Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein interaction networks at the host–microbe interface in Diaphorina citri, the insect vector of the citrus greening pathogen

The Asian citrus psyllid (Diaphorina citri) is the insect vector responsible for the worldwide spread of ‘Candidatus Liberibacter asiaticus’ (CLas), the bacterial pathogen associated with citrus greening disease. Developmental changes in the insect vector impact pathogen transmission, such that D. citri transmission of CLas is more efficient when bacteria are acquired by nymphs when compared with adults. We hypothesize that expression changes in the D. citri immune system and commensal microbiota occur during development and regulate vector competency. In support of this hypothesis, more proteins, with greater fold changes, were differentially expressed in response to CLas in adults when compared with nymphs, including insect proteins involved in bacterial adhesion and immunity. Compared with nymphs, adult insects had a higher titre of CLas and the bacterial endosymbionts Wolbachia, Profftella and Carsonella. All Wolbachia and Profftella proteins differentially expressed between nymphs and adults are upregulated in adults, while most differentially expressed Carsonella proteins are upregulated in nymphs. Discovery of protein interaction networks has broad applicability to the study of host–microbe relationships. Using protein interaction reporter technology, a D. citri haemocyanin protein highly upregulated in response to CLas was found to physically interact with the CLas coenzyme A (CoA) biosynthesis enzyme phosphopantothenoylcysteine synthetase/decarboxylase. CLas pantothenate kinase, which catalyses the rate-limiting step of CoA biosynthesis, was found to interact with a D. citri myosin protein. Two Carsonella enzymes involved in histidine and tryptophan biosynthesis were found to physically interact with D. citri proteins. These co-evolved protein interaction networks at the host–microbe interface are highly specific targets for controlling the insect vector responsible for the spread of citrus greening.
Vacuolar Processing Enzymes Are Essential for Proper Processing of Seed Storage Proteins in Arabidopsis thaliana*

The proprotein precursors of storage proteins are post-translationally processed to produce their respective mature forms within the protein storage vacuoles of maturing seeds. To investigate the processing mechanism in vivo, we isolated Arabidopsis mutants that accumulate detectable amounts of the precursors of the storage proteins, 12 S globulins and 2 S albumins, in their seeds. All six mutants isolated have a defect in the βVPE gene. VPE (vacuolar processing enzyme) is a cysteine proteinase with substrate specificity toward an asparagine residue. We further generated various mutants lacking different VPE isoforms: αVPE, βVPE, and/or γVPE. More than 90% of VPE activity is abolished in the βvpe-3 seeds, and no VPE activity is detected in the αvpe-1/βvpe-3/γvpe-1 seeds. The triple mutant seeds accumulate no properly processed mature storage proteins. Instead, large amounts of storage protein precursors are found in the seeds of this mutant. In contrast to βvpe-3 seeds, which accumulate both precursors and mature storage proteins, the other single (αvpe-1 and γvpe-1) and double (αvpe-1/γvpe-1) mutants accumulate no precursors in their seeds at all. Therefore, the vegetative VPEs, αVPE and γVPE, are not necessary for precursor processing in the presence of βVPE, but partly compensates for the deficiency in βVPE in βvpe-3 seeds. In the absence of functional VPEs, a proportion of pro2S albumin molecules are alternatively cleaved by aspartic proteinase. This cleavage by aspartic proteinase is promoted by the initial processing of pro2S albumins by VPE. Our overall results suggest that seed-type βVPE is most essential for the processing of storage proteins, and that the vegetative-type VPEs and aspartic proteinase complement βVPE activity in this processing.
Toxics, Toyotas, and Terrorism: The Behavioral Economics of Fear and Stigma

