Miracle-dz/UniFAR-FTUs huggingface dataset:
Oceanographic dynamics and the end of the last interglacial in the subpolar North Atlantic

Significance The last interglacial, ∼125,000 y ago, was the last extended warm period the earth has known before our Common Era of the past 11,000 y. Its end came after ∼15,000 y, paced by the decline in northern summer insolation, and followed by a glacial age lasting 100,000 y. Yet the ocean dynamics contributing to this glacial initiation and its global propagation are not fully understood, nor are their general role in climate evolution understood. This study assesses the role of the ocean’s gyre systems and fronts as dynamical components in large-scale climate change. Using microfossils, we document progressive southward advances of Arctic and polar hydrographic fronts into the subpolar North Atlantic Ocean, which trigger regional coolings and accelerate the transition into the glacial age. The last interglacial interval was terminated by the inception of a long, progressive glaciation that is attributed to astronomically influenced changes in the seasonal distribution of sunlight over the earth. However, the feedbacks, internal dynamics, and global teleconnections associated with declining northern summer insolation remain incompletely understood. Here we show that a crucial early step in glacial inception involves the weakening of the subpolar gyre (SPG) circulation of the North Atlantic Ocean. Detailed new records of microfossil foraminifera abundance and stable isotope ratios in deep sea sediments from Ocean Drilling Program site 984 south of Iceland reveal repeated, progressive cold water-mass expansions into subpolar latitudes during the last peak interglacial interval, marine isotope substage 5e. These movements are expressed as a sequence of progressively extensive southward advances and subsequent retreats of a hydrographic boundary that may have been analogous to the modern Arctic front, and associated with rapid changes in the strength of the SPG. This persistent millennial-scale oceanographic oscillation accompanied a long-term cooling trend at a time of slowly declining northern summer insolation, providing an early link in the propagation of those insolation changes globally, and resulting in a rapid transition from extensive regional warmth to the dramatic instability of the subsequent ∼100 ka.
Candida glabrata candidemia: An emerging threat in critically ill patients

Background: Candidemia is an important nosocomial blood stream infection in critically ill patients. Although several studies have addressed candidemia, very few have reviewed the impact of Candida glabrata candidemia in Intensive Care Unit (ICU) patients. Materials and Methods: The medical records of ICU patients between 2006 and 2010 were reviewed retrospectively. The epidemiology, clinical features and mortality related risk factors among our adult ICU patients were seen. Results: Among 144 episodes of candidemia, C. glabrata (n = 26; 18.05%) was the third most common species isolated. The incidence of C. glabrata candidemia was 0.21/1000 ICU admissions. The most common risk factors were prior exposure to broad spectrum antibiotics (100%), central venous catheter (100%), mechanical ventilation (76.9%), diabetes mellitus (50%), age >65 years (46.15%). Urine (23%) was the most common source of C. glabrata candidemia. Overall in hospital 30 days mortality rate due to C. glabrata fungemia was 53.8%. Patients who were treated with fluconazole showed better outcome than patients treated with amphotericin B. Renal failure requiring hemodialysis was the significantly associated with mortality in our study. Conclusion: Candida glabrata was the 3rd most common Candida causing candidemia in our ICUs with a incidence of 0.21/1000 ICU admissions. The outcome of ICU acquired C. glabrata candidemia was poor with 30 days mortality rate of 53.8%. Renal failure requiring hemodialysis was the only risk factor associated with mortality. Further studies are required to identify the other risk factors associated with mortality in C. glabrata candidemia.
Core Oligosaccharide of Plesiomonas shigelloides PCM 2231 (Serotype O17) Lipopolysaccharide—Structural and Serological Analysis

The herein presented complete structure of the core oligosaccharide of lipopolysaccharide (LPS) P. shigelloides Polish Collection of Microorganisms (PCM) 2231 (serotype O17) was investigated by 1H, 13C NMR spectroscopy, mass spectrometry, chemical analyses and serological methods. The core oligosaccharide is composed of an undecasaccharide, which represents the second core type identified for P. shigelloides serotype O17 LPS. This structure is similar to that of the core oligosaccharide of P. shigelloides strains 302-73 (serotype O1) and 7-63 (serotype O17) and differs from these only by one sugar residue. Serological screening of 55 strains of P. shigelloides with the use of serum against identified core oligosaccharide conjugated with bovine serum albumin (BSA) indicated the presence of similar structures in the LPS core region of 28 O-serotypes. This observation suggests that the core oligosaccharide structure present in strain PCM 2231 could be the most common type among P. shigelloides lipopolysaccharides.
The ablation of glial fibrillary acidic protein‐positive cells from the adult central nervous system results in the loss of forebrain neural stem cells but not retinal stem cells

