Miracle-dz/UniFAR-FTUs huggingface dataset:
A Hypothesis for the Evolution of Nuclear-Encoded, Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenase Genes in “Chromalveolate” Members

Eukaryotes bearing red alga-derived plastids — photosynthetic alveolates (dinoflagellates plus the apicomplexan Toxoplasma gondii plus the chromerid Chromera velia), photosynthetic stramenopiles, haptophytes, and cryptophytes — possess unique plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (henceforth designated as “GapC1”). Pioneering phylogenetic studies have indicated a single origin of the GapC1 enzymes in eukaryotic evolution, but there are two potential idiosyncrasies in the GapC1 phylogeny: Firstly, the GapC1 tree topology is apparently inconsistent with the organismal relationship among the “GapC1-containing” groups. Secondly, four stramenopile GapC1 homologues are consistently paraphyletic in previously published studies, although these organisms have been widely accepted as monophyletic. For a closer examination of the above issues, in this study GapC1 gene sampling was improved by determining/identifying nine stramenopile and two cryptophyte genes. Phylogenetic analyses of our GapC1 dataset, which is particularly rich in the stramenopile homologues, prompt us to propose a new scenario that assumes multiple, lateral GapC1 gene transfer events to explain the incongruity between the GapC1 phylogeny and the organismal relationships amongst the “GapC1-containing” groups. Under our new scenario, GapC1 genes uniquely found in photosynthetic alveolates, photosynthetic stramenopiles, haptophytes, and cryptopyhytes are not necessarily a character vertically inherited from a common ancestor.
Sharp analysis of low-rank kernel matrix approximations

We consider supervised learning problems within the positive-definite kernel framework, such as kernel ridge regression, kernel logistic regression or the support vector machine. With kernels leading to infinite-dimensional feature spaces, a common practical limiting difficulty is the necessity of computing the kernel matrix, which most frequently leads to algorithms with running time at least quadratic in the number of observations n, i.e., O(n^2). Low-rank approximations of the kernel matrix are often considered as they allow the reduction of running time complexities to O(p^2 n), where p is the rank of the approximation. The practicality of such methods thus depends on the required rank p. In this paper, we show that in the context of kernel ridge regression, for approximations based on a random subset of columns of the original kernel matrix, the rank p may be chosen to be linear in the degrees of freedom associated with the problem, a quantity which is classically used in the statistical analysis of such methods, and is often seen as the implicit number of parameters of non-parametric estimators. This result enables simple algorithms that have sub-quadratic running time complexity, but provably exhibit the same predictive performance than existing algorithms, for any given problem instance, and not only for worst-case situations.
Heat stress of two tropical seagrass species during low tides - impact on underwater net photosynthesis, dark respiration and diel in situ internal aeration.

Seagrasses grow submerged in aerated seawater but often in low O2 sediments. Elevated temperatures and low O2 are stress factors. Internal aeration was measured in two tropical seagrasses, Thalassia hemprichii and Enhalus acoroides, growing with extreme tides and diel temperature amplitudes. Temperature effects on net photosynthesis (PN ) and dark respiration (RD ) of leaves were evaluated. Daytime low tide was characterized by high pO2 (54 kPa), pH (8.8) and temperature (38°C) in shallow pools. As PN was maximum at 33°C (9.1 and 7.2 μmol O2 m(-2) s(-1) in T. hemprichii and E. acoroides, respectively), the high temperatures and reduced CO2 would have diminished PN , whereas RD increased (Q10 of 2.0-2.7) above that at 33°C (0.45 and 0.33 μmol O2 m(-2) s(-1) , respectively). During night-time low tides, O2 declined resulting in shoot base anoxia in both species, but incoming water containing c. 20 kPa O2 relieved the anoxia. Shoots exposed to 40°C for 4 h showed recovery of PN and RD , whereas 45°C resulted in leaf damage. These seagrasses are 'living near the edge', tolerant of current diel O2 and temperature extremes, but if temperatures rise both species may be threatened in this habitat.
Peripheral blood stem cells collection on spectra optia apheresis system using the continuous mononuclear cell collection protocol: A single center report of 39 procedures

The aim of the study was to assess the performance of the new Continuous Mononuclear Cell Collection (CMNC) protocol on the Spectra Optia Apheresis System for collecting autologous Peripheral Blood Stem Cells (PBSC) in adult patients with respect to collection variables, CD34+ cells harvest prediction and engraftment data. In this retrospective study, 39 CMNC procedures on 23 mobilized patients with multiple myeloma and lymphoma were analyzed. CD34+ cells and blood cells yields, collection efficiencies (CE1 and CE2), cell losses were calculated. Engraftment data of 17 autologous transplantations were collected.
ATLANTIC DIP: Insulin Therapy for Women With IADPSG-Diagnosed Gestational Diabetes Mellitus. Does It Work?

