Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

The direct “metagenomic” sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights into the structure of microbial communities. For example, analysis of metagenomic data has revealed the existence of previously unknown microbial taxa whose spatial distributions are limited by environmental conditions, ecological competition, and dispersal mechanisms. However, differences in genotypes that might lead biologists to designate two microbes as taxonomically distinct need not necessarily imply differences in ecological function. Hence, there is a growing need for large-scale analysis of the distribution of microbial function across habitats. Here, we present a framework for investigating the biogeography of microbial function by analyzing the distribution of protein families inferred from environmental sequence data across a global collection of sites. We map over 6,000,000 protein sequences from unassembled reads from the Global Ocean Survey dataset to protein families, generating a protein family relative abundance matrix that describes the distribution of each protein family across sites. We then use non-negative matrix factorization (NMF) to approximate these protein family profiles as linear combinations of a small number of ecological components. Each component has a characteristic functional profile and site profile. Our approach identifies common functional signatures within several of the components. We use our method as a filter to estimate functional distance between sites, and find that an NMF-filtered measure of functional distance is more strongly correlated with environmental distance than a comparable PCA-filtered measure. We also find that functional distance is more strongly correlated with environmental distance than with geographic distance, in agreement with prior studies. We identify similar protein functions in several components and suggest that functional co-occurrence across metagenomic samples could lead to future methods for de-novo functional prediction. We conclude by discussing how NMF, and other dimension reduction methods, can help enable a macroscopic functional description of marine ecosystems.
The changing psychological contract at work

Revisiting the job demands-control model The old adage that “change is here to stay” epitomises the workplace over the past three decades. And yet research in the field of occupational stress has been rooted in simple two or three dimensional models such as the job demands-control model. The article by de Croon and colleagues1 in this issue is important, even with some of its methodological shortcomings (self report, cross sectional design) and the increasing movement towards more complex stress-strain models,2 by generating and highlighting more occupation specific stressors in the process. This was started by Sparks and Cooper,3 in a range of occupational groups where it was shown that job demand and job control were only two among a range of factors that predicted job related strain outcomes. This is a significant development, because if we are to intervene effectively to minimise or eliminate “organisational sources” of stress, we must have a comprehensive and accurate assessment of the range of stressors that …
Regulation by epidermal growth factor of human squamous cell carcinoma plasminogen activator-mediated proteolysis of extracellular matrix.

The interaction of epidermal growth factor (EGF) with specific cell surface receptors initiates biochemical events in target cells which result in cellular proliferation and differentiation. In this report the regulation of extracellular-associated plasminogen activator (PA) production by EGF in human squamous cell carcinomas and its influence on tumor cell-mediated degradation of extracellular matrix (ECM) is described. The studies utilized the vulvar carcinoma cell line A431, which possesses an unusually large number of EGF receptors (EGF-Rs), and two A431 EGF-R expression variants (A5 and A7), which contain up to 20-fold fewer cell surface EGF-Rs. EGF enhanced the production of urokinase (u) PA activity by two- to threefold in A431 tumor cells, in a concentration-dependent manner, following a 24-h treatment, as determined by substrate hydrolysis assays, while no changes in tissue-type PA occurred. In contrast, A5 and A7 tumor cells failed to demonstrate such a response. Time course studies of the EGF-mediated induction of uPA activity in A431 tumor cells indicated that within 8 h after exposure to EGF, a twofold increase above basal untreated control levels was observed using the substrate hydrolysis assay. EGF increased the steady state levels of uPA mRNA threefold in A431 tumor cells following a 24-h treatment, while in contrast, no such response was observed in EGF-R variant tumor cells. In accord with an EGF enhancement of uPA mRNA levels in A431 tumor cells, a similar increase of two- to threefold in the de novo synthesis of [35S]methionine-radiolabeled uPA was observed by immunoprecipitation following EGF treatment, while no measurable increase was observed in the EGF-R tumor variants. A431 tumor cells progressively degraded [3H]glucosamine-radiolabeled bovine corneal subendothelial ECM in the presence of EGF, resulting in 8.7-, 4.3-, and 1.7-fold increases above untreated control values, after a 48-h exposure to 100, 10, and 1 ng/ml of EGF, respectively. In contrast, A5 and A7 tumor cells did not demonstrate an increase in ECM degradation in the presence of EGF, even though these tumor cells possessed the ability to degrade ECM in the absence of the growth factor. The observed increase in ECM degradation mediated by EGF in A431 tumor cells was dependent upon the presence of plasminogen and could be inhibited by an anticatalytic uPA monoclonal antibody. (ABSTRACT TRUNCATED AT 400 WORDS)
Venous Invasion in Colorectal Cancer: Impact of an Elastin Stain on Detection and Interobserver Agreement Among Gastrointestinal and Nongastrointestinal Pathologists

