Miracle-dz/UniFAR-FTUs huggingface dataset:
Degradation of pentachlorophenol by nanoscale Fe and Ni/Fe particles

Pentachlorophenol (PCP), a notoriously recalcitrant and toxic organic contaminant, was investigated for its degradation with nanoscale Fe and Ni/Fe particles. Compared with the bare nano Fe, the bimetallic Ni/Fe nanoparticles exhibited much higher reactivity. The rate of PCP transformation can be described by pseudo first-order kinetics, and the apparent rate constants were calculated to be 0.04 and 1.19 h−1 with the nanoscale Fe and Ni/Fe, respectively. The enhanced performance of the bimetallic nanoparticles may be attributed to the increased of surface area, generation, storage and activation of hydrogen, and also unique nano- and subnano- scale structures formed on the nanoparticle surface.
Simultaneous Amplification and Identification of 25 Human Papillomavirus Types with Templex Technology

ABSTRACT The majority of existing human papillomavirus (HPV) genotyping assays are based on multiplex PCR using consensus or degenerate primers. We developed a Templex HPV assay that simultaneously detects and identifies 25 common HPV genotypes in a single-tube reaction using type-specific primers for the HPV-specific E6 and E7 genes. The analytical sensitivities of the Templex assay for HPV type 16 (HPV-16), -18, and -56 were 20, 100, and 20 copies per reaction mixture, respectively. The Templex assay provides semiquantitative information on each type when multiple HPV types coexist in one reaction. We tested 109 clinical cervical specimens previously evaluated with the Digene HC2 high-risk HPV DNA test and found 95.4% concordance between the assay results. The Templex assay provided type-specific results and found multiple types in 29.2% (14 of 48) of high-risk HPV-positive samples. The entire Templex procedure, including DNA extraction, can be completed within 5 hours, providing a rapid and reliable diagnostic tool for HPV detection and typing that is amenable to automation.
Triangle-free subgraphs with large fractional chromatic number

It is well known that for any integers k and g, there is a graph with chromatic number at least k and girth at least g. In 1960s, Erdös and Hajnal conjectured that for any k and g, there exists a number h(k,g), such that every graph with chromatic number at least h(k,g) contains a subgraph with chromatic number at least k and girth at least g. In 1977, Rödl proved the case when $g=4$ , for arbitrary k. We prove the fractional chromatic number version of Rödl’s result.
Functional Roles of microRNAs in Cancer: microRNomes and oncomiRs Connection

Cancer is a complex group of diseases characterized by the presence of cells with uncontrolled growth, and high proliferation capacity. The complexity of cancer properties was outlined as the “hallmarks of cancer” a decade ago by Hanahan and Weinberg [1], and it comprises six alterations in cell physiology that dictate malignant growth including: (i) self-sufficiency in growth signals and uncontrolled growth of cells; (ii) insensitivity to antigrowth signals; (iii) evasion of apoptosis; 4 (iv) limitless replicative potential; (v) sustained angiogenesis; and (vi) acquisition of invasive properties to adjacent tissues and organs [1, 2]. These processes are regulated by protein-encoding genes whose expression switches-on or off during development and in response to cellular environment. Altered versions of the genes (tumor-suppressor genes and proto-oncogenes) which control the normal cellular processes arise from mutations, or expression deregulation in a multistep process resulting in cancer [3]. At the end of the transformation process, the malignant cells acquire growth independence, invasiveness and resistance to senescence and apoptosis. The acquired capabilities of cells to metastasize to other tissues and organs represent the most deadly hallmark of cancer [4-6].
Inhibition of mRNA translation extends lifespan in Caenorhabditis elegans

