Miracle-dz/UniFAR-FTUs huggingface dataset:
Clostridium botulinum: A Bug with Beauty and Weapon

Abstract Clostridium botulinum, a Gram-positive, anaerobic sporeforming bacteria, is distinguished by its significant clinical applications as well as its potential to be used as bioterror agent. Growing cells secrete botulinum neurotoxin (BoNT), the most poisonous of all known poisons. While BoNT is the causative agent of deadly neuroparalytic botulism, it also serves as a remarkably effective treatment for involuntary muscle disorders such as blepharospasm, strabismus, hemifacial spasm, certain types of spasticity in children, and other ailments. BoNT is also used in cosmetology for the treatment of glabellar lines, and is well-known as the active component of the anti-aging medications Botox® and Dysport®. In addition, recent reports show that botulinum neurotoxin can be used as a tool for pharmaceutical drug delivery. However, BoNT remains the deadliest of all toxins, and is viewed by biodefense researchers as a possible agent of bioterrorism (BT). Among seven serotypes, C. botulinum type A is responsible for the highest mortality rate in botulism, and thus has the greatest potential to act as biological weapon. Genome sequencing of C. botulinum type A Hall strain (ATCC 3502) is now complete, and has shown the genome size to be 3.89 Mb with a G+C content of approximately 28.2%. The bacterium harbors a 16.3 kb plasmid with a 26.8% G+C content—slightly lower than that of the chromosome. Most of the virulence factors in C. botulinum are chromosomally encoded; bioinformatic analysis of the genome sequence has shown that the plasmid does not harbor toxin genes or genes for related virulence factors. Interestingly, the plasmid does harbor genes essential to replication, including dnaE, which encodes the alpha subunit of DNA polymerase III which has close similarity with its counterpart in C. perfringens strain 13. The plasmid also contains similar genes to those that encode the ABC-type multidrug transport ATPase, and permease. The presence of ABC-type multidrug transport ATPase, and permease suggests putative involvement of efflux pumps in bacteriocin production, modification, and export in C. botulinum. The C. botulinum plasmid additionally harbors genes for LambdaBa04 prophage and site-specific recombinase that are similar to those found in the Ames strain of Bacillus anthracis; these genes and their products may play a role in genomic rearrangement. Completion of genome sequencing for C. botulinum will provide an opportunity to design genomic and proteomic-based systems for detecting different serotypes of C. botulinum strains in the environment. The completed sequence may also facilitate identification of potential virulence factors and drug targets, as well as help characterize neurotoxin-complexing proteins, their polycistronic expression, and phylogenetic relationships between different serotypes.
Evolution of Multiple Additive Loci Caused Divergence between Drosophila yakuba and D. santomea in Wing Rowing during Male Courtship

In Drosophila, male flies perform innate, stereotyped courtship behavior. This innate behavior evolves rapidly between fly species, and is likely to have contributed to reproductive isolation and species divergence. We currently understand little about the neurobiological and genetic mechanisms that contributed to the evolution of courtship behavior. Here we describe a novel behavioral difference between the two closely related species D. yakuba and D. santomea: the frequency of wing rowing during courtship. During courtship, D. santomea males repeatedly rotate their wing blades to face forward and then back (rowing), while D. yakuba males rarely row their wings. We found little intraspecific variation in the frequency of wing rowing for both species. We exploited multiplexed shotgun genotyping (MSG) to genotype two backcross populations with a single lane of Illumina sequencing. We performed quantitative trait locus (QTL) mapping using the ancestry information estimated by MSG and found that the species difference in wing rowing mapped to four or five genetically separable regions. We found no evidence that these loci display epistasis. The identified loci all act in the same direction and can account for most of the species difference.
Modeling transient behaviour in vocal fold vibration using bifurcating nonlinear ordinary differential equation systems

Transient behaviour in the human voice is discussed, with particular reference to pitch breaks. Several nonlinear models for vocal fold vibration are proposed and discussed. One particular pitch break where a triple period emerges out of a double period — and vice versa — is modeled with a simple third order system similar to the Rössler system. For a given parameter value, the proposed model system has two intertwined attractors, one with a double and the other with a triple period. A model system more closely related to the physics of the vocal folds and the laryngograph Lx signal is also proposed. The possibilities of producing pitch breaks with this system are discussed, with particular attention to the hypothesis that pitch breaks are due to a constriction of the airflow above the vocal folds.
The Function of Fiction is the Abstraction and Simulation of Social Experience

