Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny of Microorganisms Populating a Thick, Subaerial, Predominantly Lithotrophic Biofilm at an Extreme Acid Mine Drainage Site

ABSTRACT An unusually thick (∼1 cm) slime developed on a slump of finely disseminated pyrite ore within an extreme acid mine drainage site at Iron Mountain, near Redding, Calif. The slime was studied over the period of 1 year. The subaerial form of the slime distinguished it from more typical submerged streamers. Phylogenetic analysis of 16S rRNA genes revealed a diversity of sequences that were mostly novel. Nearest relatives to the majority of sequences came from iron-oxidizing acidophiles, and it appears that iron oxidation is the predominant metabolic characteristic of the organisms in the slime. The most abundant of the 16S rRNA genes detected were from organisms related toLeptospirillum species. The dominant sequence (71% of clones) may represent a new genus. Sequences within theArchaea of the Thermoplasmales lineage were detected. Most of these were only distantly related to known microorganisms. Also, sequences affiliating withAcidimicrobium were detected. Some of these were closely related to “Ferromicrobium acidophilus,” and others were affiliated with a lineage only represented by environmental clones. Unexpectedly, sequences that affiliated within the delta subdivision of the Proteobacteria were detected. The predominant metabolic feature of bacteria of this subdivision is anaerobic sulfate or metal reduction. Thus, microenvironments of low redox potential possibly exist in the predominantly oxidizing environments of the slime. These results expand our knowledge of the biodiversity of acid mine drainage environments and extend our understanding of the ecology of extremely acidic systems.
Regulation of Histone Deposition Proteins Asf1/Hir1 by Multiple DNA Damage Checkpoint Kinases in Saccharomyces cerevisiae

CAF-1, Hir proteins, and Asf1 are histone H3/H4 binding proteins important for chromatin-mediated transcriptional silencing. We explored genetic and physical interactions between these proteins and S-phase/DNA damage checkpoint kinases in the budding yeast Saccharomyces cerevisiae. Although cells lacking checkpoint kinase Mec1 do not display defects in telomeric gene silencing, silencing was dramatically reduced in cells lacking both Mec1 and the Cac1 subunit of CAF-1. Silencing was restored in cac1Δ and cac1Δ mec1Δ cells upon deletion of Rad53, the kinase downstream of Mec1. Restoration of silencing to cac1Δ cells required both Hir1 and Asf1, suggesting that Mec1 counteracts functional sequestration of the Asf1/Hir1 complex by Rad53. Consistent with this idea, the degree of suppression of silencing defects by rad53 alleles correlated with effects on Asf1 binding. Furthermore, deletion of the Dun1 kinase, a downstream target of Rad53, also suppressed the silencing defects of cac1Δ cells and reduced the levels of Asf1 associated with Rad53 in vivo. Loss of Mec1 and Rad53 did not alter telomere lengths or Asf1 protein levels, nuclear localization, or chromosome association. We conclude that the Mec1 and Dun1 checkpoint kinases regulate the Asf1-Rad53 interaction and therefore affect the activity of the Asf1/Hir complex in vivo.
Syndecan-1 Expression – A Novel Prognostic Marker in Pancreatic Cancer

Objective: Syndecan-1 is a transmembrane receptor that participates in cell-cell and cell-matrix interactions, cell proliferation and cell migration. Expression of syndecan-1 is downregulated in many cancers, but in pancreatic ductal adenocarcinoma it is upregulated. Method: We studied the immunohistochemical expression of syndecan-1 in 144 pancreatic adenocarcinomas and evaluated the prognostic value of syndecan-1 expression. Formalin-fixed, paraffin-embedded specimens were stained with mouse monoclonal antibody B-B4 against human syndecan-1. The epithelial and stromal staining was separately evaluated and compared with patient survival, clinical stage and histological grade. Result: Epithelial immunoreactivity was observed in most of the pancreatic carcinoma samples: in 70 (49%) of the samples the epithelial staining was weak, in 48 (33%) moderate, in 18 (12%)strong and in only 8 (6%) of the samples the epithelial staining was negative. Stromal staining was weak in 24 (17%), moderate in 31 (22%), strong in 11 (8%) and negative in 78 (54%) of the pancreatic carcinoma samples. Lack of stromal expression predicted a better prognosis (p = 0.002; HR 1.7) and it was independent of stage (p = 0.01; HR = 1.5) and grade (p = 0.0004; HR 2.1) in multivariate analysis. Epithelial expression predicted better prognosis for patients that underwent surgery for cure (n = 94, p = 0.03). Conclusion: Stromal syndecan-1 expression is an independent prognostic marker in pancreatic cancer, whereas epithelial syndecan-1 expression predicts better prognosis only in resectable disease.
Effects of Land Use Change, Cultivation, and Landscape Position on Prairie Soil Organic Carbon Stocks

