Miracle-dz/UniFAR-FTUs huggingface dataset:
Seroprevalence of Chlamydia trachomatis in Inner-City Children and Adolescents—Implications for Vaccine Development

Background Prevention of Chlamydia trachomatis infection is an ideal application for a vaccine program, which should optimally be administered before sexual debut. However, there are limited epidemiologic studies of C. trachomatis infection in an unselected pediatric population since routine screening and treatment of pregnant women was implemented in the United States in 1993. Methods Anonymized serum samples were obtained from children younger than 21 years in 2 medical centers in Brooklyn, New York, from 2013 to 2015. Anti–C. trachomatis IgG antibody was determined by a validated enzyme immunoassay. Infants younger than 1 year were excluded from the final analysis due to interference of maternal antibody. Results One thousand two sera were included in the final analysis. Fifty-seven percent were females. No antibody was detected at younger than 11 years. Anti–C. trachomatis IgG antibody was detected in 11.4% and 5.6% of female and male subjects, respectively, older than 11 years (P = 0.0027), and seropositivity increased with age. There was no significant difference in the distribution of age at infection between the centers (P = 0.432), but a difference was detected between genders (P = 0.012) with a higher percentage of female subjects testing positive. Conclusions Antibody was first detected at 11 years of age, likely coinciding with sexual debut. The prevalence of antibody was higher and appeared earlier in females, mirroring national surveillance trends based on nucleic acid amplification testing. The delay in male antibody detection may be due to biological or behavioral differences between genders. These data are critical in informing potential C. trachomatis vaccine strategies.
Wings versus legs in the avian bauplan: Development and evolution of alternative locomotor strategies

Wings have long been regarded as a hallmark of evolutionary innovation, allowing insects, birds, and bats to radiate into aerial environments. For many groups, our intuitive and colloquial perspective is that wings function for aerial activities, and legs for terrestrial, in a relatively independent manner. However, insects and birds often engage their wings and legs cooperatively. In addition, the degree of autonomy between wings and legs may be constrained by tradeoffs, between allocating resources to wings versus legs during development, or between wing versus leg investment and performance (because legs must be carried as baggage by wings during flight and vice versa). Such tradeoffs would profoundly affect the development and evolution of locomotor strategies, and many related aspects of animal ecology. Here, we provide the first evaluation of wing versus leg investment, performance and relative use, in birds—both across species, and during ontogeny in three precocial species with different ecologies. Our results suggest that tradeoffs between wing and leg modules help shape ontogenetic and evolutionary trajectories, but can be offset by recruiting modules cooperatively. These findings offer a new paradigm for exploring locomotor strategies of flying organisms and their extinct precursors, and thereby elucidating some of the most spectacular diversity in animal history.
Differences between participants and nonparticipants in an exercise trial for adults with rheumatoid arthritis.

OBJECTIVE To investigate the generalizability of the results of a randomized controlled trial on the effectiveness of long-term, high-intensity exercises in the rheumatoid arthritis patients in training (RAPIT) trial by comparing the characteristics of the participants with the nonparticipants. METHODS Participants and nonparticipants were mailed questionnaires on sociodemographic characteristics, health status, reasons not to participate, and attitudes toward intensive exercise. RESULTS The questionnaires from 892 (75%) nonparticipants and 299 (97%) participants were collected. The nonparticipants were slightly older, more often male, and had longer disease duration than the participants. The nonparticipants perceived their disease as more serious, used fewer disease-modifying antirheumatic drugs, had a lower level of education, and a more negative attitude toward intensive exercise. CONCLUSION The results of the RAPIT trial might not be generalizable to the entire target population. To promote participation in long-term, high-intensity exercises, health professionals should more actively discuss the potential benefits of exercise with their RA patients while taking into consideration specific factors related to participation.
Intervention program to keep girls in the science pipeline: Outcome differences by ethnic status

