Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity

Significance Comparative analysis of multiple strains within a species is a powerful way to uncover pathoadaptive genetic acquisitions. Hundreds of genome sequences are now available for the human pathogen Staphylococcus aureus, mostly known for its antibiotic-resistant variants that threaten the emergence of panresistant superbugs. In this study, genome-scale models of metabolism are used to analyze the shared and unique metabolic capabilities of this pathogen and its strain-specific variants. The models are used to distinguish S. aureus strains responsible for severe infections based solely on growth capabilities and presence of different virulence factors. The results identify metabolic similarities and differences between S. aureus strains that provide insights into the epidemiology of S. aureus and may help to combat its spread. Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus. These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world.
Concomitant lung metastasis in patients with advanced hepatocellular carcinoma.

AIM To investigate the clinical features and prognostic factors of advanced hepatocellular carcinoma (HCC) patients presenting with lung metastasis at initial diagnosis. METHODS Between 2001 and 2010, we recruited 76 consecutive HCC patients initially presenting with lung metastasis, without co-existing metastasis from other sites. These patients were divided into three groups: untreated group (n = 22), single treatment group (n = 19), and combined treatment group (n = 35). RESULTS Metastasis of bilateral lung lobes was common and noted in 35 patients (46.1%), and most of patients (59/76, 77.6%) presented with multiple lung metastatic nodules. Nineteen patients (25.0%) received single-method treatment, including hepatectomy in 4, transcatheter arterial chemoembolization in 6, radiotherapy in 5, and oral sorafenib in 4. Thirty-five patients (46.1%) received combined treatment modalities. The overall median survival of the all patients was 8.7 ± 0.6 mo; 4.1 ± 0.3, 6.3 ± 2.5 and 18.6 ± 3.9 mo, respectively in the untreated group, single treatment group and combined treatment group, respectively, with a significant difference (log-rank test, P < 0.001). Multivariate analysis revealed that Child-Pugh score, the absence or presence of portal vein tumor thrombus, and treatment modality were three independent prognostic factors affecting survival of patients with advanced HCC and concomitant lung metastasis. CONCLUSION Combined treatment modalities tend to result in a better survival as compared with the conservative treatment or single treatment modality for HCC patients initially presenting with lung metastasis.
Policy Rules and Economic Performance

Monetary policy evaluation has evolved over time from fixed rules versus discretion to policy rules versus constrained discretion. We propose a metric to evaluate monetary policy rules by calculating quadratic loss ratios, the (inflation plus unemployment) loss in high deviations periods divided by the loss in low deviations periods, with policy rules with higher loss ratios preferred to rules with lower loss ratios. The central result of the paper is that rules with larger coefficients on inflation than on the output gap have higher loss ratios (and are therefore preferred to) rules with equal coefficients or rules with higher coefficients on the output gap. This result is robust to policy lags between one and two years, different weights on inflation loss than on unemployment loss, various definitions of high and low deviations periods, and time varying equilibrium real interest rates. We conclude that the Fed should “constrain” constrained direction by responding more strongly to inflation gaps than to output gaps.
Ultrasound-guided external jugular vein cannulation for central venous access by inexperienced trainees

Background and objective The insertion of central venous catheters via the external jugular vein (EJV) is not always practical because of the relatively frequent failure rate; thus, the internal jugular approach is generally used. Data from the literature suggest that ultrasound-guided catheterization of the internal jugular vein is superior to the surface anatomy landmark technique and, therefore, should be the method of choice. We evaluated the value of ultrasound guidance in the learning process of central venous cannulation via EJV by similarly inexperienced trainees. Methods In this prospective randomized study, 60 patients were assigned to two groups: group SA (surface anatomy; n = 30) underwent insertion of the central venous catheter using landmark guidance and group US (ultrasound; n = 30) underwent insertion using ultrasound guidance. In all patients, catheter insertion through the right EJV was performed by trainees in their second year of training. Ultrasound guidance was carried out by the same ultrasound specialist. The following parameters were evaluated in all patients: the number of successful punctures of the right EJV, the total number of attempts and the time to vein puncture; the number of successful insertions of the central venous catheter, the number of attempts and the duration of catheterization (from puncture of EJV to external fixation of the catheter); and the incidence of complications. The study was approved by the institutional ethics committee, and all patients gave written informed consent. Data were expressed as mean ± SD. Student's t-test, Mann–Whitney test and χ2-test were used for analysis and P < 0.05 was considered statistically significant. The power of the study was 85%. Results The EJV puncture was successful in 24 out of 30 (80%) patients from group SA and in 22 out of 30 (73%) patients from group US (P = NS). There were no statistically significant differences between the groups regarding the mean time to perform the vein puncture and the number of attempts. The insertion of the central venous catheter was performed successfully in 10 (33%) patients from group SA and six (20%) patients from group US. The success rate of central cannulation via the EJV approach was 10 out of 24 (42%) in group SA and six out of 22 (27%) in group US (P = NS). The total time for insertion and the number of attempts were similar in both groups (P = NS). Local haematoma occurred in 11 patients in group SA and in three patients in group US (P = NS). Conclusion Our results demonstrate no significant differences between the conventional surface anatomy landmark technique and the ultrasound-guided technique for the insertion of a central venous catheter via EJV by inexperienced trainees.
The discourse of gay men's group sex: the importance of masculinity