Temperate grassland soils are typically a sink for carbon. However, it is estimated that up to 99% of tallgrass prairies in North America have been converted to another land use. These conversions can lead to increased soil erosion and soil organic carbon (SOC) mineralization rates, turning a large carbon sink into a source. The purpose of this study was to compare by land use the retention of SOC, TSN, and fly ash on sloping landscapes with an emphasis on measuring the subsoil in addition to the surface soil. Eight paired plots were established on adjacent, sloping landscape profiles in western Iowa; one site a cropland and the other a remnant tallgrass prairie. The prairie landscape had a baseline SOC stock of 232 Mg-C ha-1. After roughly 150 years of agriculture the cropland had 52% less SOC, 39% less TSN, and 22% less fly ash which equates to annual losses of 0.55 Mg-C ha-1 yr-1, 0.04 Mg-N ha-1 yr-1, and 0.0002 Mg-fly ash ha-1 yr-1.
High-Resolution Imaging of Intravascular Atherogenic Inflammation in Live Mice

Rationale: The inflammatory processes that initiate and propagate atherosclerosis remain poorly understood, largely because defining the intravascular behavior of immune cells has been technically challenging. Respiratory and pulsatile movements have hampered in vivo visualization of leukocyte accumulation in athero-prone arteries at resolutions achieved in other tissues. Objective: To establish and to validate a method that allows high-resolution imaging of inflammatory leukocytes and platelets within the carotid artery of atherosusceptible mice in vivo. Methods and Results: We have devised a procedure to stabilize the mouse carotid artery mechanically without altering blood dynamics, which dramatically enhances temporal and spatial resolutions using high-speed intravital microscopy in multiple channels of fluorescence. By applying this methodology at different stages of disease progression in atherosusceptible mice, we first validated our approach by assessing the recruitment kinetics of various leukocyte subsets and platelets in athero-prone segments of the carotid artery. The high temporal and spatial resolution allowed the dissection of both the dynamic polarization of and the formation of subcellular domains within adhered leukocytes. We further demonstrate that the secondary capture of activated platelets on the plaque is predominantly mediated by neutrophils. Finally, we couple this procedure with triggered 2-photon microscopy to visualize the 3-dimensional movement of leukocytes in intimate contact with the arterial lumen. Conclusions: The improved imaging of diseased arteries at subcellular resolution presented here should help resolve many outstanding questions in atherosclerosis and other arterial disorders.
Limitation of Collagen Cross-Linking With Hypoosmolar Riboflavin Solution: Failure in an Extremely Thin Cornea

Purpose: We report a case of failure of corneal collagen cross-linking (CXL) for progressive keratoconus after preoperative stromal swelling with hypoosmolar riboflavin solution in an extremely thin cornea. Methods: CXL was performed using the protocol established for the treatment of thin corneas. Preoperative minimal thickness after abrasion was 268 μm and increased to 406 μm after swelling with hypoosmolar riboflavin solution. Results: Despite CXL, a distinct progression of up to 1.9 diopters was observed at 3 months after the procedure on the anterior corneal surface. At 6 months after CXL, progression had increased to 2.3 diopters. Although swelling with hypoosmolar riboflavin solution was effective and led to a preoperative thickness of more than 400 μm, the increase in biomechanical resistance was not sufficient to arrest the progression of the disease. Conclusions: Little is known about the minimal stromal thickness required for effective CXL to occur. Although swelling with hypoosmolar riboflavin solution over 400 μm and safety of the procedure can be achieved in even thinner corneas, the outcome of this case suggests that a minimal preoperative stromal thickness of 330 μm needs to be respected for a successful CXL procedure.
Metabolic fingerprints of proliferative diabetic retinopathy: an 1H-NMR-based metabonomic approach using vitreous humor.

