Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypes Associated with the Essential Diadenylate Cyclase CdaA and Its Potential Regulator CdaR in the Human Pathogen Listeria monocytogenes

ABSTRACT Cyclic diadenylate monophosphate (c-di-AMP) is a second messenger utilized by diverse bacteria. In many species, including the Gram-positive human pathogen Listeria monocytogenes, c-di-AMP is essential for growth. Here we show that the single diadenylate cyclase of L. monocytogenes, CdaA, is an integral membrane protein that interacts with its potential regulatory protein, CdaR, via the transmembrane protein domain. The presence of the CdaR protein is not required for the membrane localization and abundance of CdaA. We have also found that CdaR negatively influences CdaA activity in L. monocytogenes and that the role of CdaR is most evident at a high growth temperature. Interestingly, a cdaR mutant strain is less susceptible to lysozyme. Moreover, CdaA contributes to cell division, and cells depleted of CdaA are prone to lysis. The observation that the growth defect of a CdaA depletion strain can be partially restored by increasing the osmolarity of the growth medium suggests that c-di-AMP is important for maintaining the integrity of the protective cell envelope. Overall, this work provides new insights into the relationship between CdaA and CdaR. IMPORTANCE Cyclic diadenylate monophosphate (c-di-AMP) is a recently identified second messenger that is utilized by the Gram-positive human pathogen Listeria monocytogenes. Here we show that the single diadenylate cyclase of L. monocytogenes, CdaA, is an integral membrane protein that interacts with CdaR, its potential regulatory protein. We show that CdaR is not required for membrane localization or abundance of the diadenylate cyclase, but modulates its activity. Moreover, CdaA seems to contribute to cell division. Overall, this work provides new insights into the relationship between CdaA and CdaR and their involvement in cell growth.
Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis

Background Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ∼40% of the ∼2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ∼90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance.
TOR signaling downregulation increases resistance to the cereal killer Fusarium graminearum

ABSTRACT TOR is the master regulator of growth and development that senses energy availability. Biotic stress perturbs metabolic and energy homeostasis, making TOR a good candidate to participate in the plant response. Fusarium graminearum (Fusarium) produces important losses in many crops all over the world. To date, the role of TOR in Fusarium infection has remained unexplored. Here, we show that the resistance to the pathogen increases in different Arabidopsis mutants impaired in TOR complex or in wild-type plants treated with a TOR inhibitor. We conclude that TOR signaling is involved in plant defense against Fusarium.
Linear relationship between peak and season-long abundances in insects

An accurate quantitative relationship between key characteristics of an insect population, such as season-long and peak abundances, can be very useful in pest management programs. To the best of our knowledge, no such relationship has been established. Here we establish a predictive linear relationship between insect count Mpw during the week of peak abundance, the length of seasonal flight period, F (number of weeks) and season-long cumulative abundance A ≈ 0.41Mpw. The derivation of the equation is based on several general assumptions, and does not involve fitting to experimental data, which implies generality of the result. The equation was tested using extensive data collected on captures of male gypsy moth Lymantria dispar (L.) (Lepidoptera: Erebidae), in pheromone-baited traps during 15 years. The model was also tested using trap catch data for two species of mosquitoes, Culex pipiens (L.) (Diptera: Culicidae) and Aedes albopictus (Skuse) (Diptera: Culicidae), in Gravid and BG-sentinel mosquito traps. The simple, parameter-free equation approximates experimental data points with relative error of 13% and R2 = 0.997, across all of the species tested. For gypsy moth, we also related season-long and weekly trap catches to the daily trap catches during peak flight. We describe several usage scenarios, in which the derived relationships are employed to help link results of the small-scale field study to the operational Slow the Spread of the gypsy moth program.
Interleukin 12B (IL12B) Genetic Variation and Pulmonary Tuberculosis: A Study of Cohorts from The Gambia, Guinea-Bissau, United States and Argentina

We examined whether polymorphisms in interleukin-12B (IL12B) associate with susceptibility to pulmonary tuberculosis (PTB) in two West African populations (from The Gambia and Guinea-Bissau) and in two independent populations from North and South America. Nine polymorphisms (seven SNPs, one insertion/deletion, one microsatellite) were analyzed in 321 PTB cases and 346 controls from Guinea-Bissau and 280 PTB cases and 286 controls from The Gambia. For replication we studied 281 case and 179 control African-American samples and 221 cases and 144 controls of European ancestry from the US and Argentina. First-stage single locus analyses revealed signals of association at IL12B 3′ UTR SNP rs3212227 (unadjusted allelic p = 0.04; additive genotypic p = 0.05, OR = 0.78, 95% CI [0.61–0.99]) in Guinea-Bissau and rs11574790 (unadjusted allelic p = 0.05; additive genotypic p = 0.05, OR = 0.76, 95% CI [0.58–1.00]) in The Gambia. Association of rs3212227 was then replicated in African-Americans (rs3212227 allelic p = 0.002; additive genotypic p = 0.05, OR = 0.78, 95% CI [0.61–1.00]); most importantly, in the African-American cohort, multiple significant signals of association (seven of the nine polymorphisms tested) were detected throughout the gene. These data suggest that genetic variation in IL12B, a highly relevant candidate gene, is a risk factor for PTB in populations of African ancestry, although further studies will be required to confirm this association and identify the precise mechanism underlying it.
Association of Composite IS26-sul3 Elements with Highly Transmissible IncI1 Plasmids in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Clones from Humans