Fiction literature has largely been ignored by psychology researchers because its only function seems to be entertainment, with no connection to empirical validity. We argue that literary narratives have a more important purpose. They offer models or simulations of the social world via abstraction, simplification, and compression. Narrative fiction also creates a deep and immersive simulative experience of social interactions for readers. This simulation facilitates the communication and understanding of social information and makes it more compelling, achieving a form of learning through experience. Engaging in the simulative experiences of fiction literature can facilitate the understanding of others who are different from ourselves and can augment our capacity for empathy and social inference.
Evaluation of Fentanyl Disposition and Effects in Newborn Piglets as an Experimental Model for Human Neonates

Background Fentanyl is widely used off-label in NICU. Our aim was to investigate its cerebral, cardiovascular and pulmonary effects as well as pharmacokinetics in an experimental model for neonates. Methods Fentanyl (5 µg/kg bolus immediately followed by a 90 minute infusion of 3 µg/kg/h) was administered to six mechanically ventilated newborn piglets. Cardiovascular, ventilation, pulmonary and oxygenation indexes as well as brain activity were monitored from T = 0 up to the end of experiments (T = 225–300 min). Also plasma samples for quantification of fentanyl were drawn. Results A “reliable degree of sedation” was observed up to T = 210–240 min, consistent with the selected dosing regimen and the observed fentanyl plasma levels. Unlike cardiovascular parameters, which were unmodified except for an increasing trend in heart rate, some of the ventilation and oxygenation indexes as well as brain activity were significantly altered. The pulmonary and brain effects of fentanyl were mostly recovered from T = 210 min to the end of experiment. Conclusion The newborn piglet was shown to be a suitable experimental model for studying fentanyl disposition as well as respiratory and cardiovascular effects in human neonates. Therefore, it could be extremely useful for further investigating the drug behaviour under pathophysiological conditions.
Fumarate Hydratase Deficiency in Renal Cancer Induces Glycolytic Addiction and Hypoxia-Inducible Transcription Factor 1α Stabilization by Glucose-Dependent Generation of Reactive Oxygen Species

ABSTRACT Hereditary leiomyomatosis and renal cell cancer (HLRCC) is an inherited cancer syndrome linked to biallelic inactivation of the gene encoding the tricarboxylic acid cycle enzyme fumarate hydratase (FH). Individuals with HLRCC are at risk to develop cutaneous and uterine leiomyomas and an aggressive form of kidney cancer. Pseudohypoxic drive—the aberrant activation of cellular hypoxia response pathways despite normal oxygen tension—is considered to be a likely mechanism underlying the etiology of this tumor. Pseudohypoxia requires the oxygen-independent stabilization of the α subunit of the hypoxia-inducible transcription factor (HIF-1α). Under normoxic conditions, proline hydroxylation of HIF-1α permits VHL recognition and subsequent targeting for proteasomal degradation. Here, we demonstrate that inactivating mutations of FH in an HLRCC-derived cell line result in glucose-mediated generation of cellular reactive oxygen species (ROS) and ROS-dependent HIF-1α stabilization. Additionally, we demonstrate that stable knockdown of FH in immortalized renal epithelial cells results in ROS-dependent HIF-1α stabilization. These data reveal that the obligate glycolytic switch present in HLRCC is critical to HIF stabilization via ROS generation.
The mechanics behind DNA sequence-dependent properties of the nucleosome

Chromatin organization and composition impart sophisticated regulatory features critical to eukaryotic genomic function. Although DNA sequence-dependent histone octamer binding is important for nucleosome activity, many aspects of this phenomenon have remained elusive. We studied nucleosome structure and stability with diverse DNA sequences, including Widom 601 derivatives with the highest known octamer affinities, to establish a simple model behind the mechanics of sequence dependency. This uncovers the unique but unexpected role of TA dinucleotides and a propensity for G|C-rich sequence elements to conform energetically favourably at most locations around the histone octamer, which rationalizes G|C% as the most predictive factor for nucleosome occupancy in vivo. In addition, our findings reveal dominant constraints on double helix conformation by H3–H4 relative to H2A–H2B binding and DNA sequence context-dependency underlying nucleosome structure, positioning and stability. This provides a basis for improved prediction of nucleosomal properties and the design of tailored DNA constructs for chromatin investigations.
FGFR1 promotes the stem cell-like phenotype of FGFR1-amplified non-small cell lung cancer cells through the Hedgehog pathway