Protein synthesis is a regulated cellular process that links nutrients in the environment to organismal growth and development. Here we examine the role of genes that regulate mRNA translation in determining growth, reproduction, stress resistance and lifespan. Translational control of protein synthesis by regulators such as the cap‐binding complex and S6 kinase play an important role during growth. We observe that inhibition of various genes in the translation initiation complex including ifg‐1, the worm homologue of eIF4G, which is a scaffold protein in the cap‐binding complex; and rsks‐1, the worm homologue of S6 kinase, results in lifespan extension in Caenorhabditis elegans. Inhibition of ifg‐1 or rsks‐1 also slows development, reduces fecundity and increases resistance to starvation. A reduction in ifg‐1 expression in dauers was also observed, suggesting an inhibition of protein translation during the dauer state. Thus, mRNA translation exerts pleiotropic effects on growth, reproduction, stress resistance and lifespan in C. elegans.
Evaluating different methods of using chlorophyll meter for diagnosing nitrogen status of summer maize

Precision nitrogen (N) management has a great potential to improve N use efficiency. It will require timely and efficient diagnosis of crop N status. Chlorophyll meter sensor is one of the commonly used diagnostic tools for crop nitrogen status, and different methods have been developed, including nitrogen sufficiency index, and ratio of chlorophyll meter values at different leaf positions. Up to date, no study has compared these two different methods. Therefore, the objective of this study is to evaluate these two different methods to identify a suitable method for diagnosing N status of summer maize in North China Plain. A N rate experiment was conducted in 2009 and 2010 at the Quzhou Experiment Station of China Agriculture University in Hebei Province of North China Plain. A randomized complete block design was used with five treatments and four replications. Chlorophyll meter values (CMV) were taken from the top first to third fully expanded leaves of 30 summer maize plants in each plot at growth stages V6, V12, VT in 2009 and V6, VT in 2010. On the same day, plant samples were collected for determination of shoot biomass and N concentration using the Kjeldahl method. The results indicated that the N sufficiency index (NSI) was significantly correlated to N nutrition index (NNI), and it is a suitable indicator of N status of summer maize. Using a critical NSI threshold value of 97%, we achieved an average accuracy of 86% in diagnosing N status of summer maize using the top 2 fully expanded leaf. This approach can eliminate the impact of growth stages, seasonal variation, variety, stress and other factors. The ratio of chlorophyll meter values is not a suitable method for summer maize N status diagnosis. More studies are needed to verify these results.
Credentialing for breast lymphatic mapping: how many cases are enough?

OBJECTIVE To evaluate credentialing issues for sentinel lymphatic mapping for breast cancer. SUMMARY BACKGROUND DATA The sentinel lymph node (SLN) is defined as the first lymph node receiving lymphatic drainage from a tumor. The SLN accurately reflects the status of the axillary nodes in patients with early-stage breast cancer, and SLN mapping is gaining widespread acceptance. Few of the many published feasibility studies of lymphatic mapping for breast cancer have adequate numbers to assess credentialing issues for this new procedure. METHODS Five hundred consecutive SLN biopsies were performed at one institution, over a 20-month period, by eight surgeons, using isosulfan blue dye and technetium-labeled sulfur colloid. The authors reviewed each surgeon's success rate in finding the SLN, and false-negative rate, relative to level of experience with the technique. RESULTS Lymphatic mapping performed by an experienced surgeon (surgeon A, B, or C) was associated with a higher success rate (94%) than when it was performed by one with less experience (86%). Ten failed mapping procedures occurred in the first 100 cases. For each of the ensuing 100 cases, there were eight, six, six, and four failed mapping procedures, suggesting that increasing experience does not eradicate failed mapping procedures completely. The false-negative rate among 104 patients in whom axillary dissection was planned in advance was 10.6% (5/47). Most false-negative results occurred early in the surgeon's experience: when the first six cases of every surgeon were excluded, the false-negative rate fell to 5.2% (2/38). CONCLUSIONS With increasing experience, failed SLN localizations and false-negative SLN biopsies occur less often. Combined dye and isotope localization, enhanced histopathology, a backup axillary dissection, and judicious case selection are required to avoid the high false-negative rate of one's early experience.
Use of Complementary and Alternative Medicine by Cancer Patients at a Montreal Hospital

