Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential expression of genes in purple-shoot tea tender leaves and mature leaves during leaf growth.

BACKGROUND Tea (Camellia sinensis L.), contains high levels of secondary metabolic products with both commercial and medicinal value. At present, most cultivated tea plant have green leaves; although tea plants with purple leaves exist, their supply is inadequate. During leaf growth and maturation, the content of secondary metabolic compounds decreases, resulting in higher content in tender purple leaves (TPL), and lower content in mature green leaves (MGL). The aim of this study was to analyze the differential expression of genes in these two tissues, with a cDNA-AFLP (amplified fragment length polymorphism) approach and biochemical analysis. RESULTS Compared to MGL samples, TPL samples had higher content of anthocyanin, total polyphenols and total catechins, a higher carotenoid-to-chlorophyll ratio and lower content of soluble sugars (glucose, fructose and sucrose). TPL samples showed a lower photosynthetic ability, demonstrated by a lower CO2 assimilation and carbohydrate accumulation rate. Using cDNA-AFLP with 256 primer combinations, differential transcript profiling generated 148 matched transcript-derived fragments (TDFs). Among these TDFs, 77 genes were upregulated and 71 were downregulated. These were grouped into 11 functional categories which are important for final tea quality parameters. CONCLUSIONS Our data presented the first effort to elucidate the molecular basis of differential accumulation of key metabolites during tea leaf maturation. Our findings also provided a theoretical molecular explanation for the color change during leaf growth.
TOXICOKINETICS AND METABOLISM

Di(2-ethylhexyl) phthalate (DEHP) is used as a plastic softener in the polymer industry and is widespread in medical devices. DEHP has been incriminated as an endocrine-disrupting chemical, and the effects of DEHP in various species have included disturbances in the reproductive system. The effects of the chemical have varied, depending upon exposure routes and species. This study was performed in order to characterise the kinetics of DEHP and its metabolite mono(2-ethylhexyl) phthalate (MEHP) in the young male pig, an omnivore model-species for research in reproductive toxicology. Eight pigs were given 1000 mg DEHP/kg bodyweight by oral gavage. The concentrations of DEHP and MEHP were then measured in the plasma and tissues of the pigs at different time points after administration. There was no consistent rise above contamination levels of concentrations of DEHP in the plasma of the pigs. However, the metabolite MEHP reached the systemic blood circulation. The half-life of MEHP in the systemic blood circulation was calculated to be 6.3 h. Absorption from the intestine was biphasic in six of the eight pigs and the mono-exponential elimination-phase started 16 h after the after the administration of DEHP. To conclude, MEHP consistently reaches the systemic circulation in the pig when DEHP is administered orally. The kinetic pattern of the parent substance on the other hand is more difficult to characterise.
Survivorship of the KUDO total elbow prosthesis— comparative study of cemented and uncemented ulnar components: 89 cases followed for an average of 6 years

Background The Kudo total elbow prosthesis (TEP) is a well-established implant with good mid-term results. The ulnar component can be placed with or without cement, and the humeral component is normally placed without cement. Methods 89 Kudo type-5 total elbow prostheses were evaluated after a mean follow-up of 6 (1.7–11) years. The indication for joint replacement was rheumatoid arthritis in all cases. 49 prostheses were placed without cement. In 40 cases, the ulnar component was cemented and the humeral component was uncemented. Results In the uncemented group, 7 revisions had taken place. 3 of these ulnar components were shortstemmed and 4 were long-stemmed. No revisions had been performed in the hybrid group. In the uncemented group another 7 patients showed progressive radiolucencies, while 3 patients in the hybrid group showed progressive radiolucencies. Interpretation In this group of RA patients, the survivorship of the cemented ulnar component was better than that of the uncemented ulnar component.
A pragmatic trial of acamprosate in the treatment of alcohol dependence in primary care.