This study evaluated a 2-week residential program aimed at enhancing the science interest and persistence of high-achieving 8th-grade girls. Questionnaires were administered to 38 program participants (14 of whom were of minority ethnicity) and 173 applicants who did not attend the program, at 3 time points: preprogram, 1 year postprogram, and 4 years postprogram. Outcomes, measured postprogram, included science self-concept and interest, persistence and aspirations in science, science activities, science course-taking in high school, and plans for a science college major. There was no main effect of program participation on any of the outcome measures, but a significant ParticipationEthnicity interaction effect occurred for all but one of the outcome variables. At Time 2, and especially Time 3, nonminority participants tended to have the most positive outcomes, whereas minority participants tended to have the most negative outcomes, compared with applicants. Post hoc analyses showed that although nonminority girls overall were more advantaged, this difference did not explain results. Several interpretations for these findings are discussed, the most likely that some global feature of the program, not any intervention component, interacted over time with the girls' postprogram experience. 2003 Wiley Periodicals, Inc. J Res Sci Teach 40: 393-414, 2003
Energy Harvesting Communications Under Explicit and Implicit Temperature Constraints

With a motivation to understand the effects of temperature sensitivity on wireless data transmission performance, we consider an energy harvesting communication system, where the temperature dynamics are governed by the transmission power policy. Different from the previous work, we consider a discrete time system where transmission power is kept constant in each slot. We consider two models that capture different effects of temperature. In the first model, the temperature is constrained to be below a critical temperature at all time instants; we coin this the explicit temperature constrained model. We investigate throughput optimal power allocation for multiple energy arrivals under general, as well as temperature and energy limited regimes. We show that the optimal power allocation for the temperature limited case is monotone decreasing. In the second model, we consider the effect of the temperature on the channel quality via its influence on additive noise power; we coin this the implicit temperature constrained model. In this model, the change in the variance of the additive noise due to previous transmissions is non-negligible. In particular, transmitted signals contribute as interference for all subsequent slots and thus affect the signal to interference plus noise ratio (SINR). In this case, we investigate throughput optimal power allocation under general, as well as low and high SINR regimes. We show in the low SINR regime that the optimal allocation dictates the transmitter to save its harvested energy till the last slot. In the high SINR regime, we show that the optimal power sequence is monotone increasing. Finally, we consider the case in which implicit and explicit temperature constraints are simultaneously active and we show under certain conditions that the optimal power sequence is monotone decreasing.
Bufferless Routing in Optical Gaussian Macrochip Interconnect

In optical multichip system, called Gaussian macro chip, where embedded chips are interconnected by an optical Gaussian network. By taking advantage of the underlying Hamiltonian cycles in the Gaussian network, we design a buffer less routing algorithm for the Gaussian macro chip, which routes packets along the shortest path in the absence of deflection, and guarantees that deflected packets reach their destinations along a segment of the Hamilton cycle. Our extensive simulation results demonstrate that by adopting the proposed routing algorithm, Gaussian macro chip can support much higher inter-chip communication bandwidth, has much shorter average packet delay, and is more power efficient than the previously proposed architectures for optical multichip systems.
Efficient active learning of sparse halfspaces

We study the problem of efficient PAC active learning of homogeneous linear classifiers (halfspaces) in $\mathbb{R}^d$, where the goal is to learn a halfspace with low error using as few label queries as possible. Under the extra assumption that there is a $t$-sparse halfspace that performs well on the data ($t \ll d$), we would like our active learning algorithm to be {\em attribute efficient}, i.e. to have label requirements sublinear in $d$. In this paper, we provide a computationally efficient algorithm that achieves this goal. Under certain distributional assumptions on the data, our algorithm achieves a label complexity of $O(t \cdot \mathrm{polylog}(d, \frac 1 \epsilon))$. In contrast, existing algorithms in this setting are either computationally inefficient, or subject to label requirements polynomial in $d$ or $\frac 1 \epsilon$.
Resistance of Group A Beta-Hemolytic Streptococci to Lincomycin and Erythromycin