Objectives: To assess feasibility of methods for a future study of complementary and alternative medicine (CAM) use by cancer patients treated in conventional health care settings. Methods: Patients aged 18 years and older, fluent in English or French, and diagnosed with cancer from St. Mary’s Hospital Center, Montreal, Canada participated. Feasibility was measured by the rates of participation and CAM use in the past 1 and 12 months. Following the survey, one patient focus group was held to better understand cancer patient perspectives on discussions of CAM that occur or not with their family physicians. Results: Of 103 patients approached, 100 (97.1%; 77% female, 87% white) participated. Overall, 86% and 91% of respondents used at least one CAM in the past 1 and 12 months, respectively. More patients with breast compared with colorectal and other cancers (90.2%, 86.2%, and 80%, respectively) used CAM in the previous year. In the past 1 and 12 months, natural health products were used by 70% and 80% of respondents, respectively; mind–body therapies by 61% and 64%, respectively, and CAM practitioners by 11% and 29%, respectively. More than 98% of patients used CAM to improve quality of life and 68% disclosed CAM use to their physicians. Four of 5 focus group participants used CAM. Patient–physician CAM discussions varied from receiving a CAM referral to complete dismissal of the topic. Conclusion: Recruitment methods were well accepted but a sampling strategy stratified by sex and ethnicity will ensure sufficient representation by males and non-whites. Whereas disclosure of natural health products use is occurring, informative CAM discussion is not.
Continuous plume monitoring using wireless sensors: proof of concept in intermediate scale tank.

The current practice for monitoring of subsurface plumes involves the collection of water samples from sparsely distributed monitoring wells and laboratory analysis to determine chemical concentrations. In most field situations, cost and time constraints limit the number of samples that could be collected and analyzed for continuous monitoring of large, transient plumes. With the development of wireless sensor networks (WSNs), that allow sensors to be incorporated into a distributed wireless communication and processing system, the potential exists to develop new, efficient, economical, large-scale subsurface data collection and monitoring methods. This paper presents a proof-of-concept study conducted in a two-dimensional synthetic aquifer constructed in an intermediate scale test tank to demonstrate the feasibility of using WSN for subsurface plume monitoring. The tank was packed to represent a heterogeneous aquifer, and a sodium bromide tracer was used to create a plume. A set of ten wireless sensor nodes (motes) equipped with conductivity probes to measure electrical conductivity formed the network. Software for automated data acquisition was developed and tested. Results of two experiments conducted using this test system are presented. The lessons learned from the first experiment were used to make modifications to the way the sensors were placed, how they were calibrated and how the sensors were interfaced with the data acquisition system. The findings are used to identify future research directions and issues that need to be addressed before field implementations of a WSN based data collection system for plume monitoring.
Innumeracy and Unpacking: Bridging the Nomothetic/Idiographic Divide in Violence Risk Assessment

Structured methods to assess violence risk have proliferated in recent years, but such methods are not uncontroversial. A "core controversy" concerns the extent to which an actuarial risk estimate derived at the group level should-morally, logically, or mathematically-apply to any particular individual within the group. This study examines the related psychological question: When do people apply group-level risk estimates to the individual case? We manipulated whether an actuarial risk estimate is "unpacked;" that is, whether the risk factors on which the estimate is based are articulated. Our findings indicate that the degree of unpacking (e.g., listing six vs. three risk factors) increased the likelihood that jury-eligible citizens will apply an actuarial risk estimate in their decision to civilly commit a particular respondent. Unpacking also increased the perceived relevance of the group-level risk estimate to the individual case. We then split the sample based on self-reported numeracy, defined as "ability with or knowledge of numbers. " Numeracy moderates the unpacking effect in that unpacking only made a difference for the innumerate participants. The psychological approach we take to the question of group-to-individual inference is not limited to violence-risk assessment, and may apply to many other areas of law in which group-to-individual inferences are frequently, if controversially, made.
Low Affinity and Slow Na+ Binding Precedes High Affinity Aspartate Binding in the Secondary-active Transporter GltPh *

