Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrated Transcriptional and Metabolic Profiling in Human Endotoxemia

Abstract In this meta-study, we aimed to integrate biological insights gained from two levels of -omics analyses on the response to systemic inflammation induced by lipopolysaccharide in humans. We characterized the interplay between plasma metabolite compositions and transcriptional response of leukocytes through integration of transcriptomics with plasma metabonomics. We hypothesized that the drastic changes in the immediate environment of the leukocytes might have an adaptive effect on shaping their transcriptional response in conjunction with the initial inflammatory stimuli. Indeed, we observed that leukocytes, most notably, tune the activity of lipid- and protein-associated processes at the transcriptional level in accordance with the fluctuations in metabolite compositions of surrounding plasma. A closer look into the transcriptional control of only metabolic pathways uncovered alterations in bioenergetics and defenses against oxidative stress closely associated with mitochondrial dysfunction and shifts in energy production observed during inflammatory processes.
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

We present a simple but powerful procedure to extract Gene Ontology (GO) terms that are significantly over- or under-represented in sets of genes within the context of a genome-scale experiment (DNA microarray, proteomics, etc.). Said procedure has been implemented as a web application, FatiGO, allowing for easy and interactive querying. FatiGO, which takes the multiple-testing nature of statistical contrast into account, currently includes GO associations for diverse organisms (human, mouse, fly, worm and yeast) and the TrEMBL/Swissprot GOAnnotations@EBI correspondences from the European Bioinformatics Institute.
Prevalence of PTSD and Depression among Junior Middle School Students in a Rural Town Far from the Epicenter of the Wenchuan Earthquake in China

Context On May12th 2008, a devastating earthquake measuring 8.0 on the Richter scale, struck Wenchuan county and surrounding areas in China. The prevalence of mental illness among children and adolescents in a rural town far from the earthquake epicenter is unknown. Objective To assess the prevalence of posttraumatic stress disorder (PTSD) and depression among junior middle school students in a rural town Ningqiang county, 327 km from the earthquake epicenter. Design, Setting, and Participants A population-based mental health survey was conducted in March, 2009. Main Outcome Measure Survey Self-designed General Condition Survey Scale, Children's Revised Impact of Event Scale (CRIES-13), and the Depression Self-rating Scale for Children (DSRSC) were used to sample 1,841 junior middle school students in Ningqiang county, ten months after the Wenchuan earthquake. Results The prevalence rate of a high-risk for PTSD was 28.4%, with 32.7% among females, 23.8% among males (female vs. male, p<0.001), 38.6% in the severe exposure group and 24.3% in the mild exposure group (severe vs. mild exposure, p<0.001). For depressive symptoms, the overall prevalence was 19.5%, with 24.0% among females, 14.7% among males, 24.5% in the severe exposure group and 17.5% in the mild exposure group (female vs. male, p<0.001; severe vs. mild exposure, p<0.001, respectively). In multivariate analysis, factors such as “having felt despair”, or “danger” and “having own house destroyed or damaged” were significantly associated with PTSD symptoms. Female gender and delayed evacuation in females, and earthquake related experiences in males were significantly associated with depression. Conclusion Traumatic events experienced during the earthquake were significantly associated with symptoms of PTSD and depression in children and adolescents, ten months after the Wenchuan earthquake. These data highlight a need for mental health services for children and adolescents in rural areas, far from earthquake epicenters.
Isolation and Characterization of H4N6 Avian Influenza Viruses from Pigs with Pneumonia in Canada

ABSTRACT In October 1999, H4N6 influenza A viruses were isolated from pigs with pneumonia on a commercial swine farm in Canada. Phylogenetic analyses of the sequences of all eight viral RNA segments demonstrated that these are wholly avian influenza viruses of the North American lineage. To our knowledge, this is the first report of interspecies transmission of an avian H4 influenza virus to domestic pigs under natural conditions.
Headache in acute cerebrovascular disease