Cancer stem cell-like phenotype is critical for tumor formation and treatment resistance. FGFR1 is found to be amplified in non-small cell lung cancer, particularly in the lung squamous cell cancer (LSCC). Whether FGFR1 contributes to the maintenance of stem cell-like phenotype of FGFR1-amplified lung cancer cells remains elusive. In this study, treatment with FGFR1 inhibitor AZD4547 suppressed the growth of tumor spheres and reduced ALDH positive proportion in FGFR1-amplified lung cancer cells in vitro, as well as inhibited the growth of oncospheres and parental cells in xenograft models. Knockdown of FGFR1 recaptured the similar effect as AZD4547 in vitro. Furthermore, activation of FGFR1 and subsequently its downstream ERK signaling enhanced the expression and transcriptional activity of GLI2, which could be blocked by FGFR1 inhibitor/silencing or ERK inhibitor. Knockdown of GLI2 directly inhibited the stem-like phenotype of FGFR1-amilified cells, whereas overexpression of GLI2 sufficiently rescued the phenotype caused by FGFR1 knockdown. Notably we also identified a correlation between FGFR1 and GLI2 expressions from clinical data, as well as an inverse relationship with progression free survival (PFS). Together our study suggests that the FGFR1/GLI2 axis promotes the lung cancer stem cell-like phenotype. These results support a rational strategy of combination of FGFR1 and GLI inhibitors for treatment of FGFR1-amplified lung cancers, especially LSCC.
New Directions for Self-Destructing Data Systems

This paper seeks to advance the state of the art in practical self-destructing data systems that secure sensitive data from disclosure in our highly mobile, social-networked, cloud-computing world. Our work facilitates the automatic, timed, and simultaneous destruction of all copies of a self-destructing data object (such as a message or ﬁle) without any explicit action by the user and without relying on any single trusted third party. We make three contributions to the study of self-destructing data. First, we present Cascade , an extensible framework for integrating multiple key-storage mechanisms into a single self-destructing data system. Cascade enhances resistance to attack by combining the security advantages of a diverse set of key-storage approaches. Second, we introduce Tide , a new key-storage system for self-destructing data that leverages the ubiquity and easy deployment of Apache Web servers throughout the Internet. Third, based on our earlier work on Vanish and in light of recent attacks against the Vuze DHT, we demonstrate how to signiﬁcantly harden Vuze and other DHTs against Sybil data-harvesting attacks, making DHTs applicable as key-storage systems under Cascade. To validate our approach, we designed, implemented, deployed, and measured these systems. We prototyped the extensible Cascade system with support for Tide, Vuze, and OpenDHT. We prototyped the Tide key-storage system on Apache, deployed it on over 400 PlanetLab nodes in the Internet, and demonstrated that the structure is highly immune to attack. Finally, we designed and deployed a set of defenses to Sybil data-harvesting attacks in the live Vuze P2P system and measured them at full scale in the million-node DHT; our results demonstrate that these defenses provide a three-order-of-magnitude improvement over the original Vuze DHT, rendering data-harvesting attacks extremely impractical.
Actin filament organization in activated mast cells is regulated by heterotrimeric and small GTP-binding proteins

Rat peritoneal mast cells, both intact and permeabilized, have been used widely as model secretory cells. GTP-binding proteins and calcium play a major role in controlling their secretory response. Here we have examined changes in the organization of actin filaments in intact mast cells after activation by compound 48/80, and in permeabilized cells after direct activation of GTP-binding proteins by GTP-gamma-S. In both cases, a centripetal redistribution of cellular F-actin was observed: the content of F-actin was reduced in the cortical region and increased in the cell interior. The overall F-actin content was increased. Using permeabilized cells, we show that AIF4-, an activator of heterotrimeric G proteins, induces the disassembly of F-actin at the cortex, while the appearance of actin filaments in the interior of the cell is dependent on two small GTPases, rho and rac. Rho was found to be responsible for de novo actin polymerization, presumably from a membrane-bound monomeric pool, while rac was required for an entrapment of the released cortical filaments. Thus, a heterotrimeric G-protein and the small GTPases, rho and rac, participate in affecting the changes in the actin cytoskeleton observed after activation of mast cells.
Postpartum Amenorrhoea among Manipuri Women: A Survival Analysis