Background: GltPh couples uptake of one aspartate to the cotransport of three Na+. Results: Slow binding of Na+ takes place before aspartate binding and has high activation energy. Conclusion: Binding of Na+ is accompanied by a large conformational change enabling subsequent high affinity binding of aspartate. Significance: Insight into the binding kinetics of coupling ions is essential to deduce a mechanism of transport. GltPh from Pyrococcus horikoshii is a homotrimeric Na+-coupled aspartate transporter. It belongs to the widespread family of glutamate transporters, which also includes the mammalian excitatory amino acid transporters that take up the neurotransmitter glutamate. Each protomer in GltPh consists of a trimerization domain involved in subunit interactions and a transport domain containing the substrate binding site. Here, we have studied the dynamics of Na+ and aspartate binding to GltPh. Tryptophan fluorescence measurements on the fully active single tryptophan mutant F273W revealed that Na+ binds with low affinity to the apoprotein (Kd 120 mm), with a particularly low kon value (5.1 m−1s−1). At least two sodium ions bind before aspartate. The binding of Na+ requires a very high activation energy (Ea 106.8 kJ mol−1) and consequently has a large Q10 value of 4.5, indicative of substantial conformational changes before or after the initial binding event. The apparent affinity for aspartate binding depended on the Na+ concentration present. Binding of aspartate was not observed in the absence of Na+, whereas in the presence of high Na+ concentrations (above the Kd for Na+) the dissociation constants for aspartate were in the nanomolar range, and the aspartate binding was fast (kon of 1.4 × 105 m−1s−1), with low Ea and Q10 values (42.6 kJ mol−1 and 1.8, respectively). We conclude that Na+ binding is most likely the rate-limiting step for substrate binding.
Pain in sickle cell disease. Rates and risk factors.

BACKGROUND AND METHODS Acute episodes of pain are the principal symptom of sickle cell disease, but little is known about the epidemiologic features of these episodes or risk factors for them, nor is it known whether patients with high rates of such episodes die prematurely. We prospectively studied the natural history of sickle cell disease in 3578 patients ranging from newborns to persons up to 66 years old who were followed at clinical centers across the United States. RESULTS There were 12,290 episodes of pain in 18,356 patient-years. The average rate was 0.8 episode per patient-year in sickle cell anemia, 1.0 episode per patient-year in sickle beta 0-thalassemia, and 0.4 episode per patient-year in hemoglobin SC disease and sickle beta(+)-thalassemia. The rate varied widely within each of these four groups--e.g., 39 percent of patients with sickle cell anemia had no episodes of pain, and 1 percent had more than six episodes per year. The 5.2 percent of patients with 3 to 10 episodes per year had 32.9 percent of all episodes. Among patients with sickle cell anemia who were more than 20 years old, those with high rates of pain episodes tended to die earlier than those with low rates. High rates were associated with a high hematocrit and low fetal hemoglobin levels. alpha-Thalassemia had no effect on pain apart from its association with an increased hematocrit. CONCLUSIONS The "pain rate" (episodes per year) is a measure of clinical severity and correlates with early death in patients with sickle cell anemia over the age of 20. Even when the fetal hemoglobin level is low, one can predict that small increments in the level may have an ameliorating effect on the pain rate and may ultimately improve survival. This outcome is particularly encouraging to investigators studying hydroxyurea and other treatments designed to increase the fetal hemoglobin level.
Effects of Training on Interpretation of Emotional Ambiguity

In four experiments we investigated whether interpretative biases found in anxious patients and high-trait anxious individuals can be induced by training in unselected volunteers. Repeated exposure to emotionally valenced (threatening) meanings of homographs during training was followed by relatively faster resolution of word fragments and faster lexical decisions for targets that matched the trained valence. Similar effects were found whether participants generated the meanings themselves, or verified a particular meaning of the homograph. Finally, comparison with a baseline condition confirmed that systematic exposure to threatening—but not non—threatening-resolutions of ambiguous words led to generally faster access times for congruent meanings, thus resembling the interpretative bias seen in anxiety states.
Reducing the bond frame width in Cu/Sn SLID wafer level packaging

