Miracle-dz/UniFAR-FTUs huggingface dataset:
Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops.

BACKGROUND Xanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson is a Gram-negative bacterium that causes black rot, the most important disease of vegetable brassica crops worldwide. Intensive molecular investigation of Xcc is gaining momentum and several whole genome sequences are available. TAXONOMY Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadacea; Genus Xanthomonas; Species X. campestris. HOST RANGE AND SYMPTOMS Xcc can cause disease in a large number of species of Brassicaceae (ex-Cruciferae), including economically important vegetable Brassica crops and a number of other cruciferous crops, ornamentals and weeds, including the model plant Arabidopsis thaliana. Black rot is a systemic vascular disease. Typical disease symptoms include V-shaped yellow lesions starting from the leaf margins and blackening of the veins. RACE STRUCTURE, PATHOGENESIS AND EPIDEMIOLOGY Collections of Xcc isolates have been differentiated into physiological races based on the response of several brassica species lines. Black rot is a seed-borne disease. The disease is favoured by warm, humid conditions and can spread rapidly from rain dispersal and irrigation water. DISEASE CONTROL The control of black rot is difficult and relies on the use of pathogen-free planting material and the elimination of other potential inoculum sources (infected crop debris and cruciferous weeds). Major gene resistance is very rare in B. oleracea (brassica C genome). Resistance is more readily available in other species, including potentially useful sources of broad-spectrum resistance in B. rapa and B. carinata (A and BC genomes, respectively) and in the wild relative A. thaliana. GENOME The reference genomes of three isolates have been released. The genome consists of a single chromosome of approximately 5 100 000 bp, with a GC content of approximately 65% and an average predicted number of coding DNA sequences (CDS) of 4308. IMPORTANT GENES IDENTIFIED Three different secretion systems have been identified and studied in Xcc. The gene clusters xps and xcs encode a type II secretion system and xps genes have been linked to pathogenicity. The role of the type IV secretion system in pathogenicity is still uncertain. The hrp gene cluster encodes a type III secretion system that is associated with pathogenicity. An inventory of candidate effector genes has been assembled based on homology with known effectors. A range of other genes have been associated with virulence and pathogenicity, including the rpf, gum and wxc genes involved in the regulation of the synthesis of extracellular degrading enzymes, xanthan gum and lipopolysaccharides. USEFUL WEBSITE http://www.xanthomonas. org/
Effects of conjugated equine estrogens on breast cancer and mammography screening in postmenopausal women with hysterectomy.

CONTEXT The Women's Health Initiative Estrogen-Aone trial comparing conjugated equine estrogens (CEE) with placebo was stopped early because of an increased stroke incidence and no reduction in risk of coronary heart disease. Preliminary results suggesting possible reduction in breast cancers warranted more detailed analysis. OBJECTIVE To determine the effects of CEE on breast cancers and mammographic findings. DESIGN, SETTING, AND PARTICIPANTS Following breast cancer risk assessment, 10,739 postmenopausal women aged 50 to 79 years with prior hysterectomy were randomized to CEE or placebo at 40 US clinical centers from 1993 through 1998. Mammography screenings and clinical breast examinations were performed at baseline and annually. All breast cancers diagnosed through February 29, 2004, are included. INTERVENTION A dose of 0.625 mg/d of CEE or an identical-appearing placebo. MAIN OUTCOME MEASURES Breast cancer incidence, tumor characteristics, and mammogram findings. RESULTS After a mean (SD) follow-up of 7.1 (1.6) years, the invasive breast cancer hazard ratio (HR) for women assigned to CEE vs placebo was 0.80 (95% confidence interval [CI], 0.62-1.04; P = .09) with annualized rates of 0.28% (104 cases in the CEE group) and 0.34% (133 cases in the placebo group). In exploratory analyses, ductal carcinomas (HR, 0.71; 95% CI, 0.52-0.99) were reduced in the CEE group vs placebo group; however, the test for interaction by tumor type was not significant (P = .054). At 1 year, 9.2% of women in the CEE group had mammograms with abnormalities requiring follow-up vs 5.5% in the placebo group (P<.001), a pattern that continued through the trial to reach a cumulative percentage of 36.2% vs 28.1%, respectively (P<.001); however, this difference was primarily in assessments requiring short interval follow-up. CONCLUSIONS Treatment with CEE alone for 7.1 years does not increase breast cancer incidence in postmenopausal women with prior hysterectomy. However, treatment with CEE increases the frequency of mammography screening requiring short interval follow-up. Initiation of CEE should be based on consideration of the individual woman's potential risks and benefits. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00000611.
Social phobia in Parkinson’s disease: Prevalence and risk factors