Introduction Approximately 40% of women with gestational diabetes mellitus (GDM) diagnosed using International Association of the Diabetes and Pregnancy Study Group (IADPSG) criteria require insulin therapy. Objective We assessed whether the outcomes for women with GDM treated with insulin are comparable to women with normal glucose tolerance (NGT). Materials and Methods This retrospective cohort study included 752 women with insulin-treated GDM and 2496 women with NGT during pregnancy. Maternal and fetal outcomes were examined. Results Infants of women with insulin-treated GDM had rates of macrosomia [adjusted odds ratio (aOR), 1.19; 95% confidence interval (CI), 0.87 to 1.63; P = 0.26], large for gestational age (LGA) (aOR, 1.07; 95% CI, 0.77 to 1.47; P = 0.67), and small for gestational age (SGA) (aOR, 0.70; 95% CI, 0.38 to 1.38; P = 0.26) similar to women with NGT. They were more likely to be hypoglycemic at birth (aOR, 6.85; 95% CI, 2.31 to 20.28; P < 0.01) and to require neonatal intensive care unit care (NICU) (aOR, 12.09; 95% CI, 8.72 to 16.76; P < 0.01), predominantly for nonmedical reasons. Maternal rates of hypertensive disorders (preeclampsia: aOR, 0.64; 95% CI, 0.34 to 1.12; P = 0.17; pregnancy-induced hypertension: aOR, 1.11; 95% CI, 0.74 to 1.66; P = 0.60) and hemorrhage (ante partum hemorrhage: aOR, 0.56; 95% CI, 0.19 to 1.58; P = 0.27; postpartum hemorrhage: aOR, 1.17; 95% CI, 0.68 to 2.03; P = 0.55) were similar between groups, but the risk of polyhydramnios was increased in the GDM cohort (aOR, 7.75; 95% CI, 3.96 to 15.16; P < 0.01). Conclusions Insulin treatment of IADPSG-diagnosed GDM results in rates of macrosomia, LGA, SGA, and maternal hypertensive disorders similar to those of women with NGT. Although NICU admissions are greater in the GDM cohort, they are primarily for nonmedical reasons. Neonatal hypoglycemia and polyhydramnios remain greater among women with insulin-treated GDM.
International Frontal Sinus Anatomy Classification and Anatomic Predictors of Low-Lying Anterior Ethmoidal Arteries

Background The International Frontal Sinus Anatomy Classification (IFAC) was introduced to more accurately characterize ethmoid and frontal sinus pneumatization patterns. The prevalence of IFAC cells and their anatomic associations have not been described. Objective The goal was to examine the prevalence of IFAC cells and determine radiologic features associated with a low-lying anterior ethmoidal artery (LAEA). Methods Imaging of adult patients who underwent computed tomographies from January 2015 to March 2016 were retrospectively reviewed by using the IFAC classification. We also measured the distance from the skull base to the anterior ethmoidal artery (AEA), the height of the lateral lamella of the cribriform plate, and anterior-posterior diameter from the anterior wall of the frontal sinus to the skull base (APF). Patients with a history of sinus surgery, trauma, malignancy, or congenital anomaly were excluded. Statistical analysis was performed by using Pearson correlation coefficients and χ2 tests. Results A total of 95 patients met the inclusion criteria. There was a significant association between supraorbital ethmoid cells and an LAEA (p < 0.001), with a significant effect size (ϕ = 0.276, p = 0.007). An inverse relationship was observed between Keros type I classification I and an LAEA (p < 0.001), with a significant effect size (ϕ = -0.414, p = 0.000). Significant associations were found between the AEA distance from the skull base and the cribriform lateral lamella height (R = 0.576, p < 0.001). In addition, there was a significant association between the AEA distance from the skull base and the APF (R = 0.497, p < 0.001). Conclusion The presence of a supraorbital ethmoid cell and a wide APF were associated with an LAEA. There was a significant relationship between Keros type I classification and the AEA adjacent to the skull base. Delineation of these anatomic relationships may be helpful during endoscopic sinus surgery to avoid complications.
The Pandemic H30 Subclone of Sequence Type 131 (ST131) as the Leading Cause of Multidrug-Resistant Escherichia coli Infections in the United States (2011–2012)