Ten (0.05%) of 18,628 strains of Streptococcus pyogenes isolated from clinical specimens in the 3 years 1968 to 1970 were resistant to lincomycin and erythromycin. All 10 strains were highly resistant to lincomycin, having minimal inhibitory concentration (MIC) values of 200 μg/ml. There were two degrees of resistance to erythromycin: four strains were highly resistant, having MIC values of 200 μg or more/ml; and six strains showed slight resistance, MIC values being 0.78 to 1.56 μg/ml. There was no known epidemiological relationship between any of the patients infected with the resistant strains, which belonged to a variety of T serotypes. A zonal pattern of resistance to lincomycin occurred in four strains, all of which were only slightly resistant to erythromycin. After incubation for 24 hr in a twofold dilution series of lincomycin in broth, the strains grew in 0.05 μg or less/ml and in 50 and 100 μg/ml, but not in intermediate concentrations. Tests in agar indicated that the bacterial population of one strain, but not of the other three, was homogeneous in respect to its ability to grow readily in low and high, but not in intermediate, concentrations. The zone phenomenon is of significance in the clinical laboratory, since unawareness of it might result in a highly resistant strain being regarded as susceptible to lincomycin in tube or plate MIC tests that do not include sufficiently high concentrations of lincomycin.
Differential effects of ethanol and hexanol on the Escherichia coli cell envelope

Both ethanol and hexanol inhibited the growth of Escherichia coli, but their effects on the organization and composition of the cell envelope were quite different. Hexanol (7.8 x 10(-3) mM) increased membrane fluidity, whereas ethanol (0.67 M) had little effect. During growth in the presence of ethanol, the proportion of unsaturated fatty acids increased. The opposite change was induced by hexanol. Unlike hexanol, growth in the presence of ethanol resulted in the production of un-cross-linked peptidoglycan with subsequent lysis. Salt (0.3 M) protected cells against ethanol-induced lysis but potentiated growth inhibition by hexanol. Mutants isolated for resistance to ethanol-induced lysis synthesized cross-linked peptidoglycan during growth in the presence of ethanol but remained sensitive to hexanol. A general hypothesis was presented to explain the differential effects of ethanol and hexanol. All alcohols are viewed as similar in having both an apolar chain capable of interacting with hydrophobic environments and a hydroxyl function capable of hydrogen bonding. The differential effects of short-chain alcohols may represent effects due to the high molar concentrations of hydrogen bonding groups with an apolar end within the environment. These may replace bound water in some cases. With longer-chain alcohols such as hexanol, the effects of the acyl chain would dominate, and limitations of solubility and cellular integrity would mask these hydroxyl effects.
Scintillation Detector Timing Resolution; A Study by Ray Tracing Software

Time-of-flight positron emission tomography requires high timing resolution. In this paper, we determined the influence of scintillation properties on the detector timing resolution for crystals with non-negligible optical transit timespread. In addition to intrinsic scintillation properties, such as the light yield, decay time constant, and scintillation rise time, we also studied the relation between the timing resolution and extrinsic scintillation properties, such as the dimensions of the crystal, the absorption probability of the reflector, the dwell time of photons inside the reflector during the reflection process, and the crystal polish. For this purpose, we developed ray-tracing software. The crystals simulated in this paper are LSO:Ce, LYSO:Ce, LSO:Ce,0.2%Ca, LYSO:0.11%Ce,0.2%Mg, and LYSO:0.2%Ce,0.2%Ca, with dimensions 3 ×3 ×5 mm3, 3 ×3 ×10 mm3, 3 ×3 ×20 mm3, and 4 ×4 ×22 mm3. We furthermore studied the optical transit timespread of photons inside polished and etched crystals, which explains the differences in timing resolution.
Functional analysis of the cyclophilin PpiB role in bacterial cell division