Objective We aimed to investigate the frequency of social phobia in patients with Parkinson’s disease (PD). In addition, we explored the relationship between social phobia and the clinical characteristics of PD, and the frequency of comorbid psychiatric disorders in PD patients. Methods This study included 80 consecutive patients with PD admitted to the Parkinson’s disease and Movement Disorders Clinic at the Erenkoy Research and Training Hospital for Neurologic and Psychiatric Disorders, Istanbul, Turkey and used demographic and clinical data. The PD patients were evaluated during the “on state”, using the Hoehn and Yahr scale, the Unified Parkinson’s Disease Rating Scale, and the Schwab England Activities of Daily Living Scale. Psychiatric evaluations were conducted using the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition structured clinical interview, the Liebowitz Social Anxiety Scale (LSAS), and the Hamilton Depression Rating Scale. Results Social phobia was diagnosed in 42.5% of PD patients. Social phobia was comorbid with depression in 20 patients (58.8%), generalized anxiety disorder in 18 patients (52.9%), and panic disorder in six patients (17.6%). Social phobia was more frequent in males, early-onset PD, patients with a long duration of disease, the presence of postural instability, and with the use of a high Levodopa equivalent daily dose. A logistic regression analysis revealed the predictive factors of social phobia to be the sex of the patient (more frequent in males) and the presence of postural instability. There was a statistically significantly negative correlation between the LSAS score and the age of disease onset (r=−0.503; P=0.002) and a positive correlation between LSAS score and the duration of disease (r=0.374; P=0.023). Conclusion Social phobia is frequently observed in PD patients. Therefore, the assessment of PD patients should always include psychiatric evaluations, particularly for social phobia. The early detection and treatment of social phobia in PD patients is very important for the quality of life of patients as well as caregivers.
Computational investigation of pro-arrhythmogenesis of heart failure induced electrical remodelling in ventricles

Heart failure (HF) is one of the most common cardiac diseases that are associated with increased susceptibility of ventricular arrhythmia causing morbidity and mortality. Previous studies have found that HF causes a series of electrical and structural remodeling in the heart. The aim of this study was to determine the predominant factor of HF-induced remodeling responsible for ventricular arrhythmias. We developed a new family of cellular electrical models of canine ventricular and Purkinje fiber (PF) myocytes in control and HF condition based on experimental data. These models were validated by reproducing experimentally observed AP prolongation in HF condition. Single cell models were then incorporated into a 3D anatomical model with detailed electrical heterogeneity and structural anisotropy, as well as PF network. Re-entrant excitation waves were initiated using the phase distribution method. Role of each individual HF-induced electrical and structural remodeling on lifespan of re-entry was investigated. Among HF-induced remodeling, the reduction of intercellular conductivity plays an important role in sustaining ventricular arrhythmia. The ion channel remodeling though prolongs APD leading to increased vulnerability, it however reduces sustainability of re-entry.
Three‐Dimensional Printing of Ti3SiC2‐Based Ceramics

In the present work, we explored the feasibility of fabricating Ti3SiC2-based ceramics by a near-net-shape fabrication process of three-dimensional printing (3D printing) combined with liquid silicon infiltration (LSI). The porous ceramic preform was fabricated by 3D printing TiC powder with dextrin as a binder. The heat-treated preforms contained bimodal pore structure with interagglomerate pores (d≈23 μm) and intraagglomerate pores (d≈1 μm). Upon infiltration in Ar atmosphere at 1600°–1700°C for 1 h, silicon melt infiltrated the pores and reacted with TiC to yield Ti3SiC2, TiSi2, and SiC. The effects of silicon content and infiltration temperature on the phase composition of the Ti3SiC2-based composites were also studied. After LSI at 1700°C for 1 h, the composites with an initial TiC:Si mole ratio of 3:1.2 attained a bending strength of 293 MPa, a Vickers hardness of 7.2 GPa, and an electrical resistivity of 27.8 μΩ·cm, respectively.
Flight loss linked to faster molecular evolution in insects