Summary Among US clinical Escherichia coli isolates from 2011–2012, sequence type 131 (ST131) was even more prevalent (26.4%) than reported previously for 2007 isolates (17%). The ST131-H30 subclone (19.8% prevalence), with its H30Rx subset (6.6%), accounted for most fluoroquinolone, extended-spectrum cephalosporin, and multidrug resistance.
Risk Control of Mean-Reversion Time in Statistical Arbitrage

This paper deals with the risk of mean-reversions in statistical arbitrage. The basic concept of statistical arbitrage is to exploit short-term deviations in returns from a long-term equilibrium across several assets. This kind of strategy heavily relies on the assumption of mean-reversion of idiosyncratic returns - reverting to a long-term mean after a certain amount of time, but literature on the assessment of risk on this belief is rare. In this paper, we propose a simple scheme that controls the risk on mean-reversions, via portfolio selections and screenings. Realizing that each residual exhibits different mean-reversion time, the residuals that have fast mean-reverting speed are selected to form portfolios. In addition, further control is imposed by allowing the trading activity only when the goodness-of-fit of the estimation for trading signals is sufficiently high. Furthermore, we design the dynamic asset allocation with the market- and dollar-neutrality conditions as a constrained optimization problem, which can be solved numerically. The improved reliability and robustness of the strategy from our method is demonstrated through back-testing results. It has been found that the performance of this investment framework is robust to market fluctuations. We further provide an answer to a puzzled relation among the number of factors, lengths of estimation window, and transaction costs, which are crucial parameters that have direct impacts on the strategy.
The effects of Ramadan fasting on activity and energy expenditure.

Background Fasting during the month of Ramadan entails abstinence from eating and drinking between dawn and sunset and a major shift in meal times and patterns with associated changes in several hormones and circadian rhythms; whether there are accompanying changes in energy metabolism is unclear. Objective We have investigated the impact of Ramadan fasting on resting metabolic rate (RMR), activity, and total energy expenditure (TEE). Design Healthy nonobese volunteers (n = 29; 16 women) fasting during Ramadan were recruited. RMR was measured with the use of indirect calorimetry. In subgroups of participants, activity (n = 11; 5 women) and TEE (n = 10; 5 women) in free-living conditions were measured with the use of accelerometers and the doubly labeled water technique, respectively. Body composition was measured with the use of bioelectrical impedance. Measurements were repeated after a wash-out period of between 1 and 2 mo after Ramadan. Nonparametric tests were used for comparative statistics. Results Ramadan fasting did not result in any change in RMR (mean ± SD: 1365.7 ± 230.2 compared with 1362.9 ± 273.6 kcal/d for Ramadan and post-Ramadan respectively, P = 0.713, n = 29). However, controlling for the effects of age, sex, and body weight, RMR was higher in the first week of Ramadan than in subsequent weeks. During Ramadan, the total number of steps walked were significantly lower (n = 11, P = 0.001), while overall sleeping time was reduced and different sleeping patterns were seen. TEE did not differ significantly between Ramadan and post-Ramadan (mean ± SD: 2224.1 ± 433.7 compared with 2121.0 ± 718.5 kcal/d for Ramadan and post-Ramadan, P = 0.7695, n = 10). Conclusions Ramadan fasting is associated with reduced activity and sleeping time, but no significant change in RMR or TEE. Reported weight changes with Ramadan in other studies are more likely to be due to differences in food intake. This trial is registered at clinicaltrials.gov as NCT02696421.
Utility of a Direct 16S rDNA PCR and Sequencing for Etiological Diagnosis of Infective Endocarditis

