Miracle-dz/UniFAR-FTUs huggingface dataset:
Terrestrial cooling in Northern Europe during the Eocene–Oligocene transition

Geochemical and modeling studies suggest that the transition from the “greenhouse” state of the Late Eocene to the “icehouse” conditions of the Oligocene 34–33.5 Ma was triggered by a reduction of atmospheric pCO2 that enabled the rapid buildup of a permanent ice sheet on the Antarctic continent. Marine records show that the drop in pCO2 during this interval was accompanied by a significant decline in high-latitude sea surface and deep ocean temperature and enhanced seasonality in middle and high latitudes. However, terrestrial records of this climate transition show heterogeneous responses to changing pCO2 and ocean temperatures, with some records showing a significant time lag in the temperature response to declining pCO2. We measured the Δ47 of aragonite shells of the freshwater gastropod Viviparus lentus from the Solent Group, Hampshire Basin, United Kingdom, to reconstruct terrestrial temperature and hydrologic change in the North Atlantic region during the Eocene–Oligocene transition. Our data show a decrease in growing-season surface water temperatures (∼10 °C) during the Eocene–Oligocene transition, corresponding to an average decrease in mean annual air temperature of ∼4–6 °C from the Late Eocene to Early Oligocene. The magnitude of cooling is similar to observed decreases in North Atlantic sea surface temperature over this interval and occurs during major glacial expansion. This suggests a close linkage between atmospheric carbon dioxide concentrations, Northern Hemisphere temperature, and expansion of the Antarctic ice sheets.
Cloning, characterization, and expression of xyloglucan endotransglucosylase/hydrolase and expansin genes associated with petal growth and development during carnation flower opening

Growth of petal cells is a basis for expansion and morphogenesis (outward bending) of petals during opening of carnation flowers (Dianthus caryophyllus L.). Petal growth progressed through elongation in the early stage, expansion with outward bending in the middle stage, and expansion of the whole area in the late stage of flower opening. In the present study, four cDNAs encoding xyloglucan endotransglucosylase/hydrolase (XTH) (DcXTH1–DcXTH4) and three cDNAs encoding expansin (DcEXPA1–DcEXPA3) were cloned from petals of opening carnation flowers and characterized. Real-time reverse transcription-PCR analyses showed that transcript levels of XTH and expansin genes accumulated differently in floral and vegetative tissues of carnation plants with opening flowers, indicating regulated expression of these genes. DcXTH2 and DcXTH3 transcripts were detected in large quantities in petals as compared with other tissues. DcEXPA1 and DcEXPA2 transcripts were markedly accumulated in petals of opening flowers. The action of XTH in growing petal tissues was confirmed by in situ staining of xyloglucan endotransglucosylase (XET) activity using a rhodamine-labelled xyloglucan nonasaccharide as a substrate. Based on the present findings, it is suggested that two XTH genes (DcXTH2 and DcXTH3) and two expansin genes (DcEXPA1 and DcEXPA2) are associated with petal growth and development during carnation flower opening.
Alcohol Use, Mental Health Status and Psychological Well-being 2 Years After the World Trade Center Attacks in New York City

Over the past 30 years, studies have shown that survivors of community-wide disasters suffer from a variety of physical and mental health problems. Researchers also have documented increased substance use in the aftermath of these disasters. In the present study, we examined the relationship between alcohol use and mental health status within the context of the terrorist attacks on the World Trade Center in New York City (NYC). The data for the present report come from a 2-wave panel study of adults living in NYC on the day of the attacks. Wave 1 (W1) and Wave 2 (W2) interviews occurred one year and two years after the attacks, respectively. Overall, 2,368 individuals completed the W1 survey (cooperation rate, 63%) and 1,681 completed the W2 survey (re-interview rate, 71%). The alcohol use variables examined were binge drinking, alcohol dependence, increased days drinking, and increased drinks per day. The outcomes examined included measures of posttraumatic stress disorder (PTSD), major depression, BSI-18-Global Severity and measures of SF12-mental and physical health status. After controlling for demographic, stress, and resource factors, multivariate logistic regressions indicated that all alcohol measures were related to one or more of these outcomes. In particular, binge drinking was related to partial PTSD, while alcohol dependence was associated subsyndromal PTSD, severity of PTSD, depression, BSI-18 global severity, and SF-12 poor mental health status. Increased post-disaster drinking was positively associated with subsyndromal PTSD and negatively associated with SF-12 physical health. We discuss reasons for these results and the negative consequences that heavy alcohol use may have on the postdisaster recovery process.
Scan Architecture With Align-Encode

