Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of DNA repair in Bacillus subtilis spore resistance

Wet-heat or hydrogen peroxide treatment of wild-type Bacillus subtilis spores did not result in induction of lacZ fusions to three DNA repair-related genes (dinR, recA, and uvrC) during spore outgrowth. However, these genes were induced during outgrowth of wild-type spores treated with dry heat or UV. Wet-heat, desiccation, dry-heat, or UV treatment of spores lacking major DNA-binding proteins (termed alpha-beta- spores) also resulted in induction of the three DNA repair genes during spore outgrowth. Hydrogen peroxide treatment of alpha-beta-spores did not result in induction of dinR- and rerA-lacZ but did cause induction of uvrC-lacZ during spore outgrowth. Spores of a recA mutant were approximately twofold more UV sensitive and approximately ninefold more sensitive to dry heat than were wild-type spores but were no more sensitive to wet heat and hydrogen peroxide. In contrast, alpha-beta- recA spores were significantly more sensitive than were alpha-beta- spores to all four treatments, as well as to desiccation. Surprisingly, RecA levels were quite low in dormant spores, but RecA was synthesized during spore outgrowth. Taken together, these data (i) are consistent with previous suggestions that some treatments (dry heat and UV with wild-type spores; desiccation, dry and wet heat, hydrogen peroxide, and UV with alpha-beta- spores) that kill spores do so in large part by causing DNA damage and (ii) indicate that repair of DNA damage during spore outgrowth is an important component of spore resistance to a number of treatments, as has been shown previously for UV.
Analysis of the Genetic Diversity and Population Structure of Austrian and Belgian Wheat Germplasm within a Regional Context Based on DArT Markers

Analysis of crop genetic diversity and structure provides valuable information needed to broaden the narrow genetic base as well as to enhance the breeding and conservation strategies of crops. In this study, 95 Austrian and Belgian wheat cultivars maintained at the Centre for Genetic Resources (CGN) in the Netherlands were characterised using 1052 diversity array technology (DArT) markers to evaluate their genetic diversity, relationships and population structure. The rarefacted allelic richness recorded in the Austrian and Belgian breeding pools (A25 = 1.396 and 1.341, respectively) indicated that the Austrian germplasm contained a higher genetic diversity than the Belgian pool. The expected heterozygosity (HE) values of the Austrian and Belgian pools were 0.411 and 0.375, respectively. Moreover, the values of the polymorphic information content (PIC) of the Austrian and Belgian pools were 0.337 and 0.298, respectively. Neighbour-joining tree divided each of the Austrian and Belgian germplasm pools into two genetically distinct groups. The structure analyses of the Austrian and Belgian pools were in a complete concordance with their neighbour-joining trees. Furthermore, the 95 cultivars were compared to 618 wheat genotypes from nine European countries based on a total of 141 common DArT markers in order to place the Austrian and Belgian wheat germplasm in a wider European context. The rarefacted allelic richness (A10) varied from 1.224 (Denmark) to 1.397 (Austria). Cluster and principal coordinates (PCoA) analyses divided the wheat genotypes of the nine European countries into two main clusters. The first cluster comprised the Northern and Western European wheat genotypes, whereas the second included the Central European cultivars. The structure analysis of the 618 European wheat genotypes was in a complete concordance with the results of cluster and PCoA analyses. Interestingly, a highly significant difference was recorded between regions (26.53%). In conclusion, this is the first study to reveal the high diversity levels and structure of the uncharacterised Austrian and Belgian wheat germplasm maintained at the CGN as well as place them in a wider European context. The results should help plant breeders to utilise the most promising wheat genotypes of this study in future breeding programmes for enhancing wheat cultivars.
Soluble, Prefibrillar α-Synuclein Oligomers Promote Complex I-dependent, Ca2+-induced Mitochondrial Dysfunction*