Background Cases of infective endocarditis (IE) require prompt etiological diagnosis for effective treatment. Molecular methods can aid in rapid and reliable diagnosis of culture-negative IE cases. We evaluated the utility of 16S rDNA PCR and sequencing in determining the causative agents of IE in valve tissues, especially when specimens were obtained after initiation of antimicrobial therapy. Methods We performed 16S rDNA PCR and sequencing in heart valve specimens and medical records review of 80 patients who underwent protocol-based cardiac surgery from 2013 to 2015. One patient did not meet the criteria for IE. Sixty-five (81.3%) and 14 pa-tients (17.5%) were diagnosed as having definite IE and possible IE, respectively. Blood and heart valve biopsy tissue were examined by using routine microbiological methods. Results Blood cultures in our hospital were IE-positive for 33 patients (41.8%), whereas 49 patients (62.0%) showed positive blood cultures when initial blood cultures performed at the referring hospital were included. Eighteen (22.8%) and 40 patients (50.6%) were IE-positive in valve tissue cultures and 16S rDNA PCR, respectively. Bacteria in the Streptococcus mitis group (n=26) were the most common etiological agents of IE. Eight (10.1%) culture-negative specimens tested positive by 16S rDNA PCR. In five of eight PCR-positive and culture-negative cases, fastidious or anaerobic organisms were the cause of IE. Conclusions Direct 16S rDNA PCR and sequencing can be used as a supplementary method to conventional blood and biopsy culture testing, especially in culture-negative IE cases that are negative for IE by culture.
Indian Bt Cotton Varieties Do Not Affect the Performance of Cotton Aphids

Cotton varieties expressing Cry proteins derived from the soil bacterium Bacillus thuringiensis (Bt) are grown worldwide for the management of pest Lepidoptera. To prevent non-target pest outbreaks and to retain the biological control function provided by predators and parasitoids, the potential risk that Bt crops may pose to non-target arthropods is addressed prior to their commercialization. Aphids play an important role in agricultural systems since they serve as prey or host to a number of predators and parasitoids and their honeydew is an important energy source for several arthropods. To explore possible indirect effects of Bt crops we here examined the impact of Bt cotton on aphids and their honeydew. In climate chambers we assessed the performance of cotton aphids, Aphis gossypii Glover (Hemiptera: Aphididae) when grown on three Indian Bt (Cry1Ac) cotton varieties (MECH 12, MECH 162, MECH 184) and their non-transformed near isolines. Furthermore, we examined whether aphids pick up the Bt protein and analyzed the sugar composition of aphid honeydew to evaluate its suitability for honeydew-feeders. Plant transformation did not have any influence on aphid performance. However, some variation was observed among the three cotton varieties which might partly be explained by the variation in trichome density. None of the aphid samples contained Bt protein. As a consequence, natural enemies that feed on aphids are not exposed to the Cry protein. A significant difference in the sugar composition of aphid honeydew was detected among cotton varieties as well as between transformed and non-transformed plants. However, it is questionable if this variation is of ecological relevance, especially as honeydew is not the only sugar source parasitoids feed on in cotton fields. Our study allows the conclusion that Bt cotton poses a negligible risk for aphid antagonists and that aphids should remain under natural control in Bt cotton fields.
Impact of an Electronic Monitoring Intervention to Improve Adherence to Inhaled Medication in Patients with Asthma and Chronic Obstructive Pulmonary Disease: Study Protocol for a Randomized Controlled Trial

Background Despite progress in pharmacological and non-pharmacological treatment in recent years, the burden of disease among patients with asthma and chronic obstructive pulmonary disease (COPD) is high and patients are frequently hospitalized due to exacerbations. Reasons for uncontrolled diseases are manifold, but are often associated with poor inhalation technique and non-adherence to the prescribed treatment plan. This causes substantial mortality, morbidity, and costs to the healthcare system. In this respect, the study of causes for non-adherence and the development of measures to increase and maintain treatment adherence in chronic diseases is of major clinical importance. Objective The primary objective of this study is to investigate the impact of using specific, validated electronic devices on adherence to inhaled medication in patients with chronic obstructive lung diseases such as asthma and COPD. Furthermore, it aims to assess the impact of a reminder and close supervision of the course of disease and quality of life. Methods In this ongoing prospective, single-blind, randomized controlled study, adherence to inhaled medication is analyzed over a 6-month period in at least 154 in- and outpatients with asthma or COPD who have experienced at least 1 exacerbation during the last year. Adherence is measured using electronic data capture devices, which save the date and time of each inhalative device actuation and transfer these data daily via a wireless connection to a Web-based database. Patients are randomly assigned to either the intervention or the control group. The clinical intervention consists of an automated and personal reminder. The intervention group receives an audio reminder and support calls in case medication has not been taken as prescribed or if rescue medication is used more frequently than pre-specified in the study protocol. During the study, participants are assessed every 2 months in the form of clinical visits. Results Recruitment started in January 2014. To date, a total of 169 patients have been recruited. Follow-up assessments are still ongoing. The study will be concluded in the first quarter of 2017. Data analysis will take place during 2017. Conclusions Few studies have investigated medication adherence in patients with chronic obstructive lung diseases. With this prospective study design and the use of state-of-the-art devices for measuring adherence, we expect scientifically relevant and clinically meaningful results that will have a substantial and positive impact on the provision of healthcare in chronically ill patients suffering from asthma or COPD. Trial Registration ClinicalTrials.gov: NCT02386722; https://clinicaltrials.gov/ct2/show/NCT02386722 (Archived by WebCite at http://www.webcitation.org/6oJq1fel0)
Using a UK Virtual Supermarket to Examine Purchasing Behavior Across Different Income Groups in the United Kingdom: Development and Feasibility Study