Group sex has consistently been identified as one of a group of risk behaviours among gay men associated with HIV seroconversion. This paper presents a detailed description of how gender, and specifically masculinity, operates as an aspect of the discourse of gay men's group sex. The findings presented in this paper are one part of a multi-aspected discourse analysis through which we are aiming to develop an account of the discourse of gay men's group sex as it was produced in a series of qualitative interviews conducted with gay men who participate in group sex. The interviews were conducted as part of the Three or More Study (TOMS), a larger project that involved a substantial quantitative component. The overarching intent of the discourse analysis is to provide as comprehensive a mapping as possible of this discursive terrain to facilitate the targeted development of HIV and sexual health educational initiatives. The discourse of gay men's group sex reproduces some key formations of masculinity within discourses of gender, which present specific challenges for HIV prevention education. These challenges are outlined at the conclusion of this paper.
Carbamazepine therapy in trigeminal neuralgia: clinical effects in relation to plasma concentration.

Seven patients with trigeminal neuralgia were treated with carbamazepine at three dose levels, each period lasting for six days. A single-blind technique was used, the patients being unaware of the dose changes. During the last three days of each dose treatment, the pain score was determined by the patients and the plasma concentrations of carbamazepine and its epoxide metabolite were measured. There was a correlation between the dose and plasma level of carbamazepine (r = .56; P < .01). At the carbamazepine doses studied (200 to 1,400 mg/day), no indication of saturation kinetics was seen. As the ratio between the plasma levels of the epoxide and carbamazepine was relatively low and constant, it was not possible to evaluate the potency of the epoxide. In six of the patients studied a plasma level-effect relationship was found. The best effect was seen at carbamazepine levels between 24 and 43 mu mole/L (5.7 and 10.1 microgram/mL). In one patient who was studied twice, the plasma level-response curve was different on the two occasions. Side effects were recorded in two patients, both with carbamazepine plasma levels above 33 mu mole/L (7.9 microgram/mL).
Serving those who served: retention of newly returning veterans from Iraq and Afghanistan in mental health treatment.

OBJECTIVE There are growing concerns about the mental health status of returning veterans from the recent conflicts in Iraq (Operation Iraq Freedom [OIF]) and Afghanistan (Operation Enduring Freedom [OEF]) and about retention in mental health treatment of veterans with posttraumatic stress disorder (PTSD). This study obtained data from veterans who had a new diagnosis of PTSD from fiscal year (FY) 2004 to FY 2007 and determined whether retention in PTSD treatment and the number of mental health visits were comparable among OIF-OEF veterans and veterans from other service eras. METHODS Data from the Department of Veterans Affairs and the Department of Defense were combined to identify veterans who were newly diagnosed as having PTSD (N=204,184) and their service era. Survival analysis assessed dropout from mental health treatment within one year from initial diagnosis, and Poisson regression assessed the association between war era and number of mental health visits. RESULTS Although a smaller proportion of OIF-OEF veterans than Vietnam-era veterans remained in treatment for more than one year (37.6% versus 46.0%), when the analyses adjusted for demographic characteristics and comorbid diagnoses, OIF-OEF veterans were less likely than Vietnam-era veterans to discontinue psychiatric treatment for PTSD within one year. OIF-OEF veterans attended fewer mental health visits than Vietnam-era veterans did (8.15 versus 13.37). However, multivariate analysis indicated that, after the analyses adjusted for confounding factors, OIF-OEF veterans had significantly more visits than Vietnam-era veterans associated with PTSD treatment. CONCLUSIONS Retention and numbers of visits were found to be lower among OIF-OEF veterans primarily as a function of age and comorbid conditions and not as a function of the particular war era. Interventions should be designed to target specific barriers to care that may interfere with continued engagement in mental health services.
In Vitro Activity of Cephalexin against Community-Acquired Urinary Escherichia coli , Klebsiella and Proteus species Isolates