PURPOSE To explore the metabolic profile of vitreous fluid of patients with proliferative diabetic retinopathy (PDR) using 1H-NMR-based metabonomic analysis. METHODS 1H-NMR spectra were acquired from vitreous samples obtained during vitrectomy from 22 patients with type 1 diabetes with PDR and from 22 nondiabetic patients with macular hole (control group). Data analysis included a principal component analysis and partial least squares discriminant analysis (PLS-DA). In addition, 1H-(1)H and 1H-(13)C HMQC correlation spectra were acquired for the identification of metabolites. Furthermore, the main metabolites accounting for the differences in metabolic profile were assessed by current biochemical methods. RESULTS Lactate was the most abundant metabolite, and it was present at higher levels in samples from PDR patients than from nondiabetic patients (P=0.02). Glucose was significantly higher in samples from PDR patients than nondiabetic patients (P=0.03). After removing the lactate peak at 1.35 ppm and with the use of PLS-DA, a model was obtained that was able to correctly classify 19 of 22 patients with PDR and 18 of 22 controls, resulting in a sensitivity of 86% and a specificity of 81%. The main metabolites involved in this specific pattern recognition were galactitol and ascorbic acid (AA); levels of both were significantly lower in PDR patients. CONCLUSIONS 1H-NMR-based metabonomic analysis of vitreous fluid permits the obtainment of a metabolic signature of PDR. Apart from the higher abundance of lactate and glucose, significant deficits of galactitol and AA are the main metabolic fingerprints of vitreous fluid from PDR patients.
Prospective Study of Anxiety and Incident Stroke

Background and Purpose— Higher levels of anxiety are associated with increased risk for coronary heart disease. However, few studies have investigated whether anxiety is associated with stroke risk. The purpose of this study was to examine the association between anxiety symptoms and incident stroke in a nationally representative longitudinal study of the US population. Methods— Participants (n=6019) in the First National Health and Nutrition Examination Survey were assessed at baseline and followed for 16.29±4.75 years. Multivariate Cox proportional hazards regression models were used to estimate hazard ratios and 95% confidence intervals of incident stroke associated with a 1 SD increase in anxiety symptoms. Models were adjusted for standard cardiovascular risk factors and additionally for depression. Results— A total of 419 incident stroke cases were identified from hospital/nursing home discharge reports and death certificates. Reporting more anxiety symptoms at baseline was associated with increased risk of incident stroke after adjusting for standard biological and behavioral cardiovascular risk factors (hazard ratio, 1.14; 95% confidence interval, 1.03–1.25). Findings persisted when additionally controlling for depression. Exploratory analyses considering the role of potential confounding versus pathway variables suggested that behavioral factors may be a key pathway linking anxiety to stroke risk. Conclusions— Higher anxiety symptom levels were associated prospectively with increased risk for incident stroke independent of other risk factors, including depression. Anxiety is a modifiable experience that is highly prevalent among the general population. Its assessment and treatment may contribute to developing more effective preventive and intervention strategies for improving overall cardiovascular health.
Nurses' descriptions of caring for culturally diverse clients.