The loss of flight ability has occurred thousands of times independently during insect evolution. Flight loss may be linked to higher molecular evolutionary rates because of reductions in effective population sizes (Ne) and relaxed selective constraints. Reduced dispersal ability increases population subdivision, may decrease geographical range size and increases (sub)population extinction risk, thus leading to an expected reduction in Ne. Additionally, flight loss in birds has been linked to higher molecular rates of energy-related genes, probably owing to relaxed selective constraints on energy metabolism. We tested for an association between insect flight loss and molecular rates through comparative analysis in 49 phylogenetically independent transitions spanning multiple taxa, including moths, flies, beetles, mayflies, stick insects, stoneflies, scorpionflies and caddisflies, using available nuclear and mitochondrial protein-coding DNA sequences. We estimated the rate of molecular evolution of flightless (FL) and related flight-capable lineages by ratios of non-synonymous-to-synonymous substitutions (dN/dS) and overall substitution rates (OSRs). Across multiple instances of flight loss, we show a significant pattern of higher dN/dS ratios and OSRs in FL lineages in mitochondrial but not nuclear genes. These patterns may be explained by relaxed selective constraints in FL ectotherms relating to energy metabolism, possibly in combination with reduced Ne.
How and where do criminals operate? Using Google to track Mexican drug trafficking organizations

How and where do criminals operate? Using Google to track Mexican drug trafficking organizations Michele Coscia ∗ CID, Harvard Kennedy School Viridiana Rios † Department of Government, Harvard University October 23, 2012 Abstract We develop a tool that uses Web content to obtain quantitative infor- mation about the mobility and modus operandi of criminal groups, infor- mation that would otherwise require the operation of large scale, expensive intelligence exercises to be obtained. Exploiting indexed reliable sources such as online newspapers and blogs, we use unambiguous query terms and Google’s search engine to identify the areas of operation of criminal organizations, and to extract information about the particularities of their mobility patters. We apply our tool to Mexican criminal organizations to identify their market strategies, their preferred areas of operation, and the way in which these have evolved over the last two decades. By extracting this knowledge, we provide crucial information for academics and policy makers increasingly interested in organized crime. Our findings provide evidence that criminal organizations are more strategic and operate in more differentiated ways than current academic literature had suggested
Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database

Network pharmacology elucidates the relationship between drugs and targets. As the identified targets for each drug increases, the corresponding drug-target network (DTN) evolves from solely reflection of the pharmaceutical industry trend to a portrait of polypharmacology. The aim of this study was to evaluate the potentials of DrugBank database in advancing systems pharmacology. We constructed and analyzed DTN from drugs and targets associations in the DrugBank 4.0 database. Our results showed that in bipartite DTN, increased ratio of identified targets for drugs augmented density and connectivity of drugs and targets and decreased modular structure. To clear up the details in the network structure, the DTNs were projected into two networks namely, drug similarity network (DSN) and target similarity network (TSN). In DSN, various classes of Food and Drug Administration-approved drugs with distinct therapeutic categories were linked together based on shared targets. Projected TSN also showed complexity because of promiscuity of the drugs. By including investigational drugs that are currently being tested in clinical trials, the networks manifested more connectivity and pictured the upcoming pharmacological space in the future years. Diverse biological processes and protein-protein interactions were manipulated by new drugs, which can extend possible target combinations. We conclude that network-based organization of DrugBank 4.0 data not only reveals the potential for repurposing of existing drugs, also allows generating novel predictions about drugs off-targets, drug-drug interactions and their side effects. Our results also encourage further effort for high-throughput identification of targets to build networks that can be integrated into disease networks.
An Offloading Strategy in Mobile Cloud Computing Considering Energy and Delay Constraints