Scan architectures that provide compression capabilities have become mandatory due to the unbearable test costs imposed by high test data volume and prolonged test application. To alleviate these test costs, a stimulus decompressor and a response compactor block are inserted between the tester channels and the scan chains. As a result, a few tester channels drive a larger number of scan chains. In such an architecture, whether a particular test pattern can be delivered depends on the care bit distribution of that pattern. In this paper, we introduce a hardware block to be utilized in conjunction with a combinational stimulus decompressor block. This block, namely, Align-Encode, provides a deterministic per pattern control over care bit distribution of test vectors, improving pattern deliverability, and thus, the effectiveness of the particular stimulus decompressor. Align-Encode is reconfigured on a per pattern basis to delay the shift-in operations in selected scan chains. The number of cycles that a chain may be delayed can be between zero and the maximum allowable value, in order to align the scan slices in such a way that originally undeliverable test vectors become encodable. The reconfigurability of Align-Encode provides a test pattern independent solution, wherein any given set of test vectors can be analyzed to compute the proper delay information. We present efficient techniques for computing the scan chain delay values that lead to pattern encodability. Experimental results also justify the test pattern encodability enhancements that Align-Encode delivers, enabling significant test quality improvements and/or test cost reductions.
'The anatomy underlying acute versus chronic spatial neglect' also depends on clinical tests.

Sir, We would like to make a few comments on the interesting paper recently published in Brain by Karnath et al. (2011). We were impressed by the careful assessment of spatial neglect during acute and chronic phase, which was combined with a solid voxel-wise lesion symptom mapping technique in a series of 54 patients with right-hemisphere stroke. Anatomical data indicated that lesions in the superior and middle temporal gyri, the basal ganglia, as well as the inferior occipitofrontal fasciculus are responsible for spatial neglect in both acute and chronic phases. We also had the opportunity to evaluate 69 patients with right brain lesions longitudinally. Our patients were admitted after a first right-hemisphere stroke (mean delay: 7.5 ± 14.6 days), at a mean age of 64.95 ± 14.6 years. Mean delay between the acute and chronic phase was 350.21 ± 184.7 days. These demographic data are comparable with the patients of Karnath et al . (2011). Neglect was considered as present when patients failed at least two out of eight tests (Table 1)—unlike diagnoses based on two out three tests in Karnath et al . (2011). In the acute phase, 31 patients had neglect (45%). In the chronic phase, 17 of these 31 neglect patients still showed a significant impairment (55%). Using the same voxel-wise lesion mapping as Karnath et al . (2011), we found partly different results, particularly in the acute phase (detailed below). However, we believe that major differences in the findings may depend on the clinical measures used to define neglect, since this syndrome may include heterogeneous symptoms. View this table: Table 1 Neuropsychological results on paper and pencil tests. All scores were calculated as described in Verdon et al . (2010) Bowen et al . (1999) reported that the frequency of occurrence of neglect in patients with right brain damage may vary considerably and …
Ab initio gene finding in Drosophila genomic DNA.

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger. ac.uk/gf. html.
SlyA Regulates Function of Salmonella Pathogenicity Island 2 (SPI-2) and Expression of SPI-2-Associated Genes

ABSTRACT During the systemic phase of murine infection with Salmonella enterica serovar Typhimurium, bacterial virulence is correlated with the ability to grow and survive within host macrophages. Salmonella pathogenicity island 2 (SPI-2), encoding a type three secretion system, has emerged as an important contributor to Salmonella intracellular growth. SPI-2 mutants have been proposed to be more accessible than wild-type Salmonella to oxyradicals generated by the NADPH phagocyte oxidase. We performed mixed infections of mice to investigate the relationship between SPI-2 and SlyA, a transcriptional regulator that confers resistance to oxyradicals. In mixed-infection experiments, the SPI-2 null mutant was severely attenuated in virulence, whereas slyA mutants were only mildly attenuated. Surprisingly, further experiments indicated that the function of SPI-2 was partially dependent on slyA. The intracellular behavior of a slyA mutant in infected cells was consistent with inefficient SPI-2 expression, as formation of Salmonella-induced filaments and the intracellular F-actin meshwork, features that depend on SPI-2, were present at abnormally low frequencies. Furthermore, the translocated levels of the SPI-2 effector SseJ were severely reduced in a strain carrying a mutation in slyA. We used flow cytometry to investigate the role of SlyA in expression of green fluorescent protein (GFP) from transcriptional fusions with promoters of either of two other SPI-2 effector genes, sifB and sifA. The slyA mutant exhibited reduced GFP expression from both promoters. Combining mutations in slyA and other regulators of SPI-2 indicated that SlyA acts through the SsrAB two-component regulatory system. SlyA exhibits partial functional redundancy with OmpR-EnvZ and contributes to the transcriptional response to low osmolarity and the absence of calcium, two environmental stimuli that promote SPI-2 gene expression.
Sheep cheese naturally enriched in α-linolenic, conjugated linoleic and vaccenic acids improves the lipid profile and reduces anandamide in the plasma of hypercholesterolaemic subjects