The nursing profession has responded to today's cultural diversity through theory development, association statements, research, and inclusion of cultural content in nursing curricula. This qualitative study was completed to explore whether this increased attention to cultural diversity is resulting in culturally sensitive nursing care. In this preliminary description of cross-cultural care, eight recently graduated nurses were each interviewed twice. Caring for culturally diverse clients is reflected by these participants as complex and challenging, due to the interrelatedness of multiple personal and contextual factors. Nurses' commitment to caring for culturally diverse clients varies, ranging from "resistant" to "generalist" to "impassioned. " Contextual factors include the setting of health care, the support of colleagues, the institutional climate, the foundation of education, and the presence of racism. Despite the nursing profession's attention directed toward issues of cultural diversity, it seems that the goal of culturally sensitive care remains a distant ideal.
A Flooding Method for Exchanging Routing Information in Power&#8211; Law Networks

Recent measurement studies of the Internet topology show that the connectivities of nodes exhibit power-law attributes. This topology has two main characteristics: many nodes have a small number of links while a few nodes have a large number of links; and there are fewer hop-counts between nodes. Previous studies of routing mechanisms have evaluated their validity or effectiveness in relatively small networks. However, an evaluation of power-law networks is also needed to clarify their actual validity. In this paper, we evaluate some of the flooding mechanisms used in routing protocols. Our simulation results show that in a power-law network, the flooding mechanism does not scale well due to the concentration of message, whereas random networks that do not have power-law attributes actually scale well. To reduce the concentration of messages, we propose an efficient flooding method for power-law networks. Our method uses probabilistic flooding in which each node relays routing information with a certain probability. Routing information is also exchanged periodically to prevent information mismatches between nodes. The simulation results showed that, compared to conventional flooding approaches, our method reduced the amount of traffic by 50%
Role of uncontrolled HIV RNA level and immunodeficiency in the occurrence of malignancy in HIV-infected patients during the combination antiretroviral therapy era: Agence Nationale de Recherche sur le Sida (ANRS) CO3 Aquitaine Cohort.

BACKGROUND Human immunodeficiency virus (HIV)-infected patients are at higher risk of malignancies. In addition to traditional determinants, a specific deleterious effect of HIV and immunodeficiency is speculated. We aimed at studying the association between immunological and virological characteristics of HIV-infected patients in care and the risk of acquired immunodeficiency syndrome (AIDS)-defining and non-AIDS-defining malignancies. METHODS Patients consecutively enrolled in the hospital-based Agence Nationale de Recherche sur le Sida (ANRS) CO3 Aquitaine Cohort were included if the duration of follow-up was >3 months during the period 1998-2006. Multivariate modeling used an extended Cox proportional hazards model for time-dependent covariates and delayed entry. RESULTS The 4194 patients included in the study developed 251 first malignancies during 22,389 person-years. A higher incidence of AIDS-defining malignancies (107 cases) was independently associated with (1) both longer and current exposures to a plasma HIV RNA level >500 copies/mL (hazard ratio [HR], 1.27 per year [P<.001] and 3.30 [P<.001], respectively) and (2) both longer and current exposure to a CD4(+) cell count <200 cells/mm(3) (HR, 1.36 per year [P<.001] and 6.33 [P<.001], respectively). A higher incidence of non-AIDS-defining malignancies (144 cases) was independently associated with longer and current exposure to a CD4(+) cell count <500 cells/mm(3) (HR, 1.13 per year [P=.01] and 2.07 [P<.001], respectively) and male sex (HR, 1.69; P=.02) but not with plasma HIV RNA level (P=.49 and P=.10 for cumulative and current exposures, respectively). CONCLUSIONS Uncontrolled plasma HIV RNA level was independently associated with a higher likelihood of developing AIDS-defining malignancies, whereas immunosuppression was associated with a higher risk of developing any type of malignancies. Antiretroviral treatment should aim at reaching and maintaining a CD4(+) count >500 cells/mm(3) to prevent the occurrence of malignancy, this should be integrated to malignancy-prevention policies.
Characterising the Use of Encapsulation in Object Oriented Systems November