The adult mammalian forebrain subependyma contains neural stem cells (NSCs) capable of self‐renewal and multilineage differentiation. The in vivo identification of NSCs has not been definitively addressed using a loss of function approach. Using a transgenic mouse expressing herpes‐simplex virus thymidine kinase from the glial fibrillary acidic protein (GFAP) promotor, we have selectively killed dividing GFAP‐positive cells in the presence of ganciclovir (GCV) and shown a > 95% loss in the numbers of NSCs, as assayed by the formation of clonally derived neurospheres in vitro. This loss is seen following 3 days of GCV exposure in vivo or in vitro only and cannot be rescued by coculturing with pure astrocyte populations or control (green fluorescent protein‐expressing) subependymal cells. Exposure to GCV in vitro has no effect on adult retinal stem cells hence, we conclude that adult forebrain NSCs comprise a subpopulation of the GFAP‐positive cells within the subependyma.
The N2K Consortium. II. A Transiting Hot Saturn around HD 149026 with a Large Dense Core

Doppler measurements from Subaru and Keck have revealed radial velocity variations in the V = 8.15, G0 IV star HD 149026 consistent with a Saturn-mass planet in a 2.8766 day orbit. Photometric observations at Fairborn Observatory have detected three complete transit events with depths of 0.003 mag at the predicted times of conjunction. HD 149026 is now the second-brightest star with a transiting extrasolar planet. The mass of the star, based on interpolation of stellar evolutionary models, is 1.3 ± 0.1 M☉; together with the Doppler amplitude K1 = 43.3 m s-1, we derive a planet mass M sin i = 0.36MJ and orbital radius 0.042 AU. HD 149026 is chromospherically inactive and metal-rich with spectroscopically derived [Fe/H] = +0.36, Teff = 6147 K, log g = 4.26, and v sin i = 6.0 km s-1. Based on Teff and the stellar luminosity of 2.72 L☉, we derive a stellar radius of 1.45 R☉. Modeling of the three photometric transits provides an orbital inclination of 85. °3 ± 1. °0 and (including the uncertainty in the stellar radius) a planet radius of (0.725 ± 0.05)RJ. Models for this planet mass and radius suggest the presence of a ~67 M⊕ core composed of elements heavier than hydrogen and helium. This substantial planet core would be difficult to construct by gravitational instability.
A Word-Based Naïve Bayes Classifier for Confidence Estimation in Speech Recognition

Confidence estimation has been largely used in speech recognition to detect words in the recognized sentence that have been likely misrecognized. Confidence estimation can be seen as a conventional pattern classification problem in which a set of features is obtained for each hypothesized word in order to classify it as either correct or incorrect. We propose a smoothed naïve Bayes classification model to profitably combine these features. The model itself is a combination of word-dependent (specific) and word-independent (generalized) naïve Bayes models. As in statistical language modeling, the purpose of the generalized model is to smooth the (class posterior) estimates given by the specific models. Our classification model is empirically compared with confidence estimation based on posterior probabilities computed on word graphs. Empirical results clearly show that the good performance of word graph-based posterior probabilities can be improved by using the naïve Bayes combination of features.
Increasing volume of food by incorporating air reduces energy intake*

Major challenges with weight management using weight-loss diets include hunger and rapid consumption of food, both of which lead to poor owner compliance. The aim of the present study was to determine the effect of increasing volume, by incorporating air, into dry expanded food, on satiety in dogs. Three studies have been performed. The first study aimed to measure the effect of volume of food on meal duration in dogs fed at their maintenance energy requirement. The purpose of the second study was to determine the effect of volume of food on satiety. The aim of the third study was to compare the satiety effect of the test diet with a maintenance dry diet commonly used in adult dogs. Throughout the studies, faecal score remained optimal. As volume of diet increased, the duration of food intake significantly increased (P < 0·001) and energy intake significantly decreased (P = 0·012). The present study has demonstrated that incorporating air into food to increase the volume of diet induces a satiety effect, independent of macronutrient profile, possibly by slowing food intake. Consequently, incorporating air into food might be a useful strategy for weight management in companion animals.
Urinary excretion of N-methylhistamine as a marker of disease activity in inflammatory bowel disease

