Miracle-dz/UniFAR-FTUs huggingface dataset:
SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

ABSTRACT Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle. Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.
How accurate is the estimation of anthropogenic carbon in the ocean? An evaluation of the ΔC* method

The ΔC* method of Gruber et al. (1996) is widely used to estimate the distribution of anthropogenic carbon in the ocean; however, as yet, no thorough assessment of its accuracy has been made. Here we provide a critical re‐assessment of the method and determine its accuracy by applying it to synthetic data from a global ocean biogeochemistry model, for which we know the “true” anthropogenic CO2 distribution. Our results indicate that the ΔC* method tends to overestimate anthropogenic carbon in relatively young waters but underestimate it in older waters. Main sources of these biases are (1) the time evolution of the air‐sea CO2 disequilibrium, which is not properly accounted for in the ΔC* method, (2) a pCFC ventilation age bias that arises from mixing, and (3) errors in identifying the different end‐member water types. We largely support the findings of Hall et al. (2004), who have also identified the first two bias sources. An extrapolation of the errors that we quantified on a number of representative isopycnals to the global ocean suggests a positive bias of about 7% in the ΔC*‐derived global anthropogenic CO2 inventory. The magnitude of this bias is within the previously estimated 20% uncertainty of the method, but regional biases can be larger. Finally, we propose two improvements to the ΔC* method in order to account for the evolution of air‐sea CO2 disequilibrium and the ventilation age mixing bias.
Investigating the Microstructure of Network Evolution: Alliance Formation in the Mobile Communications Industry

Theories of network evolution frequently focus on “network endogeneity,” which stresses predictable, path-dependent evolution rooted in previous network structure. However, theories of technological evolution and innovation remind us that networks may undergo significant change as technological discontinuities exert pressures on existing relationships and firms engage in exploratory search. How can we incorporate sources of change into our theories of network evolution instead of focusing so squarely on sources of inertia? By using recent advances in graph theory, we develop a more flexible theory of network evolution by examining two patterns of partner selection that have the potential to change networks: “shortcut” formation between relatively unconnected partner clusters, and the entry of new firms into the “main component” of incumbent partners. Our findings suggest an important contingency for the endogeneity perspective: structural homophily predicts shortcut formation but not alliance formation within clusters. Furthermore, we demonstrate that the pattern of alliance formation between incumbents and new entrants to the alliance network is driven by a combination of endogenous and exogenous mechanisms. New entrants attach to more prominent incumbents, but they are more likely to attach with an alliance deal that comprises multiple partners. We demonstrate these findings in an industry where systemic technology encourages cooperation and where network entry is prevalent—the mobile communications industry from 1993–2002.
Avoiding Counterproductive Results: An Experimental Pretest of a Harm Reduction Intervention on Attitude Toward Party Drugs Among Users and Nonusers

In two experimental studies, the authors tested written health education materials on the personal acceptance of party drug use. Following a harm reduction strategy, the materials provided information on minimizing potential hazards associated with drug use. Among users and nonusers, potential aversive effects of these materials were examined on measures of attitude, intention, and outcome expectancy toward party drug use. Participants were recruited in the city center of Maastricht, The Netherlands, in nightlife settings that were popular among young people. In the first experiment, a leaflet on ecstasy use was evaluated among ecstasy users and nonusers. Results showed neither health promoting effects, nor counterproductive results on the outcome measures. In the second experiment, the effects of two different formats (leaflet vs. infocard) about two different kinds of party drugs (ecstasy vs. GHB) were compared within a nonusing population. Again, results showed no positive changes on the outcome measures toward ecstasy use as a result of exposure to the ecstasy materials. However, exposure to the GHB materials resulted into a more negative attitude toward GHB use (leaflet and infocard) and lower estimates of the likelihood of positive outcomes of use (infocard). The study's limitations and implications are discussed, including the need for experimental pretesting.
Low-dose bortezomib increases the expression of NKG2D and DNAM-1 ligands and enhances induced NK and γδ T cell-mediated lysis in multiple myeloma

