Miracle-dz/UniFAR-FTUs huggingface dataset:
Functionally Redundant RXLR Effectors from Phytophthora infestans Act at Different Steps to Suppress Early flg22-Triggered Immunity

Genome sequences of several economically important phytopathogenic oomycetes have revealed the presence of large families of so-called RXLR effectors. Functional screens have identified RXLR effector repertoires that either compromise or induce plant defense responses. However, limited information is available about the molecular mechanisms underlying the modes of action of these effectors in planta. The perception of highly conserved pathogen- or microbe-associated molecular patterns (PAMPs/MAMPs), such as flg22, triggers converging signaling pathways recruiting MAP kinase cascades and inducing transcriptional re-programming, yielding a generic anti-microbial response. We used a highly synchronizable, pathogen-free protoplast-based assay to identify a set of RXLR effectors from Phytophthora infestans (PiRXLRs), the causal agent of potato and tomato light blight that manipulate early stages of flg22-triggered signaling. Of thirty-three tested PiRXLR effector candidates, eight, called Suppressor of early Flg22-induced Immune response (SFI), significantly suppressed flg22-dependent activation of a reporter gene under control of a typical MAMP-inducible promoter (pFRK1-Luc) in tomato protoplasts. We extended our analysis to Arabidopsis thaliana, a non-host plant species of P. infestans. From the aforementioned eight SFI effectors, three appeared to share similar functions in both Arabidopsis and tomato by suppressing transcriptional activation of flg22-induced marker genes downstream of post-translational MAP kinase activation. A further three effectors interfere with MAMP signaling at, or upstream of, the MAP kinase cascade in tomato, but not in Arabidopsis. Transient expression of the SFI effectors in Nicotiana benthamiana enhances susceptibility to P. infestans and, for the most potent effector, SFI1, nuclear localization is required for both suppression of MAMP signaling and virulence function. The present study provides a framework to decipher the molecular mechanisms underlying the manipulation of host MAMP-triggered immunity (MTI) by P. infestans and to understand the basis of host versus non-host resistance in plants towards P. infestans.
The Isoform of Protein Kinase C Mediates Transcriptional Activation of the Human Transglutaminase 1 Gene (*)

Transglutaminase 1 (TGase 1) is expressed during the terminal differentiation of keratinized squamous epithelium to form cornified cell envelope in differentiated keratinocytes by the -(-glutamyl) cross-linking reaction. The gene for human TGase 1 is responsible for autosomal recessive lamellar ichthyosis, a severe hereditary keratinizing disorder of the skin. We examined the transcriptional activity of the gene in FRSK, rat keratinocytic cells, transfected with the luciferase reporter gene under control of the 5′ upstream region of human TGase 1 gene. Transfection of the reporter gene with an expression vector for the isoform of novel protein kinase C (nPKC), as well as exposure to 12-O-tetradecanoylphorbol-13-acetate, markedly increased the luciferase activity in FRSK, but not in HT-1080 fibrosarcoma cells, although exogenous nPKC was expressed in both. The induction was suppressed by deleting the TGase 1 upstream sequence from −95 to −67 and by deleting the kinase domain from exogenous nPKC. In comparison with other PKC isoforms, nPKC most effectively induced the luciferase activity. We suggest that nPKC, an epithelium-specific isoform of PKC, mediates the activation of the TGase 1 transcription.
Collagen Metabolism in the Myocardium from Streptozotocin-diabetic Rats

The effect of diabetes on myocardial collagen metabolism was investigated in rats. Diabetes was induced by an i.v. injection of streptozotocin (60 mg/kg). The animals were killed after 3, 6, 18, or 26 wk of diabetes. Urinary glucose levels were measured by Tes-Tape. The myocardium was quickly removed and homogenized. Collagen was estimated by hydroxyproline content. Collagen synthesis was measured by 14C-proline incorporation. Myocardial collagen concentration and collagen synthesis was not altered in the diabetic rats. Collagen concentration did appear to increase in the 18- and 26-wk rats, but this was probably an age-related phenomenon. These results suggest that diabetes does not alter collagen metabolism in rats.
Adherence of enteroaggregative Escherichia coli to the ileal and colonic mucosa: an in vitro study utilizing the scanning electron microscopy.