With the expansion of wireless networks throughout the world and the high growth rate of the use of sophisticated programs in mobile devices, users’ expectations for the services provided by these devices have increased. Mobile devices have some limitations, such as battery life time and processing power for delivering all types of services to users. In recent years, mobile cloud computing, which is a phenomenal branch of cloud computing, has achieved considerable evolution in the computing community. By considering the advantage of offloading to the cloud, the limitations of mobile devices can be overcome to a great extent. A mobile device can be converted to a powerful device by applying cloud resources. The outstanding challenges in offloading are finding an optimum solution for the offloading problem to overcome these limitations. In this paper, offloading is modeled via a mathematical graph where both Wi-Fi and 3G links are topics of concern. Finding the best solution for offloading is equivalent to finding the constrained shortest path in this graph. By considering the K-LARAC and M-LARAC heuristic algorithms, a new heuristic algorithm is introduced to find the optimized path that can assess energy and delay, at a minimum, financial cost. This path is an appropriate solution for the offloading problem. The obtained results indicate that the designed algorithm can find an arbitrary approximation solution for the offloading problem with low complexity in comparison to existing algorithms.
CTRP3 is a novel biomarker for diabetic retinopathy and inhibits HGHL-induced VCAM-1 expression in an AMPK-dependent manner

Objectives Diabetic retinopathy (DR) is a severe complication of chronic diabetes. The C1q/TNF-related protein family (CTRPs) has been demonstrated to exert protective effects against obesity and atherosclerosis in animal studies. Heretofore, the association between circulating CTRPs and DR patients has been unexplored. In the current study, we attempt to define this association, as well as the effect of CTRPs upon DR pathophysiology. Design The present investigation is a case control study that enrolled control subjects and type 2 diabetes mellitus (T2DM) patients diagnosed with DR. Serum CTRPs and sVACM-1 were determined by ELISA. Results Serum CTRP3 and CTRP5 levels were markedly decreased in patients with T2DM compared to controls (p<0.05) and inversely associated with T2DM. Furthermore, mutivariate regression and ROC analysis revealed CTRP3 deficiency, not CTRP5, was associated with proliferative diabetic retinopathy (PDR). Spearman’s rank correlation assay demonstrated an inverse association between CTRP3 and sVCAM-1. Finally, exogenous CTRP3 administration attenuated high glucose high lipid (HGHL)-induced VCAM-1 production in an AMPK-dependent manner in cultured human retinal microvascular endothelial cells (HRMECs). Conclusion CTRP3 may serve as a novel biomarker for DR severity. CTRP3 may represent a future novel therapeutic against DR, a common ocular complication of diabetes.
Mitochondrial dysfunction induces dendritic loss via eIF2α phosphorylation

Mitochondria are key contributors to the etiology of diseases associated with neuromuscular defects or neurodegeneration. How changes in cellular metabolism specifically impact neuronal intracellular processes and cause neuropathological events is still unclear. We here dissect the molecular mechanism by which mitochondrial dysfunction induced by Prel aberrant function mediates selective dendritic loss in Drosophila melanogaster class IV dendritic arborization neurons. Using in vivo ATP imaging, we found that neuronal cellular ATP levels during development are not correlated with the progression of dendritic loss. We searched for mitochondrial stress signaling pathways that induce dendritic loss and found that mitochondrial dysfunction is associated with increased eIF2&agr; phosphorylation, which is sufficient to induce dendritic pathology in class IV arborization neurons. We also observed that eIF2&agr; phosphorylation mediates dendritic loss when mitochondrial dysfunction results from other genetic perturbations. Furthermore, mitochondrial dysfunction induces translation repression in class IV neurons in an eIF2&agr; phosphorylation-dependent manner, suggesting that differential translation attenuation among neuron subtypes is a determinant of preferential vulnerability.
Eavesdropping prevention for heterogeneous Internet of Things systems