AIMS To assess the effectiveness of pharmacotherapy with acamprosate in alcohol-dependent patients treated in a naturalistic setting in primary care in France. METHODS The ARES (Acamprosate et Repercussions Economiques et Sociales; Acamprosate and Economic and Social Repercussions) study was performed by 149 general practitioners interested in treating alcohol use disorders in France who included patients fulfilling DSM-IV criteria for alcohol dependence. The only exclusion criteria concerned contra-indications to acamprosate, co-medication with naltrexone and multiple substance abuse. Eligible patients were randomized to one of two treatment arms, either standard care alone or standard care with acamprosate, using an open-label design and followed up quarterly for a period of 1 year. The primary outcome variable was the change from baseline on the Alcohol-Related Problems Questionnaire. Secondary efficacy variables were abstinence, Clinical Global Impression, quality of life measured with the SF-36 and incidence of adverse events. An intent-to-treat population was used for outcome analysis. RESULTS 422 patients were included, of whom 348 (82%) completed the protocol as planned. At the end of the study, patients randomized to the acamprosate group had significantly better outcomes in terms of total ARPQ score, change from baseline (-2.61 vs -3.44) and number of subjects with no alcohol-related problem. On average, patients treated with acamprosate had one less alcohol-related problem than did the controls. The number needed to treat in order to save one additional patient from alcohol-related problems compared to standard care was 7.14. Statistically significant differences in favour of the acamprosate group were observed for all secondary efficacy outcome measures including quality of life. CONCLUSIONS Adjunctive therapy with acamprosate in primary care is associated with significantly better functional outcome. Pragmatic trials in alcohol dependence are both feasible and informative.
Connectivity within and among a Network of Temperate Marine Reserves

Networks of marine reserves are increasingly being promoted as a means of conserving marine biodiversity. One consideration in designing systems of marine reserves is the maintenance of connectivity to ensure the long-term persistence and resilience of populations. Knowledge of connectivity, however, is frequently lacking during marine reserve design and establishment. We characterise patterns of genetic connectivity of 3 key species of habitat-forming macroalgae across an established network of temperate marine reserves on the east coast of Australia and the implications for adaptive management and marine reserve design. Connectivity varied greatly among species. Connectivity was high for the subtidal macroalgae Ecklonia radiata and Phyllospora comosa and neither species showed any clear patterns of genetic structuring with geographic distance within or among marine parks. In contrast, connectivity was low for the intertidal, Hormosira banksii, and there was a strong pattern of isolation by distance. Coastal topography and latitude influenced small scale patterns of genetic structure. These results suggest that some species are well served by the current system of marine reserves in place along this temperate coast but it may be warranted to revisit protection of intertidal habitats to ensure the long-term persistence of important habitat-forming macroalgae. Adaptively managing marine reserve design to maintain connectivity may ensure the long-term persistence and resilience of marine habitats and the biodiversity they support.
A Social-Ecological Framework of Theory, Assessment, and Prevention of Suicide

The juxtaposition of increasing suicide rates with continued calls for suicide prevention efforts begs for new approaches. Grounded in the Centers for Disease Control and Prevention (CDC) framework for tackling health issues, this personal views work integrates relevant suicide risk/protective factor, assessment, and intervention/prevention literatures. Based on these components of suicide risk, we articulate a Social-Ecological Suicide Prevention Model (SESPM) which provides an integration of general and population-specific risk and protective factors. We also use this multi-level perspective to provide a structured approach to understanding current theories and intervention/prevention efforts concerning suicide. Following similar multi-level prevention efforts in interpersonal violence and Human Immunodeficiency Virus (HIV) domains, we offer recommendations for social-ecologically informed suicide prevention theory, training, research, assessment, and intervention programming. Although the SESPM calls for further empirical testing, it provides a suitable backdrop for tailoring of current prevention and intervention programs to population-specific needs. Moreover, the multi-level model shows promise to move suicide risk assessment forward (e.g., development of multi-level suicide risk algorithms or structured professional judgments instruments) to overcome current limitations in the field. Finally, we articulate a set of characteristics of social-ecologically based suicide prevention programs. These include the need to address risk and protective factors with the strongest degree of empirical support at each multi-level layer, incorporate a comprehensive program evaluation strategy, and use a variety of prevention techniques across levels of prevention.
Coexistence of Different Genotypes in the Same Bat and Serological Characterization of Rousettus Bat Coronavirus HKU9 Belonging to a Novel Betacoronavirus Subgroup