CONTEXT Enteroaggregative Escherichia coli strains have been associated with persistent diarrhea in several developing countries. In vivo procedures with animal models, in vitro assays with cellular lines and in vitro organ culture with intestinal fragments have been utilized to study these bacteria and their pathogenicity. OBJECTIVE The present experimental research assessed the pathogenic interactions of three enteroaggregative Escherichia coli strains, using the in vitro organ culture, in order to show the adherence to different regions of both, the ileal and the colonic mucosa and demonstrate possible mechanisms that could have the participation in the prolongation of diarrheiogenic process. METHODS This study used intestinal fragments from terminal ileum and colon that were excised from pediatric patients undergoing intestinal surgeries and from adult patients that underwent to colonoscopic procedures. Each strain was tested with three intestinal fragments for each region. Tissue was fixed for scanning electron microscopic analysis. RESULTS These bacteria colonized ileal and colonic mucosa in the typical stacked-brick configuration in the ileum and colon. In both regions, the strains were seen over a great amount of mucus and sometimes over the intact epithelium. In some regions, there is a probable evidence of effacement of the microvilli. It was possible to see adhered to the intestinal surface, bacteria fimbrial structures that could be responsible for the adherence process. CONCLUSION In order to cause diarrhea, enteroaggregative Escherichia coli strains adhere to the intestinal mucosa, create a mucoid biofilm on the small bowel surface that could justify the digestive-absorptive abnormalities and consequently, prolonging the diarrhea.
Von Willebrand Factor, ADAMTS13, and the Risk of Mortality: The Rotterdam Study

Objective—Von Willebrand Factor (VWF) is a plasma protein that plays a major role in platelet adhesion and aggregation. Large VWF multimers are cleaved into smaller, less coagulant forms by the metalloprotease ADAMTS13 (A Disintegrin And Metalloprotease with ThromboSpondin motif repeats 13). Previous studies have shown that high VWF and low ADAMTS13 levels are associated with cardiovascular disease, but whether these factors are associated with mortality is unclear. Our aim is to establish the association between VWF antigen (VWF:Ag) levels, ADAMTS13 activity, and mortality. Approach and Results—We included 6130 participants of the Rotterdam study, a population-based cohort study among individuals aged ≥55 years. We determined the association between ADAMTS13 activity, VWF:Ag levels, and all-cause and cardiovascular mortality by Cox proportional hazard regression analysis. During a median follow-up time of 11.3 years and a total of 90 635 person years, 1868 of the 6130 individuals died (30.5%), of whom 442 (23.7%) died because of cardiovascular disease. In individuals with low ADAMTS13 activity, the risk of cardiovascular mortality (hazard ratio, 1.46; 95% confidence interval, 1.09–1.96) was higher than that in individuals with high ADAMTS13 activity. The risk of cardiovascular mortality (hazard ratio, 1.29; 95% confidence interval 0.98–1.70) was higher in individuals with the highest VWF:Ag levels than in those with the lowest levels. In individuals with both low ADAMTS13 activity and high VWF:Ag levels, the risk of cardiovascular mortality was even higher (hazard ratio, 1.73 95% confidence interval, 1.28–2.35). Conclusions—In this large prospective cohort study, ADAMTS13 activity and VWF:Ag levels are both associated with an increased risk of all-cause and cardiovascular mortality.
Preoperative evaluation and management of the pancreatic head mass

The differential diagnosis of a pancreatic head mass encompasses a wide range of clinical entities that include both solid and cystic lesions. This chapter focuses on our approach to the patient presenting with a newly found pancreatic head mass with the main goals of determining the risk of the lesion being malignant or premalignant, resectability if the patient is appropriate for surgical intervention, assessment of need for multimodality treatment and determination the patient's surgical risk. J. Surg. Oncol. 2013;107:23–32. © 2012 Wiley Periodicals, Inc.
Ambivalence in Monkey Mothering: Infant Abuse Combined with Maternal Possessiveness