Economists have traditionally viewed the behavioral response to risk as continuous and proportional. In contrast, psychologists have often contended that people have little control over their response to risk that is dichotomous, nonproportional, visceral, and fear based. In extreme cases, this automatic response results in the stigmatization of a product, technology, or choice, which seemingly cannot be eliminated or reduced. In resolving these contrasting perspectives, we review four recent studies that blend behavioral economics and psychology. Together, they provide evidence for a dual‐process decision model for risk that incorporates both reason and fear. They show consumers’ responses to perceived risk as a mix of proportional and dichotomous (safe/unsafe) responses that are relatively more continuous in situations where deliberation is possible, and more dichotomous in emotional or stressful circumstances. These findings reconcile mixed results in past studies, and, more importantly, the dual‐process model allows a clear definition of stigma, and suggests new ways to mitigate stigma and to help manage potentially damaging overreactions to it.
Detection of glutamate, glutamine, and glutathione by radiofrequency suppression and echo time optimization at 7 tesla

To achieve detection of glutamate (Glu), glutamine (Gln), and glutathione (GSH) by minimizing the N‐acetyl‐aspartate (NAA) multiplet signals at 2.49 ppm using a echo time (TE) ‐optimized PRESS pulse sequence and a novel J‐suppression radiofrequency pulse.
Association between pain severity, depression severity, and use of health care services in Japan: results of a nationwide survey

Background Depression is often associated with painful physical symptoms. Previous research has seldom assessed the relationship between the severity of physical symptoms and the severity of mental and emotional symptoms of depression or other health outcomes, and no such studies have been conducted previously among individuals with depression in Japan. The aim of this study was to assess the relationship between the severity of physical pain and depression and other outcomes among individuals in Japan diagnosed with depression. Methods Data for individuals aged 18 and older in Japan who reported being diagnosed with depression and also reported physical pain were obtained from the Japan National Health and Wellness Survey. These respondents were characterized on sociodemographics and health characteristics, and the relationship between ratings of severity on pain in the last week and health outcomes were assessed using bivariate correlations and generalized linear models. Measures included the Patient Health Questionnaire for depression severity, Medical Outcomes Study 12-Item Short Form Survey Instrument for health-related quality of life, the Work Productivity and Activity Impairment for work and activity impairment, and 6-month report of health care use. Results More severe physical pain in the past week was correlated with more severe depression, worse health-related quality of life, lower health utility, greater impairment at work, and more health care provider visits. These relationships remained significant after incorporating sociodemographics and health characteristics in the statistical models. Conclusion Individuals whose depression is accompanied by more severe physical pain have a higher burden of illness than those whose depression includes less severe pain, suggesting that even partially ameliorating painful physical symptoms may significantly benefit patients with depression. Clinicians should take the presence and severity of physical pain into account and consider treating both the physical and emotional symptoms of these patients.
Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition

Human thanatomicrobiome studies have established that an abundant number of putrefactive bacteria within internal organs of decaying bodies are obligate anaerobes, Clostridium spp. These microorganisms have been implicated as etiological agents in potentially life-threatening infections; notwithstanding, the scale and trajectory of these microbes after death have not been elucidated. We performed phylogenetic surveys of thanatomicrobiome signatures of cadavers’ internal organs to compare the microbial diversity between the 16S rRNA gene V4 hypervariable region and V3-4 conjoined regions from livers and spleens of 45 cadavers undergoing forensic microbiological studies. Phylogenetic analyses of 16S rRNA gene sequences revealed that the V4 region had a significantly higher mean Chao1 richness within the total microbiome data. Permutational multivariate analysis of variance statistical tests, based on unweighted UniFrac distances, demonstrated that taxa compositions were significantly different between V4 and V3-4 hypervariable regions (p < 0.001). Of note, we present the first study, using the largest cohort of criminal cases to date, that two hypervariable regions show discriminatory power for human postmortem microbial diversity. In conclusion, here we propose the impact of hypervariable region selection for the 16S rRNA gene in differentiating thanatomicrobiomic profiles to provide empirical data to explain a unique concept, the Postmortem Clostridium Effect.
Capacity pre-log of SIMO correlated block-fading channels