ABSTRACT Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9), a recently identified coronavirus of novel Betacoronavirus subgroup D, from Leschenault's rousette, was previously found to display marked sequence polymorphism among genomes of four strains. Among 10 bats with complete RNA-dependent RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes sequenced, three and two sequence clades for all three genes were codetected in two and five bats, respectively, suggesting the coexistence of two or three distinct genotypes of Ro-BatCoV HKU9 in the same bat. Complete genome sequencing of the distinct genotypes from two bats, using degenerate/genome-specific primers with overlapping sequences confirmed by specific PCR, supported the coexistence of at least two distinct genomes in each bat. Recombination analysis using eight Ro-BatCoV HKU9 genomes showed possible recombination events between strains from different bat individuals, which may have allowed for the generation of different genotypes. Western blot assays using recombinant N proteins of Ro-BatCoV HKU9, Betacoronavirus subgroup A (HCoV-HKU1), subgroup B (SARSr-Rh-BatCoV), and subgroup C (Ty-BatCoV HKU4 and Pi-BatCoV HKU5) coronaviruses were subgroup specific, supporting their classification as separate subgroups under Betacoronavirus. Antibodies were detected in 75 (43%) of 175 and 224 (64%) of 350 tested serum samples from Leschenault's rousette bats by Ro-BatCoV HKU9 N-protein-based Western blot and enzyme immunoassays, respectively. This is the first report describing coinfection of different coronavirus genotypes in bats and coronavirus genotypes of diverse nucleotide variation in the same host. Such unique phenomena, and the unusual instability of ORF7a, are likely due to recombination which may have been facilitated by the dense roosting behavior and long foraging range of Leschenault's rousette.
Evaluation of Nucleoside Phosphonates and Their Analogs and Prodrugs for Inhibition of Orthopoxvirus Replication

ABSTRACT In the event of a bioterrorism attack using smallpox virus, there currently is no approved drug for the treatment of infections with this virus. We have reported previously that (S)-1-[3-hydroxy-2-(phosphonomethoxy)propyl]cytosine (HPMPC) (also known as cidofovir [CDV]) has good activity against poxvirus infections; however, a major limitation is the requirement for intravenous administration. Two related acyclic nucleoside phosphonates (ANPs), adefovir (PMEA) and tenofovir (PMPA), are active against human immunodeficiency virus or hepatitis B virus but do not have activity against the orthopoxviruses. Therefore, we have evaluated a number of analogs and potential oral prodrugs of these three compounds for their ability to inhibit the replication of vaccinia virus or cowpox virus in tissue culture cells. The most-active compounds within the CDV series were (S)-HPMPA and (butyl l-alaninyl) cyclic HPMPC, with 50% effective concentrations (EC50s) from 4 to 8 μM, compared with 33 to 43 μM for CDV. Although PMEA itself was not active, adefovir dipivoxil {bis[(pivaloyl)oxymethyl] PMEA} and bis(butyl l-alaninyl) PMEA were active against both viruses, and bis(butyl l-alaninyl) PME-N6-(cyclopropyl)DAP and (isopropyl l-alaninyl)phenyl PME-N6-(cyclopropyl)DAP were the most active compounds tested, with EC50s of 0.1 to 2.6 μM. In the PMPA series, none of the analogs tested had significantly better activity than PMPA itself. These data indicate that a number of these ANP derivatives have activity against vaccinia virus and cowpox virus in vitro and should be evaluated for their efficacies in animal models.
Influence of inhaled corticosteroids on community-acquired pneumonia in patients with bronchial asthma.