Multiple myeloma (MM) is an incurable hematological malignancy, although bortezomib has markedly improved its outcomes. Growing clinical evidence indicates that enhancing induced natural killer (NK) or γδ T cells for infusion is useful in the treatment of MM. However, whether combination treatment with bortezomib and induced NK and γδ T cells further improves outcomes in MM, and how the treatments should be combined, remain unclear. Herein, we found that low-dose bortezomib did not suppress the viability of induced NK and γδ T cells, but did induce MM cell apoptosis. Importantly, low-dose bortezomib increased the expression of NKG2D and DNAM-1 ligands on MM cells, which sensitized the multiple myeloma cells to lysis by induced NK and γδ T cells. Our results suggested that combination treatment with low-dose bortezomib and induced NK or γδ T cells had a synergistic cytotoxic effect on MM cells. This study provided a proof of principle for the design of future trials and investigation of this combination therapeutic strategy for MM treatment.
5G network slicing: A multi-tenancy scenario

The 5G mobile network is expected to meet increasing user demands. The increase in number of users is accompanied by varying user requirements in different network scenarios. Hence the 5G mobile network should be as flexible as possible. Network slicing offers a promising solution to the flexibility need of the 5G mobile network. Network slicing is the logical partitioning of a physical network into independent virtual mobile networks which enables the multi-tenancy paradigm. However, realising independent virtual mobile networks via network slicing in multi-tenancy requires efficient resource allocation. This is important to ensure that multi-tenancy enhances network capacity. In this paper, we investigate the resource allocation problem of achieving maximum capacity with the transmit power, allocated bandwidth as part of the constraints in a sliced multi-tenant network. Through our simulations, we demonstrate (i) how the number of users in a slice affects the capacity of an MVNO, (ii) how the transmit power improves the capacity of the MVNO and also how the number of slices affects the capacity.
Lattice Constant Tuning and Disorder Effects in 3D Colloidal Photonic Crystals

This paper uses the plane-wave expansion and finite-difference time-domain methods to study tunable 3D photonic crystals for use in display applications. The paper calculates particle diameter and refractive index for operation across the visible spectrum and estimates the reflectivity achievable for one to five layers of particles. The effects of disorder in particle position and diameter are then studied and the results show the system to be robust against such effects. Finally, the paper discusses the potential performance of this display technology in terms of reflectivity, color gamut, and contrast ratio.
Structure Analysis and Conformational Transitions of the Cell Penetrating Peptide Transportan 10 in the Membrane-Bound State

Structure analysis of the cell-penetrating peptide transportan 10 (TP10) revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan) was found to exhibit prominent characteristics of (i) amphiphilic α-helices, (ii) intrinsically disordered peptides, as well as (iii) β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state 19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L - or D -enantiomer of 3-(trifluoromethyl)-bicyclopent-[1.1. 1]-1-ylglycine (CF3 -Bpg) as a reporter group for 19F-NMR. Using the L -epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D -CF3 -Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D -CF3 -Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the unfolded N-terminus to self-assemble into β-pleated fibrils.
Optimizing FPGA-based convolutional neural networks accelerator for image super-resolution