Venous invasion (VI) is an independent prognostic indicator in colorectal cancer and may prompt consideration for adjuvant chemotherapy in patients with stage II tumors. Recent evidence suggests that VI is underreported in colorectal cancer and that detection may be enhanced by an elastin stain. This study aimed (1) to determine the impact of an elastin stain on VI detection and on interobserver agreement between gastrointestinal (GI) and non-GI pathologists, and (2) to identify factors associated with increased VI detection. Forty hematoxylin and eosin (H&E)-stained slides were circulated to 6 GI and 6 non-GI pathologists who independently assessed the VI status as positive, negative, or equivocal. Six weeks later, 40 corresponding Movat-stained slides were recirculated together with the original H&E slides and reassessed for VI status. Detection of VI was >2-fold higher with a Movat stain compared with an H&E stain alone (46.4% vs. 19.6%, P=0.001). GI pathologists detected VI more frequently than non-GI pathologists on both H&E (30.0% vs. 9.2%, P=0.029) and Movat (58.3% vs. 34.6%, P=0.018) stains. There was higher interobserver agreement in the case of a Movat stain, particularly for extramural VI (H&E: &kgr;=0.23 vs. Movat: &kgr;=0.41). A poststudy survey indicated that GI pathologists and non-GI pathologists applied similar diagnostic criteria but that GI pathologists more frequently applied “orphan arteriole” and “protruding tongue” signs as diagnostic clues to VI. This study confirms that VI is underdetected on H&E and highlights the role of elastin staining in improving VI detection and interobserver agreement. Strategies to improve VI detection are warranted.
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads. Availability: The FindPeaks 3.1 package and manual, containing algorithm descriptions, usage instructions and examples, are available at http://www.bcgsc.ca/platform/bioinfo/software/findpeaks Source files for FindPeaks 3.1 are available for academic use. Contact: afejes@bcgsc.ca
Promoter Methylation of Protocadherin8 is an Independent Prognostic Factor for Biochemical Recurrence of Early-Stage Prostate Cancer

Background Protocadherin8 has been demonstrated to play critical roles in initiation and progression of several human cancers. It is frequently inactivated by promoter methylation in cancers and may be used as a potential biomarker. However, the methylation status of protocadherin8 and its clinical significance in prostate cancer remains largely unknown. The purpose of this study was to evaluate the clinical significance of protocadherin8 methylation in early-stage prostate cancer. Material/Methods The promoter methylation status of protocadherin8 in 162 prostate cancer tissues and 47 normal prostate tissues was examined using methylation-specific PCR (MSP). Subsequently, the relationships between protocadherin8 methylation and clinicopathological features of prostate cancer patients and biochemical recurrence-free survival of patients were analyzed. Results We found that protocadherin8 methylation occurred frequently in prostate cancer tissues but not in normal prostate tissues. Moreover, protocadherin8 methylation was significantly associated with advanced pathologic stage, higher level of preoperative prostate specific antigen (PSA), higher Gleason score, positive lymph node metastasis, and biochemical recurrence. In addition, patients with protocadherin8 methylated have shorter biochemical recurrence-free survival time than patients without. Multivariate Cox regression analysis revealed that protocadherin8 methylation was an independent predictor of biochemical recurrence-free survival in prostate cancer patients. Conclusions Promoter methylation of protocadherin8 is a frequent event in prostate cancer, and might be used as an independent prognostic factor for biochemical recurrence-free survival in patients with prostate cancer.
Differential Transcriptomic Response in the Spleen and Head Kidney Following Vaccination and Infection of Asian Seabass with Streptococcus iniae