ABSTRACT The association of an IS440-sul3 platform with Tn21 class 1 integrons carried by IncI1 plasmids encoding extended-spectrum β-lactamases (ESBLs; mainly SHV-12 and CTX-M-14) among worldwide Escherichia coli clones of phylogroups A (ST10, ST23, and ST46), B1 (ST155, ST351, and ST359), and D/B2 (ST131) is reported. An in silico comparative analysis of sul3 elements available in the GenBank database shows the evolution of sul3 platforms by hosting different transposable elements facilitating the potential genesis of IS26 composite transposons and further insertion element-mediated promoted arrangements.
An algorithm for hiding and recovering data using matrices

We present an algorithm for the recovery of a matrix $\mathbb{M}$ % (non-singular $\in $ $\mathbb{C}^{N\times N}$) by only being aware of two of its powers, $\mathbb{M}_{k_{1}}:=\mathbb{M}^{k_{1}}$ and $\mathbb{M}% _{k_{2}}:=\mathbb{M}^{k_{2}}$ ($k_{1}>k_{2}$) whose exponents are positive coprime numbers. The knowledge of the exponents is the key to retrieve matrix $\mathbb{M}$ out from the two matrices $\mathbb{M}_{k_{i}}$. The procedure combines products and inversions of matrices, and a few computational steps are needed to get $\mathbb{M}$, almost independently of the exponents magnitudes. Guessing the matrix $\mathbb{M}$ from the two matrices $\mathbb{M}_{k_{i}}$, without the knowledge of $k_{1}$ and $k_{2}$, is comparatively highly consuming in terms of number of operations. If a private message, contained in $\mathbb{M}$, has to be conveyed, the exponents can be encrypted and then distributed through a public key method as, for instance, the DF (Diffie-Hellman), the RSA (Rivest-Shamir-Adleman), or any other.
Data-driven Enhancement of SVBRDF Reflectance Data

Analytical SVBRDF representations are widely used to represent spatially varying material appearance depending on view and light configurations. State-of-the-art industry-grade SVBRDF acquisition devices allow the acquisition within several minutes. For many materials with a surface reflectance behavior exhibiting complex effects of light exchange such as inter-reflections, self-occlusions or local subsurface scattering, SVBRDFs cannot accurately capture material appearance. We therefore propose a method to transform SVBRDF acquisition devices to full BTF acquisition devices. To this end, we use data-driven linear models obtained from a database of BTFs captured with a traditional BTF acquisition device in order to reconstruct high-resolution BTFs from the SVBRDF acquisition devices’ sparse measurements. We deal with the high degree of sparsity using Tikhonov regularization. In our evaluation, we validate our approach on several materials and show that BTF-like material appearance can be generated from SVBRDF measurements in the range
Neurexin–Neuroligin 1 regulates synaptic morphology and functions via the WAVE regulatory complex in Drosophila neuromuscular junction

Neuroligins are postsynaptic adhesion molecules that are essential for postsynaptic specialization and synaptic function. But the underlying molecular mechanisms of neuroligin functions remain unclear. We found that Drosophila Neuroligin 1 (DNlg1) regulates synaptic structure and function through WAVE regulatory complex (WRC)-mediated postsynaptic actin reorganization. The disruption of DNlg1, DNlg2, or their presynaptic partner neurexin (DNrx) led to a dramatic decrease in the amount of F-actin. Further study showed that DNlg1, but not DNlg2 or DNlg3, directly interacts with the WRC via its C-terminal interacting receptor sequence. That interaction is required to recruit WRC to the postsynaptic membrane to promote F-actin assembly. Furthermore, the interaction between DNlg1 and the WRC is essential for DNlg1 to rescue the morphological and electrophysiological defects in dnlg1 mutants. Our results reveal a novel mechanism by which the DNrx-DNlg1 trans-synaptic interaction coordinates structural and functional properties at the neuromuscular junction.
A survey of component carrier selection algorithms for carrier aggregation in long term evolution-advanced