Background: Mitochondrial dysfunction and aggregation of α-synuclein both contribute to Parkinson disease. Results: Prefibrillar α-synuclein oligomers reduce the Ca2+ retention time of isolated mitochondria respiring with complex I but not II substrates. Conclusion: Oligomeric α-synuclein promotes mitochondrial dysfunction in a Ca2+- and respiratory substrate-dependent manner. Significance: The Ca2+-dependence of α-synuclein's effects may contribute to selective neuronal vulnerability in Parkinson disease. α-Synuclein (αSyn) aggregation and mitochondrial dysfunction both contribute to the pathogenesis of Parkinson disease (PD). Although recent studies have suggested that mitochondrial association of αSyn may disrupt mitochondrial function, it is unclear what aggregation state of αSyn is most damaging to mitochondria and what conditions promote or inhibit the effect of toxic αSyn species. Because the neuronal populations most vulnerable in PD are characterized by large cytosolic Ca2+ oscillations that burden mitochondria, we examined mitochondrial Ca2+ stress in an in vitro system comprising isolated mitochondria and purified recombinant human αSyn in various aggregation states. Using fluorimetry to simultaneously measure four mitochondrial parameters, we observed that soluble, prefibrillar αSyn oligomers, but not monomeric or fibrillar αSyn, decreased the retention time of exogenously added Ca2+, promoted Ca2+-induced mitochondrial swelling and depolarization, and accelerated cytochrome c release. Inhibition of the permeability transition pore rescued these αSyn-induced changes in mitochondrial parameters. Interestingly, the mitotoxic effects of αSyn were specifically dependent upon both electron flow through complex I and mitochondrial uptake of exogenous Ca2+. Our results suggest that soluble prefibrillar αSyn oligomers recapitulate several mitochondrial phenotypes previously observed in animal and cell models of PD: complex I dysfunction, altered membrane potential, disrupted Ca2+ homeostasis, and enhanced cytochrome c release. These data reveal how the association of oligomeric αSyn with mitochondria can be detrimental to the function of cells with high Ca2+-handling requirements.
When do presidents appoint policy experts to social agencies? A study of Brazil’s National Indian Foundation, 1967-2018

This MSc thesis intends to address the factors that lead to the appointment of experts to social agencies, through the longitudinal study of the National Indian Foundation (henceforth Funai), the Brazilian national organization for indigenous affairs. Using the tenets of Qualitative Comparative Analysis, I test if the conditions theorized to have contributed to the appointment of policy experts as presidents across it 51 years of existence (1967-2018) are sufficient or necessary. These are: a democratic regime, the ideology of the incumbent, the absence of military influence over the incumbent, the absence of economic crises, and pressure from social movements. Regarding the findings of the configurational analysis, democracy, non-rightist incumbents and the absence of economic crises combined were sufficient factors for the appointment of policy experts to Funai over time. Moreover, the former two were the strongest sufficient conditions to expertise. Democracy is a necessary condition for the appointment of experts to Funai. Furthermore, following the assumption of asymmetric causation, the same conditions that led to the appointment of experts, could not be extrapolated to the appointment of non-experts. As for non-expertise the combination of non-democracy, military influence, and right-wing incumbents was deemed sufficient. The results suggest that during the military regime the Executive tended to opt for appointees within their prerogatives – that is, selecting officers or engineers aligned with the developmental paradigm of the time. Also, the results of this study are in line with Dargent’s (2014) findings that show that an unbalance in the constellation of stakeholders facilitates political meddling in public agencies. Furthermore, results suggest that ideological differences between the military and indigenists have excluded the latter from their cadres during the military regime.
Dynamic Bank Capital Requirements

The Basel III Accord requires countercyclical capital buffers to protect the banking system against potential losses associated with excessive credit growth and buildups of systemic risk. In this paper, I provide a rationale for time-varying capital requirements in a dynamic general equilibrium setting. An optimal policy trades off reduced inefficient lending with reduced liquidity provision. Quantitatively, I find that the optimal Ramsey policy requires a capital ratio that mostly varies between 4% and 6% and depends on economic growth, bank supply of credit, and asset prices. Specifically, a one standard deviation increase in the bank credit-to-GDP ratio (GDP) translates into a 0.1% (0.7%) increase in capital requirements, while each standard deviation increase in the liquidity premium leads to a 0.1% decrease. The welfare gain from implementing this dynamic policy is large when compared to the gain from having an optimal fixed capital requirement.
Campaigning and election outcomes in a presidential primary election