Intake of dairy fat has long been considered as a risk factor for CVD. Pasture and dietary lipid supplementation have been reported to be reliable strategies in ruminant nutrition, in order to increase the content of α-linolenic acid (ALA), conjugated linoleic acid (CLA) and vaccenic acid (VA), and decrease SFA in milk fat. In the present study, we aimed at verifying whether consumption of a sheep cheese, naturally enriched in ALA, CLA and VA, would modify the plasma lipid and endocannabinoid profiles in mildly hypercholesterolaemic subjects. A total of forty-two adult volunteers (nineteen males and twenty-three females) with diagnosed mildly hypercholesterolaemia (total cholesterol 5·68–7·49 mmol/l) were randomly assigned to eat 90 g/d of a control or enriched cheese for 3 weeks, with a cross-over after 3 weeks of washout. Plasma lipids, endocannabinoids, adipokines and inflammatory markers were measured. The intake of enriched cheese significantly increased the plasma concentrations of CLA, VA, the n-3 fatty acids ALA and EPA, and more remarkably decreased that of the endocannabinoid anandamide. LDL-cholesterol decreased significantly (7 %). No changes were detected in the levels of inflammatory markers; however, a significant correlation was found between the plasma levels of anandamide and leptin. The control cheese modified none of the parameters measured. The results obtained do not support the view that intake of dairy fat is detrimental to hypercholesterolaemic subjects. Indeed, they show that a naturally enriched cheese possesses beneficial properties, since it ameliorates the plasma lipid profile, and more remarkably reduces endocannabinoid biosynthesis.
Improving the Data Augmentation Algorithm in the Two-Block Setup

The data augmentation (DA) approach to approximate sampling from an intractable probability density fX is based on the construction of a joint density, fX, Y, whose conditional densities, fX|Y and fY|X, can be straightforwardly sampled. However, many applications of the DA algorithm do not fall in this “single-block” setup. In these applications, X is partitioned into two components, X = (U, V), in such a way that it is easy to sample from fY|X, fU|V, Y, and fV|U, Y. We refer to this alternative version of DA, which is effectively a three-variable Gibbs sampler, as “two-block” DA. We develop two methods to improve the performance of the DA algorithm in the two-block setup. These methods are motivated by the Haar PX-DA algorithm, which has been developed in previous literature to improve the performance of the single-block DA algorithm. The Haar PX-DA algorithm, which adds a computationally inexpensive extra step in each iteration of the DA algorithm while preserving the stationary density, has been shown to be optimal among similar techniques. However, as we illustrate, the Haar PX-DA algorithm does not lead to the required stationary density fX in the two-block setup. Our methods incorporate suitable generalizations and modifications to this approach, and work in the two-block setup. A theoretical comparison of our methods to the two-block DA algorithm, a much harder task than the single-block setup due to nonreversibility and structural complexities, is provided. We successfully apply our methods to applications of the two-block DA algorithm in Bayesian robit regression and Bayesian quantile regression. Supplementary materials for this article are available online.
Evaluating video as a technology for informal communication

Collaborations in organizations thrive on communication that is informal because informal communication is frequent, interactive, and expressive. Informal communication is crucial for the coordination of work, learning an organization's culture, the perpetuation of the social relations that underlie collaboration, and, in general, any situation that requires communication to resolve ambiguity. Informal communication is traditionally mediated by physical proximity, but physical proximity cannot mediate in geographically distributed organizations. The research described here evaluates the adequacy of a version of a desktop video/audio conferencing system for supporting informal communication in a research and development laboratory. The evaluation took place during a trial in which the system was used by summer employees and their supervisor-mentors. While the system was used frequently, the most common uses and users' assessments suggest that it was used more like a telephone or electronic mail than like physically mediated face-to-face communication. However, some features of its use transcended traditional media and allowed users to gain awareness of their work environment. The paper concludes with a discussion of requirements for successful technology to support informal communication.
Suppression of matrilysin inhibits colon cancer cell invasion in vitro