Among the three major components of a closed birth interval, waiting time to conception can somehow be managed with effective contraceptives while gestation is universally constant in its duration; the duration of postpartum amenorrhoea (PPA) varies in complex nature. The present study aimed to investigate the proximate factors influencing the duration of PPA. A community-based, cross-sectional study was conducted in four valley districts of Manipur, India, during 1 August−31 December 2009, to analyze the differentials and determinants of duration of PPA, applying the survival analysis technique. In total, 1,225 ever-married women were selected through two-stage cluster sampling. The median duration of PPA was 5.7 months. Among the 11 explanatory variables of interest, only three variables—place of residence (p<0.05), infant mortality from preceding pregnancy (p<0.01), and duration of breastfeeding (p<0.01)—had a significant effect on the duration of PPA. The findings may be used as baseline information for future researchers and maternal health policy-makers.
Batroxobin Mobilizes Circulating Endothelial Progenitor Cells in Patients With Deep Vein Thrombosis

Batroxobin, a thrombin-like enzyme from Bothrops atrox moojeni venom, is associated with the reduction of fibrinogen levels in plasma and the enhancement of anticoagulation and fibrinolysis. In this study, 15 patients with deep vein thrombosis (DVT) achieved successful limb salvage after the administration of batroxobin. We found that the levels of CD34+, CD31+, CD34+/CD31+, and vascular endothelial cadherin (VE-cadherin+) cells had increased in the peripheral blood of patients at 7 days and 14 days after treatment. At 0 day, 7 days, and 14 days, the percentages of CD34+ cells, which are assumed to be hematopoietic stem cells, are 0.39% ± 0.43%, 0.71% ± 0.50%, and 1.11% ± 0.66%, respectively. The levels of CD34+ cells at 14 days are significantly higher than the levels on the first day (P = .004). The levels of CD31+ cells and VE-cadherin+ cells, which represent mature endothelial cells, at 7 days (34.15% ± 11.32%, P = .013; 1.25% ± 1.39%, P = .014) and 14 days (35.21% ± 7.66%, P = .071; 1.85% ± 2.60%, P = .117) were slightly elevated compared with those at 0 day (27.55% ± 8.65%; 0.25 ± 0.39%). The double positive of CD34 and CD31 cells are assumed to be endothelial progenitor cells (EPCs). The levels of CD34+/CD31+ cells at 7 days (0.69% ± 0.50%, P = .001) and 14 days (1.07% ± 0.66%, P = .006) are significantly higher than that on the initial day (0.28% ± 0.30%). The number of CD34+/CD31+ cells significantly increased, indicating that in addition to its role in anticoagulation and fibrinolysis, treatment with batroxobin might simultaneously activate circulating EPCs that might promote the recanalization of the damaged vessel wall.
Diabetic Retinopathy and Endothelial Dysfunction in Patients with Type 2 Diabetes Mellitus

Background We investigated the relationship between endothelial dysfunction and diabetic retinopathy (DR) in patients with type 2 diabetes. Methods We used a cross-sectional design to examine 167 patients with type 2 diabetes mellitus. All patients underwent biochemical and ophthalmological examination. We assessed endothelial dysfunction by a flow-mediated vasodilation method of the brachial artery. Changes in vasodilation (flow-mediated vasodilatation, %FMD) were expressed as percent change over baseline values. Results The mean±standard deviation of patient age was 54.1±8.6 years. The %FMD was significantly lower in patients with DR than without DR. The prevalence of retinopathy decreased across increasing tertiles of %FMD. After adjusting for patients' age, sex, diabetes duration, use of insulin, use of antihypertensive, antiplatelet, and lipid lowering medications, systolic blood pressure, fasting plasma glucose, 2-hour plasma glucose, glycated hemoglobin, and urinary albumin excretion, participants with a reduced %FMD were more likely to have DR (odds ratio, 11.819; 95% confidence interval, 2.201 to 63.461; P=0.004, comparing the lowest and highest tertiles of %FMD). Conclusion Endothelial dysfunction was associated with DR, which was most apparent when the endothelial dysfunction was severe. Our study provides insights into the possible mechanism of the influence of endothelial dysfunction on the development of DR.
The thermal-electrical properties of polyvinyl alcohol/AgNO3 films