ABSTRACT This article presents new evidence from the US presidential primary setting on the role campaigning plays in determining election outcomes. Using candidate visits as a measure of campaign intensity, I estimate a discrete choice model of voting using a differentiated products framework where I allow for abstention and create instruments for campaigning based on Democratic Party rules for delegate allocation. On average, a visit by a candidate increases the vote share of this candidate by about 2.4 percentage points and decreases the abstaining share by 0.7 percentage points.
Methylation-dependent Silencing of the Reduced Folate Carrier Gene in Inherently Methotrexate-resistant Human Breast Cancer Cells*

The molecular basis of methotrexate resistance was studied in human MDA-MB-231 breast cancer cells, which are inherently defective in methotrexate uptake and lack expression of the reduced folate carrier (RFC). Transfection of MDA-MB-231 cells with RFC cDNA restored methotrexate uptake and increased methotrexate sensitivity by ∼50-fold. A CpG island in the promoter region ofRFC was found to be methylated in MDA-MB-231 cells, but was unmethylated in RFC expressing, methotrexate-sensitive MCF-7 breast cancer cells. Chromatin immunoprecipitation with antibodies against acetylated histones H3 and H4 showed that the RFC promoter was enriched for acetylated histones on expressed, unmethylated alleles only. Treatment of MDA-MB-231 cells with 5-aza-2′-deoxycytidine restored RFC expression but also led to increased methotrexate efflux and did not reverse methotrexate resistance. This suggests that 5-aza-2′-deoxycytidine up-regulates both methotrexate uptake and some methotrexate-resistance mechanism(s). Reverse transcription-polymerase chain reaction analysis showed increased expression levels of several ATP-dependent efflux pumps in response to 5-aza-2′-deoxycytidine treatment, including P-glycoprotein and members of the multidrug resistance-associated protein family. Up-regulation of P-glycoprotein in response to 5-aza-2′-deoxycytidine was associated with demethylation of a CpG island in the MDR1 promoter, whereas the mechanism(s) for 5-aza-2′-deoxycytidine-induced up-regulation of multidrug resistance-associated proteins is probably indirect. Dipyridamole inhibited methotrexate efflux and reversed methotrexate resistance in 5-aza-2′-deoxycytidine-treated MDA-MB-231 cells.
A Bayesian Method for Synthesizing Evidence: The Confidence Profile Method

This article describes a collection of meta-analysis techniques based on Bayesian statistics for interpreting, adjusting, and combining evidence to estimate parameters and outcomes important to the assessment of health technologies. The result of an analysis by the Confidence Profile Method is a joint posterior probability distribution for the parameters of interest, from which marginal distributions for any particular parameter can be calculated. The method can be used to analyze problems involving a variety of types of outcomes, a variety of measures of effect, and a variety of experimental designs. This article presents the elements necessary for analysis, including prior distributions, likelihood functions, and specific models for experimental designs that include adjustment for biases.
On systems project abandonment: An analysis of complexity during development and evolution of FLOSS systems

Among all the reasons that leads to the success or failure of a Free/Libre Open Source Software (FLOSS) project, understanding the system's evolution can reveal important pieces of information to open source stakeholders, helping them to identify what can be improved in the software system's internal organization. Once software complexity is one of the most important attributes to determine software maintainability, controlling its level in the system evolution process makes the software easier to maintain, reducing the maintainability costs. Otherwise, uncontrolled complexity makes the maintenance and enhancement process lengthy, more costly and some times it can contribute to the system abandonment. This work investigates the evolution of complexity in discontinued FLOSS projects. After several analyses, the results showed that inactive FLOSS projects do not seem to be able to keep up with the extra work required to control the systems complexity, presenting a different behaviour of the successful active FLOSS projects.
Thermoelastic damping modeling of a Si resonant beam with nanowire strain gauges