In this paper, we present recent results on mechanical strength and reliability of Cu/Sn bond frames with reduced foot-print, for wafer-level packaging of Micro and Nano-devices. The structures of the test vehicle and intermediate multi-layer of bond frames were designed and fabricated on cap and substrate wafers. Electroplated Cu/Sn frames were bonded at temperature 270 °C in an EVG501 wafer bonder. With a tailored bonding profile (temperature and pressure), a symmetric sandwich structure with Cu3Sn between two Cu layers is formed at the bonding interface, where the amount of over flow of Sn is minimized. To reduce the bond frame foot print, the width of the bond frame is reduced from 200 to 40 μm. Mechanical die-shear and reliability testing show that the minimum bond frame width giving acceptable results is 80 μm. Thinner frames (40 μm width) result in inferior results in the present experiment. For bond frames of 80 μm width and wider, the average shear strength is high (65 MPa). Three types of reliability tests, i.e., annealing test, high temperature storage, and temperature cycling test were performed to evaluate the reliability of the bonded frames after the initial inspection. In the failed dies, we observed propagation of cracks in silicon incomplete bonds. The possible failure mechanisms are discussed and feasible improvement methods are proposed.
Combined Use of k-Mer Numerical Features and Position-Specific Categorical Features in Fixed-Length DNA Sequence Classification

To classify DNA sequences, k-mer frequency is widely used since it can convert variable-length sequences into fixed-length and numerical feature vectors. However, in case of fixed-length DNA sequence classification, subsequences starting at a specific position of the given sequence can also be used as categorical features. Through the performance evaluation on six datasets of fixed-length DNA sequences, our algorithm based on the above idea achieved comparable or better performance than other state-of-the art algorithms.
Improving PMTCT Uptake and Retention Services Through Novel Approaches in Peer-Based Family-Supported Care in the Clinic and Community: A 3-Arm Cluster Randomized Trial (PURE Malawi)

Abstract:In July 2011, Malawi introduced an ambitious public health program known as “Option B+,” which provides all HIV-infected pregnant and breastfeeding women with lifelong combination antiretroviral therapy, regardless of clinical stage or CD4 count. Option B+ is expected to have benefits for HIV-infected women, their HIV-exposed infants, and their HIV-uninfected male sex partners. However, these benefits hinge on early uptake of prevention of mother-to-child transmission, good adherence, and long-term retention in care. The Prevention of mother-to-child transmission Uptake and REtention (PURE) study is a 3-arm cluster randomized controlled trial to evaluate whether clinic- or community-based peer support will improve care-seeking and retention in care by HIV-infected pregnant and breastfeeding women, their HIV-exposed infants, and their male sex partners, and ultimately improve health outcomes in all 3 populations. We describe the PURE Malawi Consortium, the initial work conducted to inform the trial and interventions, the trial design, and the analysis plan. We then discuss concerns and expected contributions to Malawi and the region.
Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans

Phylogenetic relationships of Phytophthora infestans sensu lato in the Andean highlands of South America were examined. Three clonal lineages (US-1, EC-1, EC-3) and one heterogeneous lineage (EC-2) were found in association with different host species in genus Solanum. The EC-2 lineage includes two mitochondrial (mtDNA) haplotypes, Ia and Ic. Isolates of P. infestans sensu lato EC-2 fit the morphological description of P. infestans but are different from any genotypes of P. infestans described to date. All isolates of P. infestans sensu lato from Ecuador were amplified by a P. infestans specific primer (PINF), and restriction fragment length patterns were identical in isolates amplified with ITS primers 4 and 5. The EC-1 clonal lineage of P. infestans sensu lato from S. andreanum, S. columbianum, S. paucijugum, S. phureja, S. regularifolium, S. tuberosum and S. tuquerense was confirmed to be P. infestans based on sequences of the cytochrome oxidase I (cox I) gene and intron 1 of ras gene. The EC-2 isolates with the Ic haplotype formed a distinct branch in the same clade with P. infestans and P. mirabilis, P. phaseoli and P. ipomoeae for both cox I and ras intron 1 phylogenies and were identified as the newly described species P. andina. Ras intron 1 sequence data suggests that P. andina might have arisen via hybridization between P. infestans and P. mirabilis.