We establish an upper bound on the noncoherent capacity pre-log of temporally correlated block-fading single-input multiple-output (SIMO) channels. The upper bound matches the lower bound recently reported in Riegler et al. (2011), and, hence, yields a complete characterization of the SIMO noncoherent capacity pre-log, provided that the channel covariance matrix satisfies a mild technical condition. This result allows one to determine the optimal number of receive antennas to be used to maximize the capacity pre-log for a given block-length and a given rank of the channel covariance matrix.
Robust Error Correction for De Novo Assembly via Spectral Partitioning and Sequence Alignment

Error correction is the rst step for any de novo assembly using next generation sequencing (NGS) data. This task is quite dif- cult and most available error correction software only supports base mismatches. In this work we propose a novel approach based on spec- tral graph clustering and Smith-Waterman alignment. This approach not only supports insertions and deletions, but also do not make any assumptions about the sequenced data.
Fatigue and fracture properties of thin metallic foils

Metallic thin foils are essential structural parts in microsystems, which may be subjected to fatigue loading caused by thermal fluctuations and mechanical vibrations influencing their reliability in numerous engineering applications. It is well known that the fatigue properties of bulk material cannot be adopted for small scaled structures. For a better understanding of the `size-effect' in the present investigation fatigue crack growth near threshold in the high cycle fatigue regime and associated fracture processes were studied. Free-standing rolled and electrodeposited Cu-, Mo- and Al foils of thickness from 20 μm to 250 μm in different conditions have been tested in a special experimental set up operating at R=−1 and a testing frequency of 20 kHz. At a given constant strain value the fatigue crack growth behaviour has been recorded accompanied by intermittent observation of the change of the dislocation structure in the vicinity of the growing crack by use of the electron channeling contrast imaging (ECCI)-technique in a scanning electron microscope (SEM). In a load shedding technique fatigue threshold stress intensity factor values have been derived and compared with data of bulk material. Typical crack growth features were detected depending on thickness and grain sizes of the foils. Various criteria (compliance, extent of plastic zones and plastic strain gradients) were selected for the explanation of this anomalous behaviour. Additionally fractomicrographs of uniaxial strained and fatigued foils have been studied to obtain further insight of the effect of dimensional constraint.
The Nature of Data, Information and Knowledge Exchanges in Business Processes: Implications for Process Improvement and Organisational Learning

Suggests that a number of assumptions in the past have been made about how business process improvement, re‐engineering and organizational learning should take place in organizations. Points out that, although a number of these assumptions have been framed on theoretical models, few have been based on the empirical analysis of the nature of actual business processes. Tries to fill this gap with an analysis of data, information and knowledge exchanges in 22 business processes from three organizations. Points to a number of characteristics that appear to be contradictory to some current organizational practices, and that can be helpful to inform future developments in the fields of business process improvement, re‐engineering and organizational learning. Two relevant characteristics are a much higher proportion of data over material exchanges in business processes, and a higher proportion of knowledge exchanges in improvement over core and support processes.
Progesterone Up-Regulates Anandamide Hydrolase in Human Lymphocytes: Role of Cytokines and Implications for Fertility1

Physiological concentrations of progesterone stimulate the activity of the endocannabinoid-degrading enzyme anandamide hydrolase (fatty acid amide hydrolase, FAAH) in human lymphocytes. At the same concentrations, the membrane-impermeant conjugate of progesterone with BSA was ineffective, suggesting that binding to an intracellular receptor was needed for progesterone activity. Stimulation of FAAH occurred through up-regulation of gene expression at transcriptional and translational level, and was partly mediated by the Th2 cytokines. In fact, lymphocyte treatment with IL-4 or with IL-10 had a stimulating effect on FAAH, whereas the Th1 cytokines IL-12 and IFN-γ reduced the activity and the protein expression of FAAH. Human chorionic gonadotropin or cortisol had no effect on FAAH activity. At variance with FAAH, the lymphocyte anandamide transporter and cannabinoid receptors were not affected by treatment with progesterone or cytokines. Good FAAH substrates such as anandamide and 2-arachidonoylglycerol inhibited the release of leukemia-inhibitory factor from human lymphocytes, but N-palmitoylethanolamine, a poor substrate, did not. A clinical study performed on 100 healthy women showed that a low FAAH activity in lymphocytes correlates with spontaneous abortion, whereas anandamide transporter and cannabinoid receptors in these cells remain unchanged. These results add the endocannabinoids to the hormone-cytokine array involved in the control of human pregnancy.
HST spectrum and timing of the ultracompact X-ray binary candidate 47 Tuc X9