Convolutional neural networks (CNN) are widely used in various computer vision applications. Recently, there have been many studies on FPGA-based CNN accelerators to achieve high performance and power efficiency. Most of them have been on CNN-based object detection algorithms, but researches on image super-resolution have been rarely conducted. Fast super-resolution CNN (FSRCNN), well known for CNN-based super-resolution algorithm, are a combination of multiple convolutional layers and a single deconvolutional layer. Since the deconvolutional layer generates high-resolution (HR) output feature maps from low-resolution (LR) input feature maps, its execution cycles are larger than those of the convolutional layer. In this paper, we propose a novel architecture of the FPGA-based CNN accelerator with the efficient parallelization. We develop a method of transforming a deconvolutional layer into a convolutional layer (TDC), a new methodology for the deconvolutional neural networks (DCNN). There is a massive parallelization source in the deconvolutional layer where multiple outputs within the same output feature map are created with the same inputs. When this new parallelization technique is applied to the deconvolutional layer, it generates the LR output feature maps the same as the convolutional layer. Thus, the performance of the accelerator increases without any additional hardware resources because the kernel size required to generate the LR output feature maps is smaller. In addition, if there is a DSP underutilization problem in the deconvolutional layer that some of the processors are in an idle state, the proposed method solves this problem by allowing more output feature maps to be processed in parallel. Experimental results show that the proposed TDC method achieves up to 81 times higher throughput than the state-of-the-art DCNN accelerator with the same hardware resources. We also improve the speed by 7.8 times by having all layers in the hourglass-type FSRCNN to be processed in inter-layer parallelism without additional DSP usage.
Supporting Differentiated Instruction in Programming Courses through Permanent Progress Monitoring

Several studies showed that teacher's support is essential to the students learning process. Often it is difficult for teachers to follow all their student's evolution and make timely interventions when needed. Often, in the same class, there are students with substantially different performance levels, and many times a teacher intervention is cructial to help lower performing students. To help the teacher identify these students, we propose the use of CodeInsights, a tool able to capture autonomously and unobtrusively real-time information about the students' performance based on snapshots of their code. The information available can be used by the teachers to support the adoption of the necessary measures to address each student needs or difficulties in a more grounded manner. We present the system and some results of a field test involving students from an introductory course on PHP programming.
[Metabolic changes in aromatic amino acids and monoamines in infantile autism and development of new treatment related to the finding].

A new method for measurement of the turnover rate of aromatic amino acids and related compounds in vivo using stable isotopes was developed. Deuterium-and carbon 13-labeled phenylalanine and deuterium-labeled tryptophan were used as tracers. This method was applied for the analysis of amino acid and amine metabolism in infantile autism. Marked disturbances of uptake of deuterated phenylalanine and tryptophan from intestine into blood were found in a portion of autistic patients (group A). In another group of the patients a remarkable decrease of turnover of tyrosine in blood was found (group B). This phenomenon was confirmed by an experiment using carbon 13 labeled phenylalanine. These findings might suggest that supply of tyrosine and free tryptophan to the brain (in group A) or supply of tyrosine (group B) to the brain might be decreased. We postulated that in some of autistic patients there might exist decreases in synthesis of catecholamine or serotonin. Based on the hypothesis, we started a new treatment with L-DOPA and 5 HTP in small doses, and found significant effects in some patients. However, in some, the amino acids caused marked aggravation of the symptoms. Recently, Hayaishi and his colleagues reported that R-tetrahydrobiopterin (R-THBP) could enhance biosynthesis of catecholamine and serotonin in the brain. Therefore, we started a clinical trial concerning effects of R-THBP. In the beginning, 17 cases were treated and patients younger than 5 years old showed marked improvement. Then, a double blind trial with inactive placebo was performed. (ABSTRACT TRUNCATED AT 250 WORDS)
Assessment and Outcome in Non-Traditional Cochlear Implant Candidates

The objectives of this study were to assess: (i) patient expectations met as a measure of outcome in early-deafened, late-implanted (non-traditional) cochlear implant recipients and (ii) pre-implantation predictive factors for postoperative speech perception. The notes of 13 recipients were retrospectively reviewed. The mean age at onset of profound deafness was 1.5 years (range 0-6). The mean age at implantation was 37 years (range 22-51 years). Patient expectations were assessed pre-operatively and 1 year after implantation. They were met or exceeded in 129/140 (92%) domains overall. A higher Speech Intelligibility Rating and audiovisual City University of New York sentence score before implantation were found to be positive predictive factors for improved speech discrimination after cochlear implantation.
Adaptation of the Acute Organ Failure Score for Use in a Medicare Population