The maternal behavior of an abusive Japanese macaque multiparous female was compared with that of three primiparous normal females from the same colony to evaluate the quality of the abusive mother-infant relationship. The abusive mother-infant pair scored highest on maternal warmth, protectiveness, possessiveness, and scored lowest on maternal rejectingness. The finding that the abusive mother alternated violent abuse with attentive maternal care is not consistent with the learning defect explanation of monkey infant abuse. Rather, the intense anxiety she showed in the relationship with her infant indicates that she suffered from an emotional disorder that can be adequately described by referring to Bowlby's model of anxious attachment. The implications of this case for the development of a nonhuman primate model of child abuse are examined in the light of human data clearly showing attachment disturbances in some child-abusing mothers.
Refining Climate Change Projections for Organisms with Low Dispersal Abilities: A Case Study of the Caspian Whip Snake

Climate warming is one of the most important threats to biodiversity. Ectothermic organisms such as amphibians and reptiles are especially vulnerable as climatic conditions affect them directly. Ecological niche models (ENMs) are increasingly popular in ecological studies, but several drawbacks exist, including the limited ability to account for the dispersal potential of the species. In this study, we use ENMs to explore the impact of global climate change on the Caspian whip snake (Dolichophis caspius) as model for organisms with low dispersal abilities and to quantify dispersal to novel areas using GIS techniques. Models generated using Maxent 3.3. 3 k and GARP for current distribution were projected on future climatic scenarios. A cost-distance analysis was run in ArcGIS 10 using geomorphological features, ecological conditions, and human footprint as “costs” to dispersal of the species to obtain a Maximum Dispersal Range (MDR) estimate. All models developed were statistically significant (P<0.05) and recovered the currently known distribution of D. caspius. Models projected on future climatic conditions using Maxent predicted a doubling of suitable climatic area, while GARP predicted a more conservative expansion. Both models agreed on an expansion of suitable area northwards, with minor decreases at the southern distribution limit. The MDR area calculated using the Maxent model represented a third of the total area of the projected model. The MDR based on GARP models recovered only about 20% of the total area of the projected model. Thus, incorporating measures of species’ dispersal abilities greatly reduced estimated area of potential future distributions.
Changes of myoplasmic calcium concentration during fatigue in single mouse muscle fibers

Measurements of the intracellular free concentration of Ca2+ ([Ca2+]i) were performed during fatiguing stimulation of intact, single muscle fibers, which were dissected from a mouse foot muscle and loaded with fura-2. Fatigue, which was produced by repeated 100-Hz tetani, generally occurred in three phases. Initially, tension declined rapidly to approximately 90% of the original tension (0.9 Po) and during this period the tetanic [Ca2+]i increased significantly (phase 1). Then followed a lengthy period of almost stable tension production and tetanic [Ca2+]i (phase 2). Finally, both the tetanic [Ca2+]i and tension fell relatively fast (phase 3). The resting [Ca2+]i rose continuously throughout the stimulation period. A 10-s rest period during phase 3 resulted in a significant increase of both tetanic [Ca2+]i and tension, whereas a 10-s pause during phase 2 did not have any marked effect. Application of caffeine under control conditions and early during phase 2 resulted in a substantial increase of the tetanic [Ca2+]i but no marked tension increase, whereas caffeine applied at the end of fatiguing stimulation (tension depressed to approximately 0.3 Po) gave a marked increase of both tetanic [Ca2+]i and tension. The tetanic [Ca2+]i for a given tension was generally higher during fatiguing stimulation than under control conditions. Fatigue developed more rapidly in fibers exposed to cyanide. In these fibers there was no increase of tetanic [Ca2+]i during phase 1 and the increase of the resting [Ca2+]i during fatiguing stimulation was markedly larger. The present results indicate that fatigue produced by repeated tetani is caused by a combination of reduced maximum tension-generating capacity, reduced myofibrillar Ca2+ sensitivity, and reduced Ca2+ release from the sarcoplasmic reticulum. The depression of maximum tension- generating capacity develops early during fatiguing stimulation and it is of greatest importance for the force decline at early stages of fatigue. As fatigue gets more severe, reduced Ca2+ sensitivity and reduced Ca2+ release become quantitatively more important for the tension decline.
Respiratory health among bleachery workers exposed to ozone and chlorine dioxide.