Vaccination is an important strategy in the protection of aquaculture species from major diseases. However, we still do not have a good understanding of the mechanisms underlying vaccine-induced disease resistance. This is further complicated by the presence of several lymphoid organs that play different roles when mounting an immune response. In this study, we attempt to elucidate some of these mechanisms using a microarray-based approach. Asian seabass (Lates calcarifer) were vaccinated against Streptococcus iniae and the transcriptomic changes within the spleen and head kidney at one and seven days post-vaccination were profiled. We subsequently challenged the seabass at three weeks post-vaccination with live S. iniae and similarly profiled the transcriptomes of the two organs after the challenge. We found that vaccination induced an early, but transient transcriptomic change in the spleens and a delayed response in the head kidneys, which became more similar to one another compared to un-vaccinated ones. When challenged with the pathogen, the spleen, but not the head kidneys, responded transcriptomically at 25–29 hours post-challenge. A unique set of genes, in particular those involved in the activation of NF-κB signaling, was up-regulated in the vaccinated spleens upon pathogen challenge but not in the un-vaccinated spleens. A semi-quantitative PCR detection of S. iniae using metagenomic DNA extracted from the water containing the seabass also revealed that vaccination resulted in reduction of pathogen shedding. This result indicated that vaccination not only led to a successful immune defense against the infection, but also reduced the chances for horizontal transmission of the pathogen. In conclusion, we have provided a transcriptomic analysis of how the teleost spleen and head kidneys responded to vaccination and subsequent infection. The different responses from the two organs are suggestive of their unique roles in establishing a vaccine-induced disease resistance.
Altered PTEN expression as a diagnostic marker for the earliest endometrial precancers.

BACKGROUND PTEN tumor suppressor gene mutations are the most frequent genetic lesions in endometrial adenocarcinomas of the endometrioid subtype. Testing the hypothesis that altered PTEN function precedes the appearance of endometrial adenocarcinoma has been difficult, however, partly because of uncertainties in precancer diagnosis. METHODS Two series of endometrial cancer and precancer (endometrial intraepithelial neoplasia, as diagnosed by computerized morphometric analysis) tissue samples were studied, one for PTEN mutations by the use of denaturing gradient gel electrophoresis and another for PTEN protein expression by immunohistochemistry. Endometria altered by high estrogen levels that are unopposed by progestins-conditions known to increase cancer risk-were also studied by immunohistochemistry. Fisher's exact test was used for statistical analysis. RESULTS The PTEN mutation rate was 83% (25 of 30) in endometrioid endometrial adenocarcinomas and 55% (16 of 29) in precancers, and the difference in number of mutations was statistically significant (two-sided P =.025). No normal endometria showed PTEN mutations. Although most precancers and cancers had a mutation in only one PTEN allele, endometrioid endometrial adenocarcinomas showed complete loss of PTEN protein expression in 61% (20 of 33) of cases, and 97% (32 of 33) showed at least some diminution in expression. Cancers and most precancers exhibited contiguous groups of PTEN-negative glands, while endometria altered by unopposed estrogens showed isolated PTEN-negative glands. CONCLUSIONS Loss of PTEN function by mutational or other mechanisms is an early event in endometrial tumorigenesis that may occur in response to known endocrine risk factors and offers an informative immunohistochemical biomarker for premalignant disease. Individual PTEN-negative glands in estrogen-exposed endometria are the earliest recognizable stage of endometrial carcinogenesis. Proliferation into dense clusters that form discrete premalignant lesions follows.
The meaning of being in uncertainty after heart transplantation – an unrevealed source to distress

Background: As many as 88% of heart transplant recipients (HTRs) suffer from psychological distress. Both psychosocial factors and physical health are associated with increased psychological distress. However, the causes and impacts of psychological distress are unclear. HTRs strive for a sense of control over their health and daily lives in order to improve their psychological well-being. Perceived control was found to be related to the patients’ construction of normality, their emotional state, as well as their thoughts and feelings of uncertainty about the future. Aim: An in-depth exploration of the meaning of uncertainty during the first year after a heart transplantation (HTX). Method: A phenomenological–hermeneutic method was employed. Interviews were conducted with 14 patients, four women and ten men, with a mean age of 51 years (range: 28–67 years). Results: Being in uncertainty after HTX means losing a sense of coherence, which shatters the HTR’s whole worldview. The HTRs search for meaning and strive for coherence, which is no longer achievable. By using a nursing theory, we understand that uncertainty should be seen as a natural state among HTRs. It constitutes the starting point from which the HTRs can reorganise their self-structure and find a new view of life. When striving for normality, certainty and predictability (i.e., the healthcare professional’s perspective), we block or prolong this process, thus causing distress among HTRs because they are unable to create a new orientation in life. Conclusion: This study presents a hypothesis of the primary cause of psychological distress after HTX and provides a useful framework for how to approach this condition.
Assessment of Factors Affecting Implementation of Nursing Process Among Nurses in Selected Governmental Hospitals, Addis Ababa, Ethiopia; Cross Sectional Study