Objectives: Without widely available physiologic data, a need exists for ICU risk adjustment methods that can be applied to administrative data. We sought to expand the generalizability of the Acute Organ Failure Score by adapting it to a commonly used administrative database. Design: Retrospective cohort study. Setting: One hundred fifty-one hospitals in Pennsylvania. Patients: A total of 90,733 ICU admissions among 77,040 unique patients between January 1, 2009, and December 1, 2009, in the Medicare Provider Analysis and Review database. Measurements and Main Results: We used multivariable logistic regression on a random split cohort to predict 30-day mortality, and to examine the impact of using different comorbidity measures in the model and adding historical claims data. Overall 30-day mortality was 17.6%. In the validation cohort, using the original Acute Organ Failure Score model’s &bgr; coefficients resulted in poor discrimination (C-statistic, 0.644; 95% CI, 0.639–0.649). The model’s C-statistic improved to 0.721 (95% CI, 0.711–0.730) when the Medicare cohort was used to recalibrate the &bgr; coefficients. Model discrimination improved further when comorbidity was expressed as the COmorbidity Point Score 2 (C-statistic, 0.737; 95% CI, 0.728–0.747; p < 0.001) or the Elixhauser index (C-statistic, 0.748; 95% CI, 0.739–0.757) instead of the Charlson index. Adding historical claims data increased the number of comorbidities identified, but did not enhance model performance. Conclusions: Modification of the Acute Organ Failure Score resulted in good model discrimination among a diverse population regardless of comorbidity measure used. This study expands the use of the Acute Organ Failure Score for risk adjustment in ICU research and outcomes reporting using standard administrative data.
Title Isoflavones in treating watchful waiting benign prostatehyperplasia : a double-blinded , randomized controlled trial

Objectives: This study aims to determine the efficacy and safety of soy isoflavones in controlling the symptoms and signs of lower urinary tract symptoms due to benign prostate hyperplasia (BPH). Design: This was a prospective, randomized, double-blind, placebo-controlled pilot study. Setting: This trial was conducted at two hospitals in Hong Kong between May 2006 and September 2007. Participants: One hundred and seventy-six (176) participants diagnosed with BPH were recruited from outpatient clinics. Participants with lower urinary tract symptoms were recruited through newspaper and radio interviews, posters placed at government outpatient clinics, and a public seminar offered by the investigators. Interventions: Participants were randomly assigned to either intervention (40 mg of isoflavones daily from Soylife 40) or placebo groups in a double-blind fashion. Main outcome measures: The primary outcome parameter of peak urine flow rate and the second outcome parameters of postresidual urine volume, lower urinary tract symptoms, testosterone, prostate-specific antigen, quality of life, diet, and safety profile (liver and renal function) were collected. All parameters were assessed at baseline, 6 months, and 12 months in a 12-month study period except testosterone, prostate-specific antigen, and safety profile, which were assessed at baseline and at 12 months. Results: The peak urine flow rate (Qmax), postresidual urine volume, International Prostate Symptoms Scores (IPSS), and 36-Item Short Form Health Survey (SF-36) significantly improved from baseline to the 12th month within both groups. However, when compared between groups, Qmax ( p = 0.055) and incomplete emptying subscore in IPSS ( p = 0.05) were marginally/statistically different between the two groups from the 6th to the 12th months, in addition to the general health domain of SF-36 from the baseline to 12th month ( p = 0.02) and from the 6th month to the 12th month ( p = 0.055). Isoflavones were generally safe and well tolerated. Conclusions: This randomized control pilot study showed only slight superiority of isoflavones over placebo over 12 months with otherwise surprising beneficial effects in both groups. Tolerability of isoflavones was excellent; thus it has laid foundations for further studies of isoflavones in BPH with focus on dosage and possible specificity of the effect.
Epidemiology of diarrhoeal disease in rural Malawi-a case study of cryptosporidiosis

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