To confirm the nature of the donor star in the ultra-compact X-ray binary candidate 47 Tuc X9, we obtained optical spectra (3,000$-$10,000 {\AA}) with the Hubble Space Telescope / Space Telescope Imaging Spectrograph. We find no strong emission or absorption features in the spectrum of X9. In particular, we place $3\sigma$ upper limits on the H$\alpha$ and HeII $\lambda 4686$ emission line equivalent widths $-$EW$_{\mathrm{H\alpha}} \lesssim 14$ {\AA} and $-$EW$_{\mathrm{HeII}} \lesssim 9$ {\AA}, respectively. This is much lower than seen for typical X-ray binaries at a similar X-ray luminosity (which, for $L_{\mathrm{2-10 keV}} \approx 10^{33}-10^{34}$ erg s$^{-1}$ is typically $-$EW$_{\mathrm{H\alpha}} \sim 50$ {\AA}). This supports our previous suggestion (by Bahramian et al.) of an H-poor donor in X9. We perform timing analysis on archival far-ultraviolet, $V$ and $I$-band data to search for periodicities. In the optical bands we recover the seven-day superorbital period initially discovered in X-rays, but we do not recover the orbital period. In the far-ultraviolet we find evidence for a 27.2 min period (shorter than the 28.2 min period seen in X-rays). We find that either a neutron star or black hole could explain the observed properties of X9. We also perform binary evolution calculations, showing that the formation of an initial black hole / He-star binary early in the life of a globular cluster could evolve into a present-day system such as X9 (should the compact object in this system indeed be a black hole) via mass-transfer driven by gravitational wave radiation.
Endothelial expression of thrombomodulin is reversibly regulated by fluid shear stress.

The vascular endothelium, by virtue of its position at the interface between blood and the vessel wall, is known to play a critical role in the control of thrombosis and fibrinolysis. Thrombomodulin (TM) is a surface receptor that binds thrombin and is a potent activator of the protein C anticoagulant pathway. Although TM expression is known to be regulated by various cytokines, little is known about its response to ever-present biomechanical stimuli. We have explored the role of fluid shear stress, imparted on the luminal surface of the endothelial cell as a result of blood flow, on the expression of TM mRNA and protein in both bovine aortic endothelial (BAE) and bovine smooth muscle (BSM) cells in an in vitro system. We report in the present study that TM expression is regulated by flow. Subjecting BAE cells to fluid shear stress in the physiological range of magnitude of 15 (moderate shear stress) and 36 (elevated shear stress) dynes/cm2 resulted in a mild transient increase followed by a significant decrease in TM mRNA to 37% and 16% of its resting level, respectively, by 9 hours after the onset of flow. In contrast, shear stress at the low magnitude of 4 dynes/cm2 did not affect TM mRNA levels. The sensitivity of TM mRNA expression by flow was found to be specific to endothelium, since it was not observed in BSM cells exposed to steady laminar shear stress of 15 dynes/cm2. Furthermore, unlike BAE cells, BSM cells did not exhibit altered cell shape nor align in the direction of flow after 24 hours of shear stress at 15 dynes/cm2. (ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of host‐range and cell entry properties of the major genotypes and subtypes of hepatitis C virus