OBJECTIVES This study investigated the possibility of occupational exposure to ozone increasing the risk of obstructive airway disease among bleachery workers. : Bleachery workers (N = 129) from two Swedish pulp mills using ozone for bleaching were studied together with referents (N = 80) from adjacent paper mills. The pulp mills had previously used chlorine dioxide as the bleaching agent. Testings included spirometry, methacholine challenge testing, and questionnaires. Area samplings showed sporadic ozone levels exceeding 0.9 ppm. RESULTS There was a greater prevalence of wheezing (25%) among the bleachery workers with a history of gassings (from ozone, chlorine, or sulfur dioxide) than among those without gassings (18%) and among the referents (13%). Among the current smokers the fraction with a slightly increased bronchial responsiveness to methacholine was greater among the bleachery workers reporting gassings than among those that had not been gassed. For the period from 1992 to 1996, when the mills were using ozone, there was an increased incidence rate of wheezing among the workers in the bleachery (incidence rate ratio 2.3, 95% confidence interval 1.6-5.8). CONCLUSIONS Repeated exposure to irritants increases the risk of asthma-like symptoms. This finding reinforces the view that repeated peak exposures to irritants must be prevented in pulp mills.
Neighborhood Socioeconomic Deprivation and Mortality: NIH-AARP Diet and Health Study

Purpose Residing in deprived areas may increase risk of mortality beyond that explained by a person's own SES-related factors and lifestyle. The aim of this study was to examine the relation between neighborhood socioeconomic deprivation and all-cause, cancer- and cardiovascular disease (CVD)-specific mortality for men and women after accounting for education and other important person-level risk factors. Methods In the longitudinal NIH-AARP Study, we analyzed data from healthy participants, ages 50–71 years at study baseline (1995–1996). Deaths (n = 33831) were identified through December 2005. Information on census tracts was obtained from the 2000 US Census. Cox models estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for quintiles of neighborhood deprivation. Results Participants in the highest quintile of deprivation had elevated risks for overall mortality (HRmen = 1.17, 95% CI: 1.10, 1.24; HRwomen = 1.13, 95% CI: 1.05, 1.22) and marginally increased risk for cancer deaths (HRmen = 1.09, 95% CI: 1.00, 1.20; HRwomen = 1.09, 95% CI: 0.99, 1.22). CVD mortality associations appeared stronger in men (HR = 1.33, 95% CI: 1.19, 1.49) than women (HR = 1.18, 95% CI: 1.01, 1.38). There was no evidence of an effect modification by education. Conclusion Higher neighborhood deprivation was associated with modest increases in all-cause, cancer- and CVD-mortality after accounting for many established risk factors.
Legume cover crops and nutrient cycling in tropical fruit tree production

Legume cover crops have various important effects on nutrient cycling in tropical fruit tree production: they (i) fix atmospheric N2 and may amend the soil and trees with N, (ii) recycle nutrients, and (iii) affect soil nutrient availability. Aboveground N accumulation usually is very large in legume cover crops as seen from Pueraria phaseoloides being 8 to 14 times higher than in intercropped fruit trees. Biomass production and N turnover will often exceed these values. Nutrient cycling may be significantly enhanced by the cover, leading to less nutrient leaching and higher nutrient contents in the topsoil, such as K. The amount of biological N fixation is an important factor for the N cycling. As a result, total soil N contents may often increase and N availability is enhanced. For nutrients other than N which cannot be supplied by the legume from external sources like P, the cover crop may induce nutrient competition resulting in lower tree nutrition.
Embryonic germ cells induce epigenetic reprogramming of somatic nucleus in hybrid cells