Background The majority of food in the United Kingdom is purchased in supermarkets, and therefore, supermarket interventions provide an opportunity to improve diets. Randomized controlled trials are costly, time-consuming, and difficult to conduct in real stores. Alternative approaches of assessing the impact of supermarket interventions on food purchases are needed, especially with respect to assessing differential impacts on population subgroups. Objective The aim of this study was to assess the feasibility of using the United Kingdom Virtual Supermarket (UKVS), a three-dimensional (3D) computer simulation of a supermarket, to measure food purchasing behavior across income groups. Methods Participants (primary household shoppers in the United Kingdom with computer access) were asked to conduct two shopping tasks using the UKVS and complete questionnaires on demographics, food purchasing habits, and feedback on the UKVS software. Data on recruitment method and rate, completion of study procedure, purchases, and feedback on usability were collected to inform future trial protocols. Results A total of 98 participants were recruited, and 46 (47%) fully completed the study procedure. Low-income participants were less likely to complete the study (P=.02). Most participants found the UKVS easy to use (38/46, 83%) and reported that UKVS purchases resembled their usual purchases (41/46, 89%). Conclusions The UKVS is likely to be a useful tool to examine the effects of nutrition interventions using randomized controlled designs. Feedback was positive from participants who completed the study and did not differ by income group. However, retention was low and needs to be addressed in future studies. This study provides purchasing data to establish sample size requirements for full trials using the UKVS.
Mortality Among Hospitalized Patients With Hypoglycemia: Insulin Related and Noninsulin Related

Context: Hypoglycemia is common among hospitalized patients with and without diabetes mellitus. Objective: Investigate the association between spontaneous or insulin-related hypoglycemia and mortality in hospitalized patients. Design: Hypoglycemia was defined as blood glucose <70 mg/dl (3.9 mmol/l), including moderate (40 to 70 mg/dl, 2.2 to 3.9 mmol/l) and severe hypoglycemia (<40 mg/dl, 2.2 mmol/l). Use of insulin during hospitalization defined insulin-related hypoglycemia, thus patients were classified into 6 groups: non-insulin treated (NITC) and insulin-treated controls (ITC), insulin-related hypoglycemia (IH) or severe hypoglycemia (ISH), and non insulin-related hypoglycemia (NIH) and severe hypoglycemia (NISH). Setting and Patients: Historical prospectively data of patients ≥ 18 years of age, hospitalized in medical wards for any cause between January 2011 and December 2013. Main Outcome Measure: All-cause mortality at the end of follow-up. Results: The cohort included 33,675 patients, including 2605 with moderate hypoglycemia (IH, 1011; NIH, 1594) and 342 with severe hypoglycemia (ISH, 201; NISH,141). Overall end-of-follow-up mortality was 31.9% (NITC, 28.0%; ITC, 42.9%; NIH, 50.7%; IH, 55.3%; NISH, 70.9%; ISH, 69.1%). Compared with NITC, unadjusted hazard ratios (95% confidence intervals) for mortality were as follows: ITC, 1.7 (1.6 to 1.8), NIH, 2.2 (2.0 to 2.4), IH, 2.5 (2.2 to 2.7), NISH, 4.2 (3.5 to 5.2), and ISH, 3.8 (3.2 to 4.5); with P < 0.001. Following multivariate analysis, respective hazard ratios were 1.8, 2.1, 2.4, 3.2, and 3.6 (P < 0.001). Cause of admission did not affect the association. Conclusions: In hospitalized patients, hypoglycemia, either with insulin use or spontaneous, is associated with increased short- and long-term mortality.