Headache features were compared in 51 patients with acute subarachnoid hemorrhage (SAH), 61 with intraparenchymal hemorrhage (IPH), and 160 with ischemic stroke (IS). SAH patients had more sentinel headaches, more onset headaches, and more bilateral and severe onset headaches than patients with IPH or IS. Vomiting with onset headache was more common in SAH and IPH. In stepwise logistic regression analysis, onset headache and vomiting were direct predictors of SAH, but were inversely related to IS. Sentinel headache was not a predictor of underlying stroke mechanism. The data suggest that some headache features are more frequently associated with particular stroke subtypes and that onset headache and vomiting may be important indicators of stroke mechanism.
Evaluation of Daphnid Grazing on Microscopic Zoosporic Fungi by Using Comparative Threshold Cycle Quantitative PCR

ABSTRACT Lethal parasitism of large phytoplankton by chytrids (microscopic zoosporic fungi) may play an important role in organic matter and nutrient cycling in aquatic environments by shunting carbon away from hosts and into much smaller zoospores, which are more readily consumed by zooplankton. This pathway provides a mechanism to more efficiently retain carbon within food webs and reduce export losses. However, challenges in accurate identification and quantification of chytrids have prevented a robust assessment of the relative importance of parasitism for carbon and energy flows within aquatic systems. The use of molecular techniques has greatly advanced our ability to detect small, nondescript microorganisms in aquatic environments in recent years, including chytrids. We used quantitative PCR (qPCR) to quantify the consumption of zoospores by Daphnia in laboratory experiments using a culture-based comparative threshold cycle (CT ) method. We successfully quantified the reduction of zoospores in water samples during Daphnia grazing and confirmed the presence of chytrid DNA inside the daphnid gut. We demonstrate that comparative CT qPCR is a robust and effective method to quantify zoospores and evaluate zoospore grazing by zooplankton and will aid in better understanding how chytrids contribute to organic matter cycling and trophic energy transfer within food webs. IMPORTANCE The study of aquatic fungi is often complicated by the fact that they possess complex life cycles that include a variety of morphological forms. Studies that rely on morphological characteristics to quantify the abundances of all stages of the fungal life cycle face the challenge of correctly identifying and enumerating the nondescript zoospores. These zoospores, however, provide an important trophic link between large colonial phytoplankton and zooplankton: that is, once the carbon is liberated from phytoplankton into the parasitic zoospores, the latter are consumed by zooplankton and carbon is retained in the aquatic food web rather than exported from the system. This study provides a tool to quantify zoospores and evaluate the consumption of zoospores by zooplankton in order to further our understanding of their role in food web dynamics.
Effects of Implant Design Parameters on Cervical Disc Arthroplasty Performance and Sagittal Balance - A Finite Element Investigation

of Effects of Implant Design Parameters on Cervical Disc Arthroplasty Performance and Sagittal Balance A Finite Element Investigation by Nikhil Kulkarni Submitted to the Graduate Faculty in partial fulfillment of the requirements for the Master of Science Degree in Bioengineering The University of Toledo August 2010 Fusion has been the historic gold standard for the treatment of the degenerated disc in the spine. Fusion surgeries constra in the motion at the im planted level the re by transf erring additional load to the adjacen t lev els. Many clinical s tudies have sho wn that adjacen t segment degeneration was observed in patien ts over tim e. In order to overcom e the drawbacks of the fusion procedures, the artific ial discs are being explored to treat disc degeneration related problems. Artificial discs are designed to preserve m otion at the index level and lessen effects on the adjacent segments. More recently, the need to preserve the sagittal balance following disc replacem ent has been stressed. Ex isting devices provide m otion, but m ay not actively preserve or correct sagittal balance. A new disc design was compared with the
Non-genetic factors affecting fertility traits in South African Holstein cows