OBJECTIVE The aim of the present study was to evaluate the influence of inhaled corticosteroids (ICS) on community-acquired pneumonia (CAP) in patients with asthma. PATIENTS AND METHODS All asthmatic patients who required hospitalization for CAP from the beginning of 1989 through December 2001 were enrolled in this retrospective study. Patients who used oral corticosteroids daily were excluded. Patients were divided into two groups based on whether or not they used ICS, and we analyzed clinical characteristics of the pneumonia. Sixty-two patients (28 males, 34 females; mean age, 54.5 years) were enrolled in this study. Thirty-seven of 62 patients used ICS, with the mean dosage being 777.9 microg/day. RESULTS We found no significant differences between the two groups with regard to mean age, serum albumin level, duration of asthma, pulmonary function and frequency of intravenous infusion of corticosteroids in the outpatient department. There were no significant differences in body temperature, white blood cell count, and CRP value upon admission between the two groups. Differences were not significant in the period of resolution of the pneumonia or in the frequency of pathogens identified between the two groups. CONCLUSION ICS therapy appears to have no influence on CAP in patients with asthma. We recommend that ICS should be continued to control asthma with adequate antibiotic therapy when asthmatic patients have CAP.
Percutaneous Treatment of Lumbar Disc Herniation

Nine hundred and eighteen patients were subjected to percutaneous treatment of lumbar herniated disc. 733 of these were treated through enzymatic nucleolysis with chymopapain, for a total 883 levels (150 of whom were treated at two levels): 185 patients were treated with Onik's automate discectomy. Chemonucleolysis was carried out on 733 patients (79.8%) and automated discectomy in 185 cases (20.1%). Chemonucleolysis has led to the resolution of the symptoms in a high percentage of cases (82.2%). Nucleotomy was an effective method of management in 74.6% of the cases. The availability of several therapeutic methods has allowed us to respond in a more appropriate way to the patient's requirements and, in the case of failure, offer a more flexible therapeutic spectrum, and to consider surgery as the last resort. As regards the relation between enzymatic nucleolysis with chymopapain and disc nucleoaspiration, we feel that the two should not be in competition, for the indications are precise for both methods: in the enzymatic treatment, the hernia can be medium-large sized, in a sub- or extra-ligamentous position. The treatment of patients with moderately severe symptoms is preferable. In disc nucleoaspiration, the hernia must be small-sized.
Cooperative Spectrum Sharing Protocol with Selective Relaying System

In this paper, we propose a two-phase protocol based on cooperative relaying for a secondary system to achieve spectrum access along with a selective relaying primary system. The primary system comprises of a transmitter-receiver pair PT-PR and M relays R<sub>i</sub>, i G {1,2,⋯ , M}. The secondary system is a multi-user system with N transmitters R<sub>i</sub>, i ϵ {M +1, M + 2, ⋯ , M + N } which intend to communicate with a common receiver SR. In the proposed protocol, terminals R<sub>i</sub>, i ϵ M<sub>1</sub> = {1, 2, ⋯ , M + Q} are designated as possible candidates for assisting the primary system while the remaining secondary transmitters R<sub>i'</sub>, i' ϵ M<sub>2</sub> = {M + Q + 1, M + Q + 2, ⋯ ,M + N} are chosen as possible candidates for secondary spectrum access, where 0 ≤ Q ≤ N. The relaying terminal R<sub>p</sub>, p ϵ M<sub>1</sub> which achieves the request target rate for the primary system and has the best channel to PR, is first selected from M<sub>1</sub> to serve as a decode-and-forward (DF) relay for the primary system. With the cooperation of R<sub>p</sub>, the primary system is able to tolerate some interference lower than a certain threshold in the relaying phase, without degrading its outage performance. The secondary transmitter R<sub>s</sub>, s ϵ M<sub>2</sub> which satisfies this interference constraint and optimizes the outage performance for the secondary system, is then selected from M<sub>2</sub> to access the spectrum band simultaneously when R<sub>p</sub> is relaying the primary signal. Analytical and simulation results confirm the efficiency of the proposed spectrum sharing protocol. We show that there exists an optimal value for Q and both primary and secondary systems are able to achieve better outage performance with increasing N.
Deciding Equivalence of Top-Down XML Transformations in Polynomial Time