Escherichia coli PpiB is a peptidyl‐prolyl cis/trans isomerase (PPIase, EC: 5.2.1.8) with chaperone activity. Here, we show that the ΔppiB deletion strain and the PpiB over‐expression wild‐type strain are both characterized by defects in cell division involving milder or severe cell filamentation, respectively. Using various PpiB mutants, we show that the PPIase activity of PpiB is necessary for the observed cell filamentation, whereas other structural features apart from the active site are also important for this phenotype. Early divisome components zipA and ftsZ showed decreased expression in ΔppiB cells, whereas the corresponding proteins partially suppressed the division phenotype of ΔppiB cells as well. Although PpiB itself has no obvious specific affinity for the septal ring as a GFP translational fusion showed a diffuse cytoplasmic localization, it interacts with FtsZ employing the C‐terminal FtsZ domain, decreases its GTPase activity and when over‐expressed shows an inhibitory effect on the proper FtsZ localization at future division sites. Furthermore, additional putative PpiB prey proteins are able to partially restore the ΔppiB phenotype indicating that PpiB is able to control bacterial cell division by probably modulating the function of various other proteins which are indirectly associated with the process.
ICT tools for enabling smart grid players' flexibility through VPP and DR services

The European Climate Change Program consists of a range of measures to fight against climate change, one of which is to reach 20% of renewable energy in the total energy supply in the EU by 2020. The increasing penetration of RES and DG introduces new business cases which require innovative ICT tools and the support of appropriate communication infrastructure. This paper focuses on the Virtual Power Plant and Demand Response cases, proposing a general architecture, as well as analyzing core functionalities, information and communication requirements, along with relative standards and technologies. The architectural analysis is based on the SGAM framework, a standardized architecture for smart grid solutions and services that enables new actors in the smart grid domain to participate in the energy markets and contribute to an optimal grid operation. The document presents the use cases' modeling and gives an overview of the pilots in which the proposed models will be materialized and validated.
Prospective detection of hyperglycemia in critically ill children using continuous glucose monitoring*

Objective: To evaluate the extent of hyperglycemia in nondiabetic children admitted to a pediatric intensive care unit using an interstitial continuous glucose monitor, and to compare the ability of this interstitial continuous glucose monitoring system to detect hyperglycemia with that of intermittent laboratory monitoring. Design: Prospective observational study. Setting: Ten-bed pediatric intensive care unit in an academic referral medical center in western Massachusetts. Patients: A convenience sample of 20 nondiabetic children, aged 1–18, anticipated to require intensive care >2 days. Interventions: Placement of a subcutaneous continuous glucose monitor for 72 hrs with a subsequent second sensor placed if the patient and family agreed. Glucose levels were compared with laboratory glucose values. Measurements and Main Results: Elevated glucose levels were revealed by 16,337 sensor glucose readings over a mean of 68 ± 5.2 hrs per patient. Forty-three percent of readings were >125 mg/dL (6.9 mmol/L), 27.2% were >140 mg/dL (7.8 mmol/L), and 4.0% were >200 mg/dL (11.1 mmol/L). Laboratory glucose measurements demonstrated hyperglycemia less frequently and missed significant periods of hyperglycemia. Conclusions: Significant hyperglycemia is present in pediatric intensive care patients and may be underestimated by intermittent laboratory monitoring.
Real-time physiological identification using incremental learning and semi-supervised learning

vii Chapter 1: Introduction 1 1.1 Background 1 1.2 Problem Statement 3 1.3 Related work 4 1.3. 1 Wearable Sensors 4 1.3. 2 Human Activity Recognition 5 1.4 Experimental Setup 5 1.5 Processing framework 7 1.5. 1 Data Collection 8 1.5. 2 Data Segmentation 11 1.5. 3 Data filtering 12 1.5. 4 Feature Extraction 13 1.5. 5 Feature Selection 14 1.5. 6 Model Generation 15 Chapter 2: Proposed Methodology 16 2.1 System Architecture 16 2.2 Conventional machine learning 17 2.3 Results 19 2.4 Conclusion 20 Chapter 3: Incremental learning 21
Towards a reliable prediction of conversion from Mild Cognitive Impairment to Alzheimer's Disease: stepwise learning using time windows