Genomic reprogramming of primordial germ cells (PGCs), which includes genome‐wide demethylation, prevents aberrant epigenetic modifications from being transmitted to subsequent generations. This process also ensures that homologous chromosomes first acquire an identical epigenetic status before an appropriate switch in the imprintable loci in the female and male germ lines. Embryonic germ (EG) cells have a similar epigenotype to PGCs from which they are derived. We used EG cells to investigate the mechanism of epigenetic modifications in the germ line by analysing the effects on a somatic nucleus in the EG‐thymic lymphocyte hybrid cells. There were striking changes in methylation of the somatic nucleus, resulting in demethylation of several imprinted and non‐imprinted genes. These epigenetic modifications were heritable and affected gene expression as judged by re‐activation of the silent maternal allele of Peg1/Mest imprinted gene in the somatic nucleus. This remarkable change in the epigenotype of the somatic nucleus is consistent with the observed pluripotency of the EG‐somatic hybrid cells as they differentiated into a variety of tissues in chimeric embryos. The epigenetic modifications observed in EG‐somatic cell hybrids in vitro are comparable to the reprogramming events that occur during germ cell development.
FETs on 2-D Materials: Deconvolution of the Channel and Contact Characteristics by Four-Terminal Resistance Measurements on WSe2 Transistors

FETs made on 2-D semiconductors, typically without degenerate doping at the contacts, have a significant Schottky junction (SJ) resistance, which complicates transistor analysis. This paper evaluates the effect of the contact resistance on the 2-D-material FET characteristics through four-terminal (4-T) resistance measurements on WSe2 FETs, which allow studying the channel and contacts characteristics separately. Apart from showing the nonnegligibility of contact resistance, this paper enables a finer understanding of commonly observed phenomena, such as transistor performance improvement with dielectric-encapsulation is observed to have a stronger effect on the contact than the channel; the resistance of the forward-biased SJ is observed to be not negligible, but comparable to that of the reverse-biased junction; at biases commonly referred to as “low-bias,” the WSe2 FET resistance could be dominated by the contacts; and pinchoff can be observed at relatively lower current levels, being related to the channel-contact resistance ratio rather than their magnitudes. In the devices where true channel pinchoff can be verified, a correlation emerges between current saturating behavior and asymmetry in the output characteristics with respect to the drain–source bias polarity, a feature that may serve as a guide toward interpreting standard FET output characteristics in 2-D materials.
Publishing Sensitive Transactions for Itemset Utility

We consider the problem of publishing sensitive transaction data with privacy preservation. High dimensionality of transaction data poses unique challenges on data privacy and data utility. On one hand, re-identification attacks tend to use a subset of items that infrequently occur in transactions, called moles. On the other hand, data mining applications typically depend on subsets of items that frequently occur in transactions, called nuggets. Thus the problem is how to eliminate all moles while retaining nuggets as much as possible. A challenge is that moles and nuggets are multi-dimensional with exponential growth and are tangled together by shared items. We present a novel and scalable solution to this problem. The novelty lies in a compact border data structure that eliminates the need of generating all moles and nuggets.
Gray matter decrease of the anterior cingulate cortex in anorexia nervosa.

OBJECTIVE The brain regions that are critically involved in the pathophysiology of anorexia nervosa have not been clearly elucidated. Moreover, decrease in cerebral tissue during extreme malnutrition has been demonstrated repeatedly in anorexia nervosa, but data regarding the reversibility of this cerebral tissue decrease are conflicting. The authors examined region-specific gray matter changes and global cerebral volumes in recovered patients with anorexia nervosa. METHOD High-resolution, T1-weighted magnetic resonance imaging (MRI) and voxel-based morphometry were performed in 22 recovered women with anorexia nervosa and in 37 healthy comparison women. Recovery was defined as a body mass index above 17.0 kg/m(2) and regular menses for at least 6 months. RESULTS The global volumes of gray matter (but not white matter) were decreased in patients with anorexia nervosa by approximately 1%. Analyses of region-specific gray matter changes revealed a gray matter decrease bilaterally in the anterior cingulate cortex of approximately 5%, which remained significant after correction for global effects. This gray matter decrease correlated significantly with the lowest body mass index of lifetime but not with other clinical variables. CONCLUSIONS In anorexia nervosa, part of the global gray matter loss persists over the long run. Region-specific gray matter loss in the anterior cingulate cortex is directly related to the severity of anorexia nervosa, indicating an important role of this area in the pathophysiology of the disorder. Further research is warranted to determine the cause, specificity, and functional consequences of this structural brain change in anorexia nervosa.