Because of the lack of a robust cell culture system, relatively little is known about the molecular details of the cell entry mechanism for hepatitis C virus (HCV). Recently, we described infectious HCV pseudo‐particles (HCVpp) that were generated by incorporating unmodified HCV E1E2 glycoproteins into the membrane of retroviral core particles. These initial studies, performed with E1E2 glycoproteins of genotype 1, noted that HCVpp closely mimic the cell entry and neutralization properties of parental HCV. Because sequence variations in E1 and E2 may account for differences in tropism, replication properties, neutralization, and response to treatment in patients infected with different genotypes, we investigated the functional properties of HCV envelope glycoproteins from different genotypes/subtypes. Our studies indicate that hepatocytes were preferential targets of infection in vitro, although HCV replication in extrahepatic sites has been reported in vivo. Receptor competition assays using antibodies against the CD81 ectodomain as well as ectopic expression of CD81 in CD81‐deficient HepG2 cells indicated that CD81 is used by all the different genotypes/subtypes analyzed to enter the cells. However, by silencing RNA (siRNA) interference assays, our results show that the level of Scavenger Receptor Class‐B Type‐I (SR‐BI) needed for efficient infection varies between genotypes and subtypes. Finally, sera from chronic HCV carriers were found to exhibit broadly reactive activities that inhibited HCVpp cell entry, but failed to neutralize all the different genotypes. In conclusion, we characterize common steps in the cell entry pathways of the major HCV genotypes that should provide clues for the development of cell entry inhibitors and vaccines. (HEPATOLOGY 2005;41:265–274.)
Clustering web documents using co-citation, coupling, incoming, and outgoing hyperlinks: a comparative performance analysis of algorithms

Querying search engines with the keyword “jaguars” returns results as diverse as web sites about cars, computer games, attack planes, American football, and animals. More and more search engines offer options to organize query results by categories or, given a document, to return a list of links to topically related documents. While information retrieval traditionally defines similarity of documents in terms of contents, it seems natural to expect that the very structure of the Web carries important information about the topical similarity of documents. Here we study the role of a matrix constructed from weighted co‐citations (documents referenced by the same document), weighted couplings (documents referencing the same document), incoming, and outgoing links for the clustering of documents on the Web. We present and discuss three methods of clustering based on this matrix construction using three clustering algorithms, K‐means, Markov and Maximum Spanning Tree, respectively. Our main contribution is a cl.
Somatotopy in the Medullary Dorsal Horn As a Basis for Orofacial Reflex Behavior

The somatotopy of the trigeminocervical complex of the rat was defined as a basis for describing circuitry for reflex behaviors directed through the facial motor nucleus. Thus, transganglionic transport of horseradish peroxidase conjugates applied to individual nerves/peripheral receptive fields showed that nerves innervating oropharyngeal structures projected most rostrally, followed by nerves innervating snout, periocular, and then periauricular receptive fields most caudally. Nerves innervating mucosae or glabrous receptive fields terminated densely in laminae I, II, and V of the trigeminocervical complex, while those innervating hairy skin terminated in laminae I–V. Projections to lamina II exhibited the most focused somatotopy when individual cases were compared. Retrograde transport of FluoroGold (FG) deposited into the facial motor nucleus resulted in labeled neurons almost solely in lamina V of the trigeminocervical complex. The distribution of these labeled neurons paralleled the somatotopy of primary afferent fibers, e.g., those labeled after FG injections into a functional group of motoneurons innervating lip musculature were found most rostrally while those labeled after injections into motoneurons innervating snout, periocular and preauricular muscles, respectively, were found at progressively more caudal levels. Anterograde transport of injections of biotinylated dextran amine into lamina V at different rostrocaudal levels of the trigeminocervical complex confirmed the notion that the somatotopy of orofacial sensory fields parallels the musculotopy of facial motor neurons. These data suggest that neurons in lamina V are important interneurons in a simple orofacial reflex circuit consisting of a sensory neuron, interneuron and motor neuron. Moreover, the somatotopy of primary afferent fibers from the head and neck confirms the “onion skin hypothesis” and suggests rostral cervical dermatomes blend seamlessly with “cranial dermatomes. ” The transition area between subnucleus interpolaris and subnucleus caudalis is addressed while the paratrigeminal nucleus is discussed as an interface between the somatic and visceral nervous systems.