Predicting progression from a stage of Mild Cognitive Impairment to Alzheimer’s disease is a major pursuit in current dementia research. As a result, many prognostic models have emerged with the goal of supporting clinical decisions. Despite the efforts, the clinical application of such models has been hampered by: 1) the lack of a reliable assessment of the uncertainty of each prediction, and 2) not knowing the time to conversion. It is paramount for clinicians to know how much they can rely on the prediction made for a given patient (conversion or no conversion), and the time windows in case of conversion, in order to timely adjust the treatments. We propose a supervised learning approach using Conformal Prediction and a stepwise learning approach, where the learning model first predicts whether a patient converts to dementia, or remains stable, and then predicts the more likely progression window (short-term or long-term conversion). We used data from ADNI to test the approach and predict conversion within time windows of up to 2 years (short-term converter) and 2 to 4 years (long-term converter). The exploratory results are promising but compromised by the small number of examples for the long-term converting patients, available for training.
Functional Robustness of a Polycyclic Aromatic Hydrocarbon Metabolic Network Examined in a nidA Aromatic Ring-Hydroxylating Oxygenase Mutant of Mycobacterium vanbaalenii PYR-1

ABSTRACT In this study, we obtained over 4,000 transposon mutants of Mycobacterium vanbaalenii PYR-1 and analyzed one of the mutants, 8F7, which appeared to lose its ability to degrade pyrene while still being able to degrade fluoranthene. This mutant was identified to be defective in nidA, encoding an aromatic ring-hydroxylating oxygenase (RHO), known to be involved in the initial oxidation step of pyrene degradation. When cultured with pyrene as a sole source of polycyclic aromatic hydrocarbon (PAH), high-pressure liquid chromatography analysis revealed that the nidA mutant showed a significant decrease in the rate of pyrene degradation compared to the wild-type PYR-1, although pyrene was still being degraded. However, when incubated with PAH mixtures including pyrene, phenanthrene, and fluoranthene, the pyrene degradation rate of the mutant was higher than that of the mutant previously incubated with pyrene as a sole source of PAH. There was no significant difference between wild-type PYR-1 and the mutant in the rates of phenanthrene and fluoranthene degradation. From the whole-cell proteome analysis of mutant 8F7 induced by pyrene, we identified expression of a number of RHO enzymes which are suspected to be responsible for pyrene degradation in the nidA mutant, which had no expression of NidA. Taken together, results in this study provide direct evidence for the in vivo functional role of nidA in pyrene degradation at the level of the ring-cleavage-process (RCP) functional module but also for the robustness of the PAH metabolic network (MN) to such a genetic perturbation.
Metabolic engineering of Methanosarcina acetivorans for lactate production from methane

We previously demonstrated anaerobic conversion of the greenhouse gas methane into acetate using an engineered archaeon that produces methyl‐coenzyme M reductase (Mcr) from unculturable microorganisms from a microbial mat in the Black Sea to create the first culturable prokaryote that reverses methanogenesis and grows anaerobically on methane. In this work, we further engineered the same host with the goal of converting methane into butanol. Instead, we discovered a process for converting methane to a secreted valuable product, L‐lactate, with sufficient optical purity for synthesizing the biodegradable plastic poly‐lactic acid. We determined that the 3‐hydroxybutyryl‐CoA dehydrogenase (Hbd) from Clostridium acetobutylicum is responsible for lactate production. This work demonstrates the first metabolic engineering of a methanogen with a synthetic pathway; in effect, we produce a novel product (lactate) from a novel substrate (methane) by cloning the three genes for Mcr and one for Hbd. We further demonstrate the utility of anaerobic methane conversion with an increased lactate yield compared to aerobic methane conversion to lactate. Biotechnol. Bioeng. 2017;114: 852–861. © 2016 Wiley Periodicals, Inc.