Software is commonly very large and complex, and consequently hard to develop, understand and maintain. Encapsulation is the practice of breaking a system up into well-defined pieces and hiding internal details within each piece. It supports modularisation and information hiding, making it one of the most fundamental tools software developers have for managing complexity. Object oriented design heuristics have been proposed to help developers achieve better software designs and thus improve overall software quality; many of these design heuristics concern the use of encapsulation or are based on underlying assumptions about encapsulation. However, design advice in this area often conflicts. Little is known about how developers apply encapsulation in practice. In this work, we identify and compare two radically different schools of thought that underpin encapsulation policies and lead to the conflicting encapsulation advice. We conducted a survey to reveal which encapsulation policy is more intuitive, and found that novices’ intuition about encapsulation differs from the encapsulation mechanisms supported by languages such as Java and C#. Following the survey, we empirically analysed encapsulation in real-world software to determine which encapsulation policies are followed in practice, uncovering a general culture of confusion and inconsistency around the use of encapsulation. This finding leads us to propose refactoring tools and a visualisation for helping developers improve encapsulation in software.
The Individual Environment Nexus: Impact of Promotion Focus and the Environment on Academic Scientists’ Entrepreneurial Intentions

Using a sample of academic scientists, we show that promotion focus interacts with the work and family environments to predict academic scientists' entrepreneurial intentions. Concretely, we find that the relationship between promotion focus and entrepreneurial intentions is particularly strong when scientists' parents have owned a business and when they work in laboratories with more industry-financed research. As such, our study complements prior research into entrepreneurial intentions in academia, which has to a large extent focused on individual characteristics as determinants of such intentions. We highlight the vital role of the environment in encouraging academic entrepreneurship. Without a supportive environment, high promotion focus individuals are unlikely to become entrepreneurs. Our study has implications for the entrepreneurship literature, in particular academic entrepreneurship, and we call for more research on the individual-environment nexus.
Validation of a diagnostic multiplex polymerase chain reaction assay for infectious posterior uveitis.

OBJECTIVE To validate a multiplex polymerase chain reaction (PCR) assay capable of simultaneously screening vitreous biopsy specimens for a panel of common pathogens in posterior uveitis. METHODS A multiplex PCR assay using novel primer sets for cytomegalovirus (CMV), herpes simplex virus (HSV), varicella zoster virus (VZV), and Toxoplasma gondii was developed. The sensitivity of the assay was determined for purified pathogen DNA. Twenty-one vitreous specimens from patients with posterior uveitis were tested by both multiplex and monoplex PCR. RESULTS Fewer than 10 genomes of VZV and fewer than 100 genomes of HSV, CMV, and T gondii could be detected using the new primer sets. When used in multiplex, the assay lost less than 1 log of sensitivity. Monoplex PCR detected pathogen DNA in 18 of 21 patient samples; multiplex PCR detected pathogen DNA in 15 of the 18 samples positive by monoplex PCR. None of 10 negative control samples were positive for pathogen DNA. CONCLUSIONS Multiplex PCR has adequate sensitivity to simultaneously screen a substantial differential diagnosis for posterior uveitis in a single reaction, without loss of specificity. This assay may reduce the time and cost involved in PCR-based molecular diagnostics of infectious pathogens. CLINICAL RELEVANCE Mutiplex PCR may allow rapid diagnosis of infectious posterior uveitis.
Tree tribes and lower bounds for switching lemmas

We show tight upper and lower bounds for switching lemmas obtained by the action of random $p$-restrictions on boolean functions that can be expressed as decision trees in which every vertex is at a distance of at most $t$ from some leaf, also called $t$-clipped decision trees. More specifically, we show the following: $\bullet$ If a boolean function $f$ can be expressed as a $t$-clipped decision tree, then under the action of a random $p$-restriction $\rho$, the probability that the smallest depth decision tree for $f|_{\rho}$ has depth greater than $d$ is upper bounded by $(4p2^{t})^{d}$. $\bullet$ For every $t$, there exists a function $g_{t}$ that can be expressed as a $t$-clipped decision tree, such that under the action of a random $p$-restriction $\rho$, the probability that the smallest depth decision tree for $g_{t}|_{\rho}$ has depth greater than $d$ is lower bounded by $(c_{0}p2^{t})^{d}$, for $0\leq p\leq c_{p}2^{-t}$ and $0\leq d\leq c_{d}\frac{\log n}{2^{t}\log t}$, where $c_{0},c_{p},c_{d}$ are universal constants.