Background: Nursing Process is a systematic problem-solving approach used to identify, prevent and treat actual or potential health problems and promote wellness. It has five steps- assessment, diagnosis, planning, implementation, and evaluation. Objective: To assess factors affecting implementation of nursing process among nurses in selected governmental hospitals from February-April, 2011 at Addis Ababa, Ethiopia. Method: A cross-sectional quantitative study was conducted on selected governmental hospitals in Addis Ababa. Purposive sampling was used for selection of hospitals. Black Lion, St. Paul, Ras Desta Damitew Memorial, and Yekatit 12 hospitals were convenient for the study. The sample size was 202. Data was analyzed using SPSS 16th version. Result: Nurses working in a stressful working environment were 2.8 (adjusted OR: 0.357, 95%CI: (0.157-0.814)) times less likely to implement nursing process than disorganized working environment adjusting for facility accessibility, knowledge, and sex. Forty eight (25%) of respondents were anxious from high patient flow. Among those 15(31.3%), 22(45.8%), and 11(22.9%) have committed knowledge, executive, and slip/slap error respectively. Highly knowledgeable respondents were 38.913 (Adjusted OR: 38.913, 95%CI: (10.3-147.006) times more likely to implement nursing process than low knowledge group nurses adjusted for working environment, facility, and sex. Conclusion: The study has identified organizational factors, patient related factors, and level of knowledge and skill were among those factors highly influenced nursing process implementation. This factors cause poor quality of nursing care, disorganized caring system, conflicting role, medication error and readmission with similar problem, dissatisfaction with the care patients have received, and increased mortality.
Association of claw disorders with subclinical intramammary infections in Egyptian dairy cows

Aim: Bovine mastitis and lameness are the most common production diseases affecting dairy farms worldwide resulting in huge economic impact and impaired animal welfare. The objective of this field study was to investigate the association of infectious and non-infectious claw disorders with the occurrence of subclinical intramammary infections (IMIs) diagnosed by California mastitis test (CMT) in dairy cows under Egyptian conditions. Materials and Methods: A total of 43 dairy cows were included in this field study. Subclinical IMI was diagnosed by CMT on all lactating quarters of cows. A cow was considered to have subclinical IMI if it had at least one subclinically infected quarter (≥3). Cows were inspected carefully for claw disorders that recorded based on type and site. Locomotion and body condition scores were also recorded for each cow in addition to the limb affected. The association between the CMT and other explanatory variables was tested by Fisher’s exact test. Results: The prevalence of infectious and non-infectious claw disorders was 81.4% (35/43) and 32.6% (14/43), respectively. Digital dermatitis (DD) and heel horn erosion were the most prevalent infectious type with 79% (34/43) and 58% (25/43), respectively, while wall fissure was the most identified non-infectious one 11.6% (5/43). The prevalence of claw disorders in hind limbs was 88.4% (38/43) and 11.6% (5/43) in the forelimbs. Infectious claw disorders were significantly associated with the subclinical IMI diagnosed by CMT (p<0.05). Non-infectious claw affections, locomotion score, body condition score, and the affected limb had no association with the occurrence of subclinical IMI. Conclusion: DD is the highest prevalent claw disorder observed in dairy cows in Egypt. The hind limbs are more susceptible to claw disorders than the forelimbs. Infectious type of claw disorders is significantly associated with subclinical IMI diagnosed by CMT in dairy cows under Egyptian conditions indicating that the infectious types of claw affections may influence the udder health.
Promoting Research‐Based Nursing: The Nurse Administrator's Role

As the practice of research increasingly becomes a part of the nursing profession, nurses must develop their ability to evaluate and incorporate the findings gained through the research process. This article reports the results of a survey aimed at determining problem areas existing among nursing staffs in understanding, accepting, and incorporating research findings. The report will help nursing administrators identify specific factors that inhibit the use of research findings and improve the conditions for incorporating research in their facilities.
On Assessing Individual Differences in Rumination on Sadness

The Rumination on Sadness Scale (RSS), an individual-difference measure of rumination on sadness, was developed as an alternative to the Ruminative Responses scale of the Response Styles Questionnaire (RRRSQ; Nolen-Hoeksema & Morrow, 1991). Research has shown the RRRSQ to consist of multiple, not highly intercorrelated factors; only 1 factor explicitly addresses rumination. In Study 1, a 1-factor solution to a principal components analysis was shown to hold for responses to the RSS. The RSS was also shown to be reliable. In Study 2, convergent and discriminant validity of the RSS were assessed. In Study 3, individuals with high RSS scores exhibited more distress regarding current concerns with the introduction of a delay period (to allow them to ruminate) after a sad mood induction.