Profitable milk production and genetic improvement in dairy herds depend largely on fertile cows calving annually to initiate a new lactation period. Over the last 30 years, several studies have indicated a decline in the reproductive performance of dairy cows. From the perspectives of many farmers and veterinarians, the reproductive performance of cows is related to the calving interval (CI) and services per conception (SPC). Using these traits as cow fertility indicators is problematic as CI is dependent on subsequent calving dates, while SPC is strongly linked to inseminator proficiency. Cow fertility refers to the ability of cows to come into oestrus soon after calving, to conceive from a minimum number of services, and to stay pregnant until the next calving. In this paper, non-genetic factors affecting fertility traits other than CI in Holstein cows are discussed. Service records (n = 69 181) and pregnancy check results of 9 046 cows in 14 herds were available. Six fertility traits were derived. Means (± sd) for the interval traits, namely calving to first insemination (CFS) and the interval from calving to conception (days open (DO)) were 77 ± 30 and 134 ± 74 days, respectively, while the number of SPC was 2.55 ± 1.79. The proportion of first services occurring within 80 days post partum (FS80d) and the proportion of cows being confirmed pregnant within 100 days (PD100d) and 200 days post partum (PD200d) were 0.64 ± 0.48, 0.36 ± 0.48 and 0.71 ± 0.45, respectively. While lactation number, calving year and calving season affected reproduction traits significantly, herds (management) had the largest effect.
Innate immunity but not NLRP3 inflammasome activation correlates with severity of stable COPD

Background In models of COPD, environmental stressors induce innate immune responses, inflammasome activation and inflammation. However, the interaction between these responses and their role in driving pulmonary inflammation in stable COPD is unknown. Objectives To investigate the activation of innate immunity and inflammasome pathways in the bronchial mucosa and bronchoalveolar lavage (BAL) of patients with stable COPD of different severity and control healthy smokers and non-smokers. Methods Innate immune mediators (interleukin (IL)-6, IL-7, IL-10, IL-27, IL-37, thymic stromal lymphopoietin (TSLP), interferon γ and their receptors, STAT1 and pSTAT1) and inflammasome components (NLRP3, NALP7, caspase 1, IL-1β and its receptors, IL-18, IL-33, ST2) were measured in the bronchial mucosa using immunohistochemistry. IL-6, soluble IL-6R, sgp130, IL-7, IL-27, HMGB1, IL-33, IL-37 and soluble ST2 were measured in BAL using ELISA. Results In bronchial biopsies IL-27+ and pSTAT1+ cells are increased in patients with severe COPD compared with control healthy smokers. IL-7+ cells are increased in patients with COPD and control smokers compared with control non-smokers. In severe stable COPD IL-7R+, IL-27R+ and TSLPR+ cells are increased in comparison with both control groups. The NALP3 inflammasome is not activated in patients with stable COPD compared with control subjects. The inflammasome inhibitory molecules NALP7 and IL-37 are increased in patients with COPD compared with control smokers. IL-6 levels are increased in BAL from patients with stable COPD compared with control smokers with normal lung function whereas IL-1β and IL-18 were similar across all groups. Conclusions Increased expression of IL-27, IL-37 and NALP7 in the bronchial mucosa may be involved in progression of stable COPD.
Cervical Cancer: Community Perception and Preventive Practices in an Urban Neighborhood of Lagos (Nigeria)

Background. Cervical cancer prevention in developing countries is suboptimal compared with the developed world where there are fewer deaths and improved survival rates. This study describes the perception and preventive practices on cervical cancer by residents of an urban neighborhood of Lagos, Nigeria. Methods. A descriptive cross-sectional study was conducted on 317 consecutively recruited consenting participants at a medical outreach using a pretested, interviewer-administered, semistructured questionnaire. Data analysis was done using statistical package for social sciences version 19. Tests of significance were performed using 95% confidence interval with level of significance set at P < 0.05. Results. The majority of respondents were within 30–49 years of age (46.7%) and female (62.1%) and 70.3% had secondary level education and above. About 37.2% of respondents had heard about cervical cancer with 84.5% of the participants willing to attend a cervical cancer health education program. Among the female respondents, 4.1% had received the HPV vaccine, while 5.1% had undergone a Pap test. Awareness about cervical cancer was significantly higher with increasing age in the total population (P < 0.05). Conclusion. There is a need to improve awareness of at-risk groups and the menfolk about cervical cancer based on the immense benefit of male involvement in reproductive health matters.
Characterization of an 2x2 SCB optical switch integrated with VOA