This paper describes XStream, a Turing-complete programming language which allows the programmer to write XML transformations in a functional tree-processing style and have them evaluated in a streaming way: the output is produced incrementally while the input is still being parsed. The programmer does not need to care explicitly about buffering. We introduce the language, describe some techniques used in the implementation and present some performance results.
Functioning and health service use among elderly nursing home residents with alcohol use disorders: findings from the National Nursing Home Survey.

OBJECTIVE The author asked whether older nursing home residents with alcohol use disorders differ from demographically-matched residents without alcohol use disorders on functioning, admission characteristics, and health services use. METHOD National Nursing Home Survey data were used to compare nursing home residents with alcohol use disorders (N=216) with demographically-matched residents without alcohol use disorders (N=216) on functioning, admission characteristics, and health services use. RESULTS Residents with alcohol use disorders functioned somewhat better than did residents in the demographically-matched sample group, as indicated by performance of basic activities of daily living. However, they were significantly more likely to have lived alone before admission and to have obtained mental health and social services. There was a significant group x gender interaction on length of stay: men with alcohol use disorders had shorter lengths of stay than did men without alcohol use disorders; women with alcohol use disorders had longer lengths of stay than did women without such disorders. CONCLUSIONS Having fewer social resources may contribute to elevated admission risk and need for mental health and social services among older nursing home residents who have alcohol use disorders. Duration and severity of alcohol problems may help explain gender differences in length of stay among these residents.
LidA, a Translocated Substrate of the Legionella pneumophila Type IV Secretion System, Interferes with the Early Secretory Pathway

ABSTRACT Legionella pneumophila uses a type IV secretion system to deliver effector molecules into the host cell and establish its replication vacuole. In this study, we investigated the role of LidA, a translocated substrate associated with the surface of the L. pneumophila-containing vacuole. LidA is secreted into the host cell throughout the replication cycle of the bacteria and associates with compartments of the early secretory pathway. When overexpressed in mammalian cells or yeast, LidA interferes with the early secretory pathway, probably via a domain predicted to be rich in coiled-coil structure. Finally, during intracellular replication, the replication vacuoles are in close contact with the endoplasmic reticulum-Golgi intermediate compartment and the Golgi apparatus, suggesting a positive correlation between intracellular growth and association of the vacuole with compartments of the early secretory pathway. We propose that LidA is involved in the recruitment of early secretory vesicles to the L. pneumophila-containing vacuole and that the vacuole associates with the secretory pathway to facilitate this process.
Simultaneous Regression Shrinkage, Variable Selection, and Supervised Clustering of Predictors with OSCAR

Summary Variable selection can be challenging, particularly in situations with a large number of predictors with possibly high correlations, such as gene expression data. In this article, a new method called the OSCAR (octagonal shrinkage and clustering algorithm for regression) is proposed to simultaneously select variables while grouping them into predictive clusters. In addition to improving prediction accuracy and interpretation, these resulting groups can then be investigated further to discover what contributes to the group having a similar behavior. The technique is based on penalized least squares with a geometrically intuitive penalty function that shrinks some coefficients to exactly zero. Additionally, this penalty yields exact equality of some coefficients, encouraging correlated predictors that have a similar effect on the response to form predictive clusters represented by a single coefficient. The proposed procedure is shown to compare favorably to the existing shrinkage and variable selection techniques in terms of both prediction error and model complexity, while yielding the additional grouping information.