OBJECTIVE:Mast cells are thought to participate in the pathogenesis of inflammatory bowel disease (IBD). In this study, urinary excretion of N-methylhistamine (UMH), a stable metabolite of the mast cell mediator histamine, was evaluated as an indicator of disease activity in patients with IBD.METHODS:Urinary excretion of UMH (μg/mmol creatinine × m2 body surface area) was measured by radioimmunoassay in 55 controls, 56 patients with Crohn's disease, and in 36 patients with ulcerative colitis. Excretion rates were correlated with clinical, serological, and endoscopic disease activity, disease extent, and location.RESULTS:Urinary excretion of UMH was found to be significantly elevated in IBD. Patients with active Crohn's disease (7.1 ± 4.2, p = 0.002 vs controls) and active ulcerative colitis (8.1 ± 4.8, p = 0.02 vs controls) had higher rates of UMH excretion than patients in remission (6.3 ± 3.8 and 5.2 ± 2.3, respectively) or controls (4.6 ± 1.9). In Crohn's disease and ulcerative colitis, a significant correlation of UMH excretion with clinical disease activity was obtained (Crohn's Disease Activity Index r2= 0.58, Clinical Activity Index r2= 0.57, p < 0.0001). Serologically, orosomucoid showed the best positive correlation with disease activity (Crohn's Disease Activity Index r2= 0.80, Clinical Activity Index r2= 0.86, p < 0.0001), but UMH excretion was found to reflect disease activity more accurately than C-reactive protein (Crohn's Disease Activity Index r2= 0.46, Clinical Activity Index r2= 0.42, p < 0.0001). No association between UMH excretion and disease type or localization could be found in Crohn's disease. However, UMH excretion correlated strongly with endoscopic severity of inflammation in Crohn's disease (Crohn's Disease Endoscopic Index of Severity r2= 0.70, p < 0.0001) or disease extent in ulcerative colitis.CONCLUSIONS:Urinary excretion of the histamine metabolite UMH is enhanced in IBD. It appears to represent an integrative parameter to monitor clinical and endoscopic disease activity in IBD, which appears to be influenced most likely by mediators released from histamine-containing cells, such as intestinal mast cell subtypes.
Real‐time polymerase chain reaction for diagnosing infectious mononucleosis in pediatric patients: A systematic review and meta‐analysis

In this meta‐analysis, we evaluated the diagnostic role of Epstein‐Barr virus deoxyribonucleic acid detection and quantitation in the serum of pediatric and young adult patients with infectious mononucleosis. The primary outcome of this meta‐analysis was the sensitivity and specificity of Epstein‐Barr virus (EBV) deoxyribonucleic acid (DNA) detection and quantitation using polymerase chain reaction (PCR). A systematic review and meta‐analysis was performed by searching for articles that were published through September 24, 2014 in the following databases: Medline, Cochrane, EMBASE, and Google Scholar. The following keywords were used for the search: “Epstein‐Barr virus,” “infectious mononucleosis,” “children/young adults/infant/pediatric,” and “polymerase chain reaction or PCR. ” Three were included in this analysis. We found that for detection by PCR, the pooled sensitivity for detecting EBV DNA was 77% (95%CI, 66–86%) and the pooled specificity for was 98% (95%CI, 93–100%). Our findings indicate that this PCR‐based assay has high specificity and good sensitivity for detecting of EBV DNA, indicating it may useful for identifying patients with infectious mononucleosis. This assay may also be helpful to identify young athletic patients or highly physically active pediatric patients who are at risk for a splenic rupture due to acute infectious mononucleosis. J. Med. Virol. 88:871–876, 2016. © 2015 Wiley Periodicals, Inc.
Analysis and Modeling of the Phase Detector Hysteresis in Bang-Bang PLLs

All-digital bang-bang phase-locked-loops suffer from unwanted output spurs due to their non-linear behavior. The digital implementation of these PLLs often introduces extra delay which affects the performance of BBPLLs. This comes from the retiming and resampling of the digital data in the loop. In this work the phase detector hysteresis is investigated as a source for additional performance degradation. The jitter dependency on the loop parameters in the presence of hysteresis is analyzed, providing a new insight to be considered when designing for minimum jitter. This analysis provides a quick estimation of the deterministic jitter and the location of the spurious tones thus allowing the timing resolution of the PD to be