Resonant structures based on the combination of an electromechanical microresonator made in a thick single crystal Si layer and a differential piezoresistive detection with Si nanowires is a recent concept allowing a breakthrough in downscaling physical resonant sensors with equal to better performances. With an optimized design, the vacuum quality factor of these resonant structures will be ultimately limited by thermoelastic damping. Existing analytical models reasonably well predict the thermoelastic damping of transverse vibrations for beam resonators with and without axial stress but their limitations for resonators with more complex geometry is difficult to estimate. In this paper we investigate by Finite Element Method the effect of axial stress and of nanowire strain gages integration on the thermoelastic damping of vibrations of a beam resonator with a central inertial mass. Results show that axial stress effect depends on actuation force and that nanowires mainly alter the thermoelastic damping through an increase of resonator stiffness. As expected thermoelastic damping is reduced when torsional vibration modes are involved. Results are compared or analyzed with published analytical models.
Immunodominant Regions of a Chlamydia trachomatis Type III Secretion Effector Protein, Tarp

ABSTRACT We have previously shown that individuals infected with Chlamydia trachomatis can develop a robust antibody response to a Chlamydia type III secretion effector protein called Tarp and that immunization with Tarp induces protection against challenge infection in mice. The current study aimed to map the immunodominant regions of the Tarp protein by expressing 11 fragments of Tarp as glutathione S-transferase (GST) fusion proteins and detecting the reactivity of these fusion proteins with antisera from patients infected with C. trachomatis in the urogenital tract or in the ocular tissue and from rabbits immunized with C. trachomatis organisms. A major immunodominant region was strongly recognized by all antibodies. This region covers amino acids 152 to 302, consisting of three repeats (amino acids 152 to 201, 202 to 251, and 252 to 302). Each of the repeats contains multiple tyrosine residues that are phosphorylated by host cell kinases when Tarp is injected into host cells. Several other minor immunodominant regions were also identified, including those comprising amino acids 1 to 156, 310 to 431, and 582 to 682 (recognized by antisera from both humans and rabbits), that comprising amino acids 425 to 581 (recognized only by human antisera), and that comprising amino acids 683 to 847 (preferentially recognized by rabbit antisera). This immunodominance was also confirmed by the observations that six out of the nine monoclonal antibodies (MAbs) bound to the major immunodominant region and that the other three each bound to one of the minor fragments, comprising amino acids 1 to 119, 120 to 151, and 310 to 431. The antigenicity analyses have provided important information for further understanding the structure and function of Tarp.
Optimization of Reduced-Dose MDCT of Thoracic Aorta Using Iterative Reconstruction

Objective To evaluate the contribution of iterative reconstruction on image quality of reduced-dose multidetector computed tomography of the thoracic aorta. Methods A torso phantom was scanned using two tube potentials (80 and 120 kVp) and five different tube currents (110, 75, 40, 20, and 10 mAs). All images were reconstructed with both filtered back projection (FBP) and iterative reconstruction. Aortic attenuation, image noise within the thoracic aorta, signal-to-noise ratio, and sharpness of the aortic wall were quantified in the phantom for the two reconstruction algorithms. Data were analyzed using paired t test. A value of P < 0.05 was considered significant. Results The aortic attenuation was similar for FBP and iterative reconstruction (P > 0.05). Image noise level was lower (P < 0.0001), and image sharpness was higher (P = 0.046) with iterative reconstruction. Signal-to-noise ratios were higher with iterative reconstruction compared with those with FBP (P < 0.0001). Signal-to-noise ratio at 80 kVp with iterative reconstruction (9.8 ± 4.4) was similar to the signal-to-noise ratio at 120 kVp with FBP (8.4 ± 3.3) (P = 0.196). Conclusions Less image noise and higher image sharpness may be achieved with iterative reconstruction in reduced-dose multidetector computed tomography of the thoracic aorta.
Body composition modifications in people with chronic spinal cord injury after supervised physical activity