Problem statement: Resistance among urinary tract pathogens to conventional antibiotics has been considered a health problem worldwide. The aim of this study was to evaluate the in vitro activity of cephalexin on urinary enterobacterial isolates. Approach: Patients with community-acquired urinary tract infections were microbiologically investigated. Urine specimens were collected from each patient. The specimens were cultured on bacteriological media. The isolated urinary pathogens were subjected to antibiotic sensitivity test using modified Kirby-Bauer Disc diffusion method. The method was judged by the National Committee for Clinical Laboratories Standards (NCCLS). Results: A total of 140 enterobacterial urinary isolates were recovered. Of these 93 (66.4%) were identified as E. coli, 20 (14.3%) as Klebsiella spp. and 12 (8.6%) as Proteus spp. The results showed that urinary enterobacterial pathogens had a high rate of resistance to cephalexin amounting to 75 (53.6%), whereas susceptible and intermediate rates were 34 (24.3%) and 31 (22.1%) respectively. Conclusion: It was concluded that E. coli are the predominant organisms isolated from subjects sampled. High resistance to cephalexin activity was noticed with Klebsiella spp isolates.
Family-to-Work Conflict among Texas Law enforcement officers in the Wake of the Hurricane Rita Evacuation

Law enforcement has critical responsibilities during evacuations, taking officers away from their families to work to serve the needs of the community. The purpose of this article is to examine family-to-work conflict for law enforcement officers who worked during the evacuation of the Texas Gulf Coast in preparation for Hurricane Rita. Officers from counties along the Texas Gulf Coast were sampled. Results of OLS regression show that unmet family needs during the evacuation resulted in increased family-to-work conflict after Hurricane Rita, while the presence of children in the household resulted in less family-to-work conflict after Hurricane Rita. Law enforcement agencies and disaster managers need to consider work and family issues when training officers to prepare for disaster related events.
You're so vein: bundle sheath physiology, phylogeny and evolution in C3 and C4 plants.

Bundle sheath (BS) anatomy is found in most C4 lineages, associated with low inter-veinal distances (IVD) and high BS:mesophyll ratio (BS:MC). The origins, function and selective advantages of the BS in C3 lineages are relevant for understanding the environmental, molecular and phylogenetic determinants of C4 evolution. Suggested functions for BS have included structural support, hydraulic isolation, storage for water, ions, and carbohydrates, and photorespiratory carbon metabolism; we propose a central role for cavitation repair, consistent with the BS as a control centre on regulating stem and leaf hydraulic continuity. An analysis of BS traits in the phylogenetic lineages giving rise to C4 grasses (the 'PACMAD' clade) shows an initial enhancement in BS:MC ratio in C3 lineages, although IVD is similar to the Pooideae sister group. Using a global database, a well-developed BS in the C3 PACMAD lineages was associated with higher precipitation and temperatures in the habitat of origin on an annual basis, with the C3 to C4 progression defined by the aridity index (AI). Maintaining leaf hydraulic conductance and cavitation repair are consistent with increased evaporative demand and more seasonal precipitation as drivers, first for the C3 BS, and then C4 diversification, under declining CO(2) concentrations in the Palaeogene and Neogene.
Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity

Cytosine methylation in the genome of Drosophila melanogaster has been elusive and controversial: Its location and function have not been established. We have used a novel and highly sensitive genomewide cytosine methylation assay to detect and map genome methylation in stage 5 Drosophila embryos. The methylation we observe with this method is highly localized and strand asymmetrical, limited to regions covering ∼1% of the genome, dynamic in early embryogenesis, and concentrated in specific 5-base sequence motifs that are CA- and CT-rich but depleted of guanine. Gene body methylation is associated with lower expression, and many genes containing methylated regions have developmental or transcriptional functions. The only known DNA methyltransferase in Drosophila is the DNMT2 homolog MT2, but lines deficient for MT2 retain genomic methylation, implying the presence of a novel methyltransferase. The association of methylation with a lower expression of specific developmental genes at stage 5 raises the possibility that it participates in controlling gene expression during the maternal-zygotic transition.
Decreased reporter gene expression during latent infection with HSV LAT promoter constructs.