Matrilysin is a member of the matrix metalloproteinase gene family, which is believed to play an important role in tumor invasion and metastasis. We examined the effects of over‐ and under‐expression of matrilysin on the ability of colon cancer cells to migrate across an artificial membrane in vitro. Introduction of matrilysin caused colon cancer cells to become more invasive as assessed by an in vitro invasion assay. In contrast, expression of matrilysin was down‐regulated by all trans‐retinoic acid or by introduction of anti‐sense matrilysin in BM314 colon cancer cells. This down‐regulation caused these cells to become less invasive. We demonstrated a correlation between matrilysin level and the invasive potential of human colon cancer cells, implying an important role for matrilysin in the control of tumor invasion in vitro. © 1995 Wiley‐Liss, Inc.
The first XMM-Newton slew survey catalogue: XMMSL1

We report on the production of a large area, shallow, sky survey, from XMM-Newton slews. The great collecting area of the mirrors coupled with the high quantum efficiency of the EPIC detectors have made XMM-Newton the most sensitive X-ray observatory flown to date. We use data taken with the EPIC-pn camera during slewing manoeuvres to perform an X-ray survey of the sky. Data from 218 slews have been subdivided into small images and source searched. This has been done in three distinct energy bands; a soft (0.2-2 keV) band, a hard (2-12 keV) band and a total XMM-Newton band (0.2-12 keV). Detected sources, have been quality controlled to remove artifacts and a catalogue has been drawn from the remaining sources. A 'full' catalogue, containing 4710 detections and a 'clean' catalogue containing 2692 sources have been produced, from 14% of the sky. In the hard X-ray band (2-12 keV) 257 sources are detected in the clean catalogue to a flux limit of 4x10^-12 ergs/s/cm2. The flux limit for the soft (0.2-2 keV) band is 6x10^-13 ergs/s/cm2 and for the total (0.2-12 keV) band is 1.2x10^-12 ergs/s/cm2. The source positions are shown to have an uncertainty of 8" (1-sigma confidence).
Broad Range Amino Acid Specificity of RNA-dependent Lipid Remodeling by Multiple Peptide Resistance Factors*

Aminoacylphosphatidylglycerol synthases (aaPGSs) are multiple peptide resistance factors that transfer amino acids from aminoacyl-tRNAs to phosphatidylglycerol (PG) in the cytoplasmic membrane. Aminoacylation of PG is used by bacteria to decrease the net negative charge of the cell envelope, diminishing affinity for charged molecules and allowing for adaptation to environmental changes. Lys-PGS, which transfers lysine to PG, is essential for the virulence of certain pathogens, providing resistance to both host cationic antimicrobial peptides and therapeutic antibiotics. Ala-PGS was also recently described, but little is known about the possible activities of other members of the highly diverse aaPGS family of proteins. Systematic deletion of the predicted membrane-inserted domains of several aaPGSs revealed that the carboxyl-terminal hydrophilic domain alone is sufficient for aminoacylphosphatidylglycerol transferase catalytic activity. In contrast to previously characterized aaPGSs, the Enterococcus faecium enzyme used an expanded repertoire of amino acids to modify PG with Ala, Arg, or Lys. Reexamination of previously characterized aaPGSs also revealed broader than anticipated substrate specificity, for example Bacillus subtilis Lys-PGS was shown to also catalyze Ala-PG synthesis. The relaxed substrate specificities of these aaPGSs allows for more elaborate remodeling of membrane lipids than previously thought, potentially providing bacteria that harbor these enzymes resistance to a broad spectrum of antibiotics and environmental stresses.
Integrative Neuroscience Review Article Identifying a Network of Brain Regions Involved in Aversion-related Processing: a Cross-species Translational Investigation

The ability to detect and respond appropriately to aversive stimuli is essential for all organisms , from fruit flies to humans. This suggests the existence of a core neural network which mediates aversion-related processing. Human imaging studies on aversion have highlighted the involvement of various cortical regions, such as the prefrontal cortex, while animal studies have focused largely on subcortical regions like the periaqueductal gray and hypothalamus. However, whether and how these regions form a core neural network of aversion remains unclear. To help determine this, a translational cross-species investigation in humans (i.e., meta-analysis) and other animals (i.e., systematic review of functional neuroanatomy) was performed. Our results highlighted the recruitment of the anterior cingulate cortex, the anterior insula, and the amygdala as well as other subcortical (e.g., thalamus, midbrain) and cortical (e.g., orbitofrontal) regions in both animals and humans. Importantly, involvement of these regions remained independent of sensory modality. This study provides evidence for a core neural network mediating aversion in both animals and humans. This not only contributes to our understanding of the trans-species neural correlates of aversion but may also carry important implications for psychiatric disorders where abnormal aversive behavior can often be observed.