Given that the demand for real-time multimedia contents that require significantly high data rate are getting of high popularity, a new mobile cellular technology known as Long term Evolution-Advanced (LTE-A) was standardized. The LTE-A is envisaged to support high peak data rate by aggregating more than one contiguous or non-contiguous Component Carriers (CCs) of the same or different frequency bandwidths. This paper provides a survey on the case where the LTE-A is working in backward compatible mode as well as when the system contains only LTE-A users. Note that the backward compatible mode indicates that the LTE-A contains a mixture of the legacy Long Term Evolution Release 8 (LTE) users that support packets (re)transmission on a single CC and the LTE-A users that are capable of utilizes more than one CCs for packets (re)transmission. It can be concluded from the study that the CC selection algorithms for newly-arrived LTE users can benefit from the channel diversity and the load status whereas the carrier aggregation that does not allocate all of the available CCs to the newly arrived LTE-A users shown to be more efficient.
A novel polymorphism in protein kinase AMP‐activated catalytic subunit alpha 2 (PRKAA2) is associated with type 2 diabetes in the Han Chinese population

It has been proposed that the energy‐sensing enzyme AMP‐activated protein kinase (AMPK) is a key agent in the pathophysiology of type 2 diabetes mellitus (T2DM). The gene encoding protein kinase AMP‐activated catalytic subunit alpha 2 (PRKAA2) is located at one of the Asian T2DM loci (1p32). Therefore, the aim of the present study was to test for the association of common variants in PRKAA2 with T2DM in the Han Chinese population.
Reliability Analysis on Shifted and Random Declustering Block Layouts in Scale-Out Storage Architectures

Reliability is a critical metric in the design and development of scale-out data storage clusters. A general multiway replication-based declustering scheme has been widely used in enterprise large-scale storage systems to improve the I/O parallelism. Unfortunately, given an increasing number of node failures, how often a cluster starts losing data when being scaled-out is not well investigated. In this paper, we studied the reliability of multi-way declustering layouts by developing an extended model, more specifically abstracting the Continuous Time Markov chain to an ordinary differentiate equation group, and analyzing their potential parallel recovery possibilities. Our comprehensive simulation results on Mat lab and SHARPE show that the shifted declustering layout outperforms the random declustering layout in a multi-way replication scale-out architecture, in terms of data loss probability and system reliability by up to 63% and 85% respectively. Our study on both 5-year and 10-year system reliability equipped with various recovery bandwidth settings shows that, the shifted declustering layout surpasses the random declustering layout in both cases by consuming up to 5.2% and 11% less recovery bandwidth.
Florivory indirectly decreases the plant reproductive output through changes in pollinator attraction

Abstract Species often interact indirectly with each other via their traits. There is increasing appreciation of trait‐mediated indirect effects linking multiple interactions. Flowers interact with both pollinators and floral herbivores, and the flower‐pollinator interaction may be modified by indirect effects of floral herbivores (i.e., florivores) on flower traits such as flower size attracting pollinators. To explore whether flower size affects the flower‐pollinator interaction, we used Eurya japonica flowers. We examined whether artificial florivory decreased fruit and seed production, and also whether flower size affected florivory and the number of floral visitors. The petal removal treatment (i.e., artificial florivory) showed approximately 50% reduction in both fruit and seed set in natural pollination but not in artificial pollination. Furthermore, flower size increased the number of floral visitors, although it did not affect the frequency of florivory. Our results demonstrate that petal removal indirectly decreased 75% of female reproductive output via decreased flower visits by pollinators and that flower size mediated indirect interactions between florivory and floral visitors.
Evaluation of the advantages of platelet concentrates stored at 4°C versus 22°C

Platelet (PLT) storage at cold temperatures (4°C) can reduce bacterial contamination and lower the risk of transfusion‐related complications. We compared the effects of 22 and 4°C storage conditions for PLTs to further explore the efficiency of hemostasis in acute bleeding and extended PLT shelf life.
Optical Biomarkers of Serous and Mucinous Human Ovarian Tumor Assessed with Nonlinear Optics Microscopies

