFBP-1 from 7.6 +/- 3.8 to 19.6 +/- 2.5 micrograms/l (P < 0.01). During the clamp, levels of free IGF-I increased gradually from baseline to 1.0 +/- 0.3 micrograms/l (saline; P < 0.01) and to 19.6 +/- 4.7 micrograms/l (IGF-I; P < 0.005). Concomitantly, levels of IGFBP-1 decreased gradually from baseline to 4.1 +/- 2.3 micrograms/l (saline; P < 0.0005) and to 4.6 +/- 1.8 micrograms/l (IGF-I; P < 0.0001). Total IGF-I exhibited minor changes only during the clamp (P < 0.05), and IGFBP-3 was unchanged. In conclusion, administration of IGF-I increased total IGF-I about fourfold, whereas free IGF-I increased 20-fold. Noteworthily, in both situations a further twofold increase in free IGF-I was observed during the hyperinsulinemic clamp, concomitant with a decrease in IGFBP-1. This supports the hypothesis that IGFBP-1 is important in the short-term regulation of free IGF-I in vivo.
The Disappearing Large-Firm Wage Premium

Large firms have paid significantly higher wages for over a century. Based on administrative data we document that the large-firm wage premium (LFWP) has declined steadily over the last 30 years. Decomposing pay into worker and firm fixed effects, we then document that the LFWP can be largely explained by a rise in firm effects with firm size. The dramatic decline is due a reduction in these firm effects at large firms. These changes have been concentrated at very large employers. In contrast, worker composition has changed little. We also find the majority of the change occurs within industries.
Will the 'True' Labor Share Stand Up? An Applied Survey on Labor Share Measures

Labor's share of income is a key variable in economics. It plays a leading role in analysis of (in)equality, globalization, technical change, growth theories, etc. Notwithstanding this broad application, there are many different definitions of the labor share. Understanding and synthesizing those differences is the purpose of this applied survey. Empirical measures may vary reflecting the allocation of income components that cannot be directly ascribed to capital or labor. We examine the alternative assumptions made in the literature in this regard and quantify and motivate the resulting discrepancies. Focusing (mostly) on US data, we show that different measures can have very distinct properties in terms of the observed stochastic trends, shares of short‐, medium‐, and long‐run variation and volatilities, persistence and mean‐reversion properties, and susceptibility to structural breaks. For instance, while “short‐run” properties of the surveyed labor share measures are relatively consistent across all definitions (and countercyclical), their “medium‐” and “long‐run” trends may diverge substantially (and are procyclical). To substantiate our analysis, we document the implications of discrepancies in the empirical labor share definition for growth accounting, analyzing the effect of technology shocks, and for estimating inflation dynamics.
Military and Veterans’ Health, Health Care, and Wellbeing

Abstract The U.S. Department of Defense (DoD) and the U.S. Department of Veterans Affairs (VA) need to bridge a gap in their understanding of service members’ health outcomes and the issues involved in treatment, such as cost. In addition, clinicians and policy analysts must overcome existing knowledge barriers. Clinicians need to be aware of policy changes that will affect their patient load in numbers and in treatment needs. Policy analysts need to be aware of issues relevant to clinical treatment, such as quality and timeliness of care. Given the need for services and support to military personnel and families, and the fact that the fastest growing expenses in defense are health care costs, a multi-disciplinary line of research will help lawmakers understand the most efficient and effective resource use across the health care services.
Obesity-related insulin resistance in adolescents: a systematic review and meta-analysis of observational studies

Abstract Insulin resistance is common among obese adolescents; however, the extent of this problem is not clear. We conducted a systematic review of PubMed-Medline, CINAHL, The Web of Science, EMBASE and Scopus for observational studies evaluating components defining insulin resistance (insulin, C-peptide and homeostatic model assessment-insulin resistance [HOMA-IR]) in obese adolescents (12–18 years) versus non-obese adolescents. Our systematic review and meta-analysis followed the PRISMA guidelines. Data were combined using a random-effects model and summary statistics were calculated using the mean differences (MDs). 31 studies were included (n = 8655). In 26 studies, fasting insulin levels were higher in obese adolescents when compared to non-obese adolescents (MD = 64.11 pmol/L, 95%CI 49.48–78.75, p < 0.00001). In three studies, fasting C-peptide levels were higher in obese adolescents when compared to non-obese adolescents (MD = 0.29 nmol/L, 95%CI 0.22–0.36, p < 0.00001). In 24 studies, HOMA-IR values were higher in obese adolescents when compared to non-obese adolescents (MD = 2.22, 95%CI 1.78–2.67, p < 0.00001). Heterogeneity of effects among studies was moderate to high. Subgroup analyses showed similar results to the main analyses. Circulating insulin and C-peptide levels and HOMA-IR values were significantly higher in obese adolescents compared to those non-obese.