In this article, one cast technique to fabricate 20–40 wt %AgNO3-doped polyvinyl alcohol (PVA) composite films of which electrical resistance sharply dropped (4–5 order) in a certain temperature range was reported. The phase, structure thermal, and electrical resistivity properties of films at different heat treatment temperatures were studied by X-ray diffraction (XRD), scanning electrical microscopy (SEM) and differential scanning calorimetry (DSC). The results showed that all the AgNO3 (20–40 wt %) doped PVA films presented an exothermic peak at 182°C. And the temperature of exothermic peak kept constant for various contents of AgNO3. Meanwhile, the phase composition of the films was greatly affected by the heat treatment temperature. Ag particles were generated during the heat treatment process, and the content of Ag particles increased with increasing the temperature. The resistivity of PVA/AgNO3 films decreased with increasing the temperature. And a sharp decrease appeared at 155–165°C due to the generation and contact of a mass of Ag particles at this temperature. The thermal-electrical results suggested the applicability of these materials in temperature sensor, for example, critical temperature resistor thermistor. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Altered proliferative ability of neuronal progenitors in PlexinA1 mutant mice

Cortical interneurons are generated predominantly in the medial ganglionic eminence (MGE) and migrate through the ventral and dorsal telencephalon before taking their final positions within the developing cortical plate. Previously we demonstrated that interneurons from Robo1 knockout (Robo1−/−) mice contain reduced levels of neuropilin 1 (Nrp1) and PlexinA1 receptors, rendering them less responsive to the chemorepulsive actions of semaphorin ligands expressed in the striatum and affecting their course of migration (Hernandez‐Miranda et al. [2011] J. Neurosci. 31:6174–6187). Earlier studies have highlighted the importance of Nrp1 and Nrp2 in interneuron migration, and here we assess the role of PlexinA1 in this process. We observed significantly fewer cells expressing the interneuron markers Gad67 and Lhx6 in the cortex of PlexinA1−/− mice compared with wild‐type littermates at E14.5 and E18.5. Although the level of apoptosis was similar in the mutant and control forebrain, proliferation was significantly reduced in the former. Furthermore, progenitor cells in the MGE of PlexinA1−/− mice appeared to be poorly anchored to the ventricular surface and showed reduced adhesive properties, which may account for the observed reduction in proliferation. Together our data uncover a novel role for PlexinA1 in forebrain development. J. Comp. Neurol. 524:518–534, 2016. © 2015 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.
Low levels of relatedness on black grouse leks despite male philopatry

In lekking species, males cluster on specific areas for display (the leks) and females generally prefer to copulate with males on large aggregations. The maintenance of leks in which only a few males reproduce might be explained if subordinate males gain indirect fitness benefits. By joining a lek on which relatives are displaying, subordinates might attract more females to the lek thereby increasing the mating opportunities of their kin. In black grouse, a genetic structure among leks has previously been found suggesting that relatives could display together. Using 11 microsatellite loci, we extended this result by testing for the presence of kin structures in nine black grouse leks (101 males). The genetic differentiation among flocks was higher in males than in females, suggesting female‐biased dispersal and male philopatry. Because of this genetic structure, males were more related within than among leks. However, the mean relatedness within each lek hardly differed from zero. The lekking males were not more related than random assortments of males from the winter flocks and there were no kin clusters within leks. Thus, black grouse males do not choose to display with and close to relatives. Male philopatry alone was not sufficient to induce elevated levels of relatedness on the leks either because of male partial dispersal or a rapid turnover of the successful males. The indirect fitness benefits associated with males’ settlement decision are probably limited compared to the direct benefits of joining large aggregations such as increased current and future mating opportunities.