With the rapid growth of Internet of Things (IoT), the idea of integrating a variety of IoTs has been proposed to support a variety of novel applications. However, IoT devices are often deployed in an open environment in which IoTs are inclined to be malfunctioned. Although data reliability can be achieved by data recovery with conventional replication, the communication between IoTs is susceptible to eavesdropping. Since most of the current work focuses on designing the architectures for IoTs under the specific scenarios, the eavesdropping prevention for heterogeneous IoT systems remains unexplored. Therefore, in this paper, we consider using the network-coding-based distributed storage systems for security and show that repair bandwidth can be reduced by increasing storage per node. Moreover, we theoretically derive the relation between repair bandwidth and storage in heterogeneous IoT systems. Finally, we show the relation between storage cost and reliability with regard to different amounts of IoT devices.
New GABAergic Neurogenesis in the Hippocampal CA1 Region of a Gerbil Model of Long‐Term Survival after Transient Cerebral Ischemic Injury

We investigated the probability of newly generated neurons that could survive and mature in the ischemic hippocampal CA1 region (CA1) of a gerbil model of transient cerebral ischemia. Neuronal death was shown in the stratum pyramidale (SP) from 4 days post‐ischemia, and a significant increase in NeuN‐positive (+) neurons was found in the SP at 180 days post‐ischemia. 5‐Bromo‐2‐deoxyuridine (BrdU)+ cells were co‐stained with NeuN and glutamic decarboxylase 67 (GAD67). Brain‐derived neurotrophic factor (BDNF) immunoreactivity and protein level was shown in nonpyramidal cells from 4 days post‐ischemia, and the immunoreactivity was strong at 30 days post‐ischemia and not significantly changed until 180 days post‐ischemia. Furthermore, TrkB immunoreactivity was co‐stained with GAD67 when we examined at 180 days post‐ischemia. Myelin basic protein (MBP)+ nerve fibers were reduced at 4 days post‐ischemia and maintained until 60 days post‐ischemia, and MBP immunoreactivity and levels were significantly increased at 180 days post‐ischemia. In the passive avoidance test, cognitive dysfunction was improved at 180 days post‐ischemia. These results suggest that the differentiation of neural progenitor cells into new GABAergic neurons may be promoted via BDNF in the ischemic CA1 and that the neurogenesis may partially mediate the recovery of cognitive impairments via increasing myelinated nerve fibers.
The Influence of Vibratory Courtship on Female Mating Behaviour in Orb-Web Spiders (Argiope keyserlingi, Karsch 1878)

Web-building spiders are important models for sexual selection. While our understanding of post-copulatory mechanisms including sperm competition and cryptic female choice is considerable, our knowledge of courtship and how it influences male and female mating decisions is still extremely poor. Here, we provide the first comprehensive description of male courtship behaviour and vibrations generated in the web by the orb-web spider, Argiope keyserlingi – a recognised model species. We identified three main elements of male courtship: shudders, abdominal wags and mating thread dances (including both plucks and bounces). The vibrations generated by these behaviours are described in detail. Male shuddering behaviour appears to have a strong influence on female latency to mate acceptance, with males that shudder at high rates without compromising shudder duration being preferred. Shuddering behaviour may also mediate female aggressive behaviour, with males that generate long shudders less likely to be cannibalised after copulation. Male abdominal wagging behaviour, however, appears to have only limited influence on female mating decisions. This study provides avenues for future work that synthesises pre- and post-copulatory mechanisms in web-building spiders to generate an all-encompassing model of how sexual selection operates.
Anomalous lattice expansion of metal-hydrogen thin films

We report x-ray diffraction experiments investigating the lattice expansion due to hydrogen in Nb/Ta superlattices and thin Nb films. For low hydrogen concentrations ( c _H < 0.09 H/metal), the lattice expands only normal to the plane of the film due to the epitaxial constraints imposed by the substrate. At higher concentrations, corresponding to strains on the order of the critical strains expected for the formation of misfit dislocations, we find a structural instability which leads to the formation of two metal-H phases, one of which has a lattice expansion in the plane of the film. These results differ significantly from the expected phase diagram and properties of the bulk metal-H systems.