This work presents the characterization of an innovative micromachined 2×2 optical switch monolithically integrated with variable optical attenuators. The device uses bi-stable mechanisms for optical switching, and can be easily realized by a standard manufacturing process with a single photo mask. Also, the split-cross-bar design (SCB) is employed as the optical path configuration. The results by the analytical models of the curve-beam and V-beam actuators employed in this dual-function device are also presented.
Disc brakes for heavy vehicles: an experimental study of temperatures and cracks

A better understanding of the thermomechanical loading of brake discs is important for controlling material fatigue and crack propagation in the disc. In the present study, full-scale drag braking experiments were performed on brake discs made from eight different grey cast iron alloys. The well-performing materials were also tested with an alternative brake pad material. A testing procedure with repeated drag brakings was used. The disc and pad temperatures were registered by thermocouples embedded at selected locations, and the disc surface temperatures by a thermocamera. Extensive analyses of the measured temperatures were performed. The results for the thermocouples at the mid-radius of the disc and at the end of brake applications indicatd that the two sides of the disc have opposite deviations from the mean temperature. The temperature deviations are generally temporally alternating, but also stationary variations can be found. The thermocamera gives the possibility of identifying the phenomena behind the temperature variations found from the thermocouples. Banding of the disc–pads contact with alternating one band and two bands of high temperatures is observed for the studied brake discs exposed to severe braking load cases. Moreover, it was found that hot-spot patterns develop on the disc surface, which are spatially fixed during each brake application. However, they may be either slowly migrating or fixed relative to the disc during consecutive brake applications. Thermal images show that small cracks do not affect hot-spot migration as a hot spot migrates over the crack. However, at a critical length of the crack, the heat becomes localized at the crack and increases its growth, thus limiting the life of the disc. The tests indicate that a combination of hot-spot migration, alternating bands and small temperature differences over the disc are significant factors to be considered when improving the lifespan of the discs.
BrucellaCapt versus Classical Tests in the Serological Diagnosis and Management of Human Brucellosis

ABSTRACT The BrucellaCapt test is an immunocapture agglutination test suggested as a possible substitute for the Coombs test in the diagnosis of human brucellosis. Here it is compared with classical tests using 321 samples from 48 patients with brucellosis (6.9 ± 1.7 samples per patient), including 20 patients with focal disease and 8 patients with a total of 9 relapse episodes (mean follow-up, 18 months). The BrucellaCapt test was used according to the manufacturer's instructions, and we also used a variant of the BrucellaCapt test in which the microtiter plates were not coated with antibodies against total human immunoglobulin (BCAPV). The correlation between the BrucellaCapt and BCAPV tests was 0.982 (P < 0.001), with 260 coincident pairs of titers (81%). The areas under the receiver operating characteristic curve for the BrucellaCapt and BCAPV tests with respect to the Coombs test were 0.969 and 0.960, respectively. Upon admission, the BrucellaCapt, BCAPV, and Coombs tests and the microagglutination test (MAT) were positive for all cases: titers were 1/2,560 by the BrucellaCapt test, 1/2,560 by the BCAPV test, 1/1,280 by the Coombs test, and 1/320 by the MAT. The decreases in the BrucellaCapt and BCAPV titers over time were pronounced in comparison with the Coombs titers. Cumulative probabilities of persistence 12 months after therapy were as follows: 80% by the BrucellaCapt test, 80% by the BCAPV test, 87% by the Coombs test, and 35% by the MAT. Serological changes during relapse were detected in seven cases (88%) by the Coombs test, in five cases by the BrucellaCapt and BCAPV tests, and in three cases by the MAT. The BrucellaCapt test is a sensitive, specific, and simple test for routine use in human brucellosis. Similar results were obtained with the BCAPV test. However, in some cases of relapse and chronic forms of the disease, the slight changes observed in low-affinity antibodies alone are better detected by the Coombs test.
Inelastic Flow Behavior of Argillaceous Salt

The effects of weak clay particles on the creep response of argillaceous salt have been analyzed by considering the particles as damage initiation sites where local tensile stresses and microcracks are induced under triaxial compression. The thermodynamic driving force for the damage process is formulated in terms of an appropriate power-conjucate equivalent stress measure, and the damage kinetics are described in terms of an evolution equation formulated on the basis of the conjugate equivalent stress and the scalar damage variable from Kachanov (1958). This treatment of clay particle effects is then incorporated into the Multimechanism Deformation Coupled Fracture (MDCF) constitutive model. A summary of the constitutive model is presented with an evaluation of the model calculations against experimental data of clean and argillaceous salt. The results suggest that the higher creep rate observed in argillaceous salt compared to clean salt is the consequence of increased damage growth in argillaceous salt due to the presence of weak clay particles.
Understanding latent interactions in online social networks

Popular online social networks (OSNs) like Facebook and Twitter are changing the way users communicate and interact with the Internet. A deep understanding of user interactions in OSNs can provide important insights into questions of human social behavior, and into the design of social platforms and applications. However, recent studies have shown that a majority of user interactions on OSNs are latent interactions, passive actions such as profile browsing that cannot be observed by traditional measurement techniques. In this paper, we seek a deeper understanding of both visible and latent user interactions in OSNs. For quantifiable data on latent user interactions, we perform a detailed measurement study on Renren, the largest OSN in China with more than 150 million users to date. All friendship links in Renren are public, allowing us to exhaustively crawl a connected graph component of 42 million users and 1.66 billion social links in 2009. Renren also keeps detailed visitor logs for each user profile, and counters for each photo and diary/blog entry. We capture detailed histories of profile visits over a period of 90 days for more than 61,000 users in the Peking University Renren network, and use statistics of profile visits to study issues of user profile popularity, reciprocity of profile visits, and the impact of content updates on user popularity. We find that latent interactions are much more prevalent and frequent than visible events, non-reciprocal in nature, and that profile popularity are uncorrelated with the frequency of content updates. Finally, we construct latent interaction graphs as models of user browsing behavior, and compare their structural properties against those of both visible interaction graphs and social graphs.
THE TREATMENT OF DELIBERATE SELF-HARM IN BORDERLINE PERSONALITY DISORDER USING DIALECTICAL BEHAVIOUR THERAPY: A PILOT STUDY IN A HIGH SECURITY HOSPITAL

Deliberate self-harm (DSH) presents a significant health problem, especially as treatments have not been particularly successful in reducing repetition. Dialectical behaviour therapy (DBT; Linehan, 1993) is one approach that has reported some success in reducing self-harm rates in borderline personality disorder patients, who self-harm frequently, though it remains largely untested outside its original setting. The present study aimed to assess the effectiveness of DBT in self-harming women in an institutional setting in the United Kingdom where self-harm is common. Female patients at Rampton Hospital who were displaying self-harming behaviour and met criteria for borderline personality disorder ( N = 10) participated in the full one-year treatment package of DBT. Patients were assessed on self-harm rates and on a number of psychological variables, pre-, during- and post-therapy, including a 6-month follow-up. There was a significant reduction in DSH during therapy, which was maintained at 6-month follow-up. This was paralleled by a reduction in dissociative experiences and an increase in survival and coping beliefs, alongside improvements in depression, suicide ideation, and impulsiveness. The findings are preliminary but the results suggest that DBT might provide an effective treatment for severe self-harm in institutional settings, and also highlight some of the psychological mechanisms that might mediate these improvements in self-harming behaviour.