Abstract Background Quantification of body composition variables is important for planning of better activities in relation to individuals with spinal cord injury (SCI). Objectives (1) To evaluate changes in body composition in patients with SCI after a supervised physical activity process; (2) To correlate total body fat with time since injury. Design Pre-post intervention. Setting Sarah Rehabilitation Hospital Network, Brazil. Participants Fifty-three men with SCI aged 18–52 years with duration of injury >3 years. Interventions The subjects were divided into three groups: tetraplegia (TT) (C5–C8), high paraplegia (HP) (T1–T6), and low paraplegia (LP) (T7–L2). Body composition was estimated in the first and last weeks of hospitalization. Outcome measures Body weight (kg), skinfolds sum (mm), absolute (kg), and relative (%) fat and lean body mass. Results Body weight increased in TT and decreased in HP (0.8 kg, 95%CI 0.1–1.5; and −1.0 kg, 95%CI −2.0 to 0.0, respectively; P < 0.05). Skinfolds sum decreased only in HP (−13.1 mm, 95%CI −20.7 to −5.5; P < 0.05). Absolute and relative body fat decreased significantly in the paraplegia groups. Lean body mass (LBM) percentage increased significantly in the paraplegia groups. Absolute LBM increased in TT and LP (0.8 kg, 95%CI 0.3–1.3; and 1.3 kg, 95%CI 0.8 to 1.8, respectively; P < 0.05). There was no correlation between time since injury and skinfolds sum for the three groups (P < 0.05). Conclusion TT, HP, and LP demonstrated favorable changes in body composition after 29 days of supervised physical activity. However, these changes were different in direction and magnitude.
Directed Search Over the Life Cycle

We develop a life-cycle model of the labor market in which different worker-firm matches have different quality and the assignment of the right workers to the right firms is time consuming because of search and learning frictions. The rate at which workers move between unemployment, employment and across different firms is endogenous because search is directed and, hence, workers can choose whether to seek low-wage jobs that are easy to find or high-wage jobs that are hard to find. We calibrate our theory using data on labor market transitions aggregated across workers of different ages. We validate our theory by showing that it correctly predicts the pattern of labor market transitions for workers of different ages. Finally, we use our theory to decompose the age profiles of transition rates, wages and productivity into the effects of age variation in work-life expectancy, human capital and match quality.
Evoked EMG and Muscle Fatigue During Isokinetic FES‐Cycling in Individuals With SCI

Purpose: This study investigated whether muscle fatigue during functional electrical stimulation (FES)‐induced cycling was associated with changes occurring in evoked electromyographic signals (eEMG, M‐waves) in individuals with spinal cord injury. We also explored the effects of recovery intervals between exercise sessions on the relationship between eEMG and muscle torque.
Constituents of Agaricus xanthodermus Genevier: The First Naturally Endogenous Azo Compound and Toxic Phenolic Metabolites

Abstract Extraction of fresh sporophores of the fungus Agaricus xanthodermus yields 4,4′-dihydroxy-azobenzene, phenol, p-quinol, and 4,4′-dihydroxybiphenyl. This is the first report of an azo compound arising endogenously in nature, while phenol, p-quinol and 4,4′-dihydroxybiphenyl have not previously been isolated from higher fungi. Phenol is present in fruitbodies in sufficiently high concentration to account for the toxicity of A. xanthodermus.
Normal hospital and low-bacterial diet in patients with cytopenia after intensive chemotherapy for hematological malignancy: a study of safety.

BACKGROUND The purpose of this randomized, controlled pilot study is to address the question whether normal hospital diet (NHD) is safe when compared with low-bacterial diet (LBD) given to prevent infections in cytopenic patients who receive antimicrobial prophylaxis (AP). PATIENTS AND METHODS The patients were randomized into two groups: one group to receive AP and LBD, the other to receive the same AP and NHD. The primary outcome parameter is colonization of the digestive tract with aerobic gram-negative bacilli and yeasts. Secondary outcome parameters were infections and total societal costs. RESULTS No statistically significant differences between treatment groups were observed regarding the primary outcome parameter, gut colonization by yeasts or gram-negative bacilli, or infections, use of antimicrobials, days with fever and total societal costs. CONCLUSION On the basis of the results of this pilot study, NHD appears to be as safe as LBD in patients with chemotherapy-induced cytopenia. Furthermore, the results indicate that LBD may offer no additional benefit as an infection preventive measure to the measures already implemented, such as AP. Thus, a larger randomized study, powered adequately to determine noninferiority of NHD to LBD is warranted and safe to be carried out.