The latency-associated transcripts (LAT), which code from an 8.5 kb segment of the internal repeat region of the HSV genome, are the only viral transcripts that are present during HSV latent infection. However, little is known about the relative contribution of promoter activity, degradative processes, and elements or regions affecting long term expression of these transcripts in latently infected neurons. To begin to address this question we investigated LAT promoter activity during acute and latent infection. Mouse footpads were infected with KOS/62-3, an engineered herpes simplex virus in which both copies of the LAT promoter are used to drive expression of the Escherichia coli lac Z gene. Four days post-inoculation (p.i.) abundant beta-galactosidase (beta-gal) protein and transcripts were present within ganglionic neurons as assayed by enzyme histochemistry and in situ hybridization. In contrast, by Day 21 (at which time a latent infection had been established) no beta-gal transcripts were present in infected ganglia, even when assayed by the polymerase chain reaction (PCR). These findings indicate a significant drop in LAT promoter activity between Day 4 and Day 21 p.i. To provide confirmatory evidence for this conclusion we infected mice with a second viral construct, KOS/67-7, in which the LAT promoter was used to drive expression of the nerve growth factor (NGF) gene. Four days p.i. , abundant NGF antigen and transcripts were present in infected ganglionic neurons, but no evidence of transcription of the cloned NGF gene could be found in latently infected ganglia. Our findings suggest that LAT promoter activity is severely restricted during the latent phase of ganglionic infection.
LT2 Cryptosporidium data: what do they tell us about Cryptosporidium in surface water in the United States?

Beginning in 2006 a United States Federal regulation required public water suppliers using surface water serving more than 10,000 population to analyze for Cryptosporidium in at least 24 consecutive monthly samples from each surface water source. In July 2012, the U.S. EPA released the resulting data consisting of ca. 45,000 records. No Cryptosporidium were found in 93% of samples and no Cryptosporidium were found in any samples analyzed from over half of 1670 locations sampled. Nevertheless, at 250 locations representing every region of the U.S., Cryptosporidium were found in sufficient numbers of samples to provide a picture of their occurrence nationwide. Data from about 100 sites reporting the highest numbers were examined in detail. Although analysis of matrix spikes was required for quality control, the results do not permit estimating organism concentrations. The data reported at each of the individual sample locations were analyzed in the form of cumulative probability distributions to describe key risk-related features of median level and variability. Taken as a whole, the data describe a spectrum of median Cryptosporidium occurrence in surface waters of the U.S. ranging from ca. 0.005 to ca. 0.5 oocysts/L. The variability at individual sites ranged from ca. 1 to 15 r.s. d. Based on the LT2 positive data, comparison to measurements of other water quality parameters, and independent means of estimating organism production from watersheds reported in the literature, the hypothesis is offered that Cryptosporidium may be found in surface water anywhere worldwide continuously and within the spectrum defined above.
Toward an aggregated understanding of enzymatic hydrolysis of cellulose: Noncomplexed cellulase systems

Information pertaining to enzymatic hydrolysis of cellulose by noncomplexed cellulase enzyme systems is reviewed with a particular emphasis on development of aggregated understanding incorporating substrate features in addition to concentration and multiple cellulase components. Topics considered include properties of cellulose, adsorption, cellulose hydrolysis, and quantitative models. A classification scheme is proposed for quantitative models for enzymatic hydrolysis of cellulose based on the number of solubilizing activities and substrate state variables included. We suggest that it is timely to revisit and reinvigorate functional modeling of cellulose hydrolysis, and that this would be highly beneficial if not necessary in order to bring to bear the large volume of information available on cellulase components on the primary applications that motivate interest in the subject. © 2004 Wiley Periodicals, Inc.