Background Nonlinear optical (NLO) microscopy techniques have potential to improve the early detection of epithelial ovarian cancer. In this study we showed that multimodal NLO microscopies, including two-photon excitation fluorescence (TPEF), second-harmonic generation (SHG), third-harmonic generation (THG) and fluorescence lifetime imaging microscopy (FLIM) can detect morphological and metabolic changes associated with ovarian cancer progression. Methodology/Principal Findings We obtained strong TPEF + SHG + THG signals from fixed samples stained with Hematoxylin & Eosin (H&E) and robust FLIM signal from fixed unstained samples. Particularly, we imaged 34 ovarian biopsies from different patients (median age, 49 years) including 5 normal ovarian tissue, 18 serous tumors and 11 mucinous tumors with the multimodal NLO platform developed in our laboratory. We have been able to distinguish adenomas, borderline, and adenocarcinomas specimens. Using a complete set of scoring methods we found significant differences in the content, distribution and organization of collagen fibrils in the stroma as well as in the morphology and fluorescence lifetime from epithelial ovarian cells. Conclusions/Significance NLO microscopes provide complementary information about tissue microstructure, showing distinctive patterns for serous and mucinous ovarian tumors. The results provide a basis to interpret future NLO images of ovarian tissue and lay the foundation for future in vivo optical evaluation of premature ovarian lesions.
PAPR reduction of DC biased optical OFDM using combined clipping and PTS techniques

Visible light communications (VLC) has attracted increasing attention recently from both the industry and academic fields due to its untamed free bandwidth, which can be used to provide ultra-high speed wireless communications. However, high peak to average power ratio (PAPR) is a major issue in VLC system that is based on orthogonal frequency division multiplexing (OFDM) technology. PAPR causes nonlinearities in the transmitted signal and increases the complexity in retrieving the original signal at the receiver. In this paper, a new and hybrid PAPR reduction scheme is proposed for the OFDM-based VLC system using combined signal clipping techniques and partial transmit sequence (PTS). For this proposed hybrid scheme, the signal clipping method is combined with a modified PTS method that is suitable for VLC transmission in order to further reduce the PAPR as well as the bit error rate (BER) of the OFDM-based VLC system. Evaluation of the proposed hybrid scheme has been conducted for different modulation orders and the results has been compared to the clipping methods as well as conventional PTS techniques. The simulation results obtained show that the proposed hybrid scheme provides more than 3 dB PAPR reduction gain as compared to the basic VLC-OFDM signal at a CCDF of 10−1. In comparison with the signal clipping and conventional PTS method, the proposed method obtained PAPR reduction gain of approximately 0.4 dB and 2 dB, respectively. Moreover, the proposed scheme also outperforms the other methods in terms of BER performance for all scenarios.
Transferring object grasping knowledge and skill across different robotic platforms

This study describes the transfer of object grasping skills between two different humanoid robots with different software frameworks. We realize such a knowledge and skill transfer between the humanoid robots iCub and ARMAR-III. These two robots have different kinematics and are programmed using different middlewares, YARP and ArmarX. We developed a bridge system to allow for the execution of grasping skills of ARMAR-III on iCub. As the embodiment differs, the known feasible grasps for the one robot are not always feasible for the other robot. We propose a reactive correction behavior to detect failure of a grasp during its execution, to correct it until it is successful, and thus adapt the known grasp definition to the new embodiment.
Knowledge Extraction from Source Code Based on Hidden Markov Model: Application to EPICAM

Large software systems evolve rapidly and these evolutions are usually integrated directly into source code without updating the conceptual model. As a consequence, implementation platforms evolve faster than business logic. Thus, when extracting knowledge to enrich or build an ontology, business logic is not always a complete data source. To solve this problem, some authors have suggested to adopt an ontology learning approach in order to extract knowledge from the source code. In this paper, we show how to realize this task using Hidden Markov Models. experiments on EPICAM, a tuberculosis surveillance system shows the relevance of this approach.
Precise response functions in all-electron methods: Application to the optimized-effective-potential approach

The optimized-effective-potential (OEP) method is a special technique to construct local Kohn-Sham potentials from general orbital-dependent energy functionals. In a recent publication [M. Betzinger, C. Friedrich, S. Bl\"ugel, A. G\"orling, Phys. Rev. B 83, 045105 (2011)] we showed that uneconomically large basis sets were required to obtain a smooth local potential without spurious oscillations within the full-potential linearized augmented-plane-wave method (FLAPW). This could be attributed to the slow convergence behavior of the density response function. In this paper, we derive an incomplete-basis-set correction for the response, which consists of two terms: (1) a correction that is formally similar to the Pulay correction in atomic-force calculations and (2) a numerically more important basis response term originating from the potential dependence of the basis functions. The basis response term is constructed from the solutions of radial Sternheimer equations in the muffin-tin spheres. With these corrections the local potential converges at much smaller basis sets, at much fewer states, and its construction becomes numerically very stable. We analyze the improvements for rock-salt ScN and report results for BN, AlN, and GaN, as well as the perovskites CaTiO3, SrTiO3, and BaTiO3. The incomplete-basis-set correction can be applied to other electronic-structure methods with potential-dependent basis sets and opens the perspective to investigate a broad spectrum of problems in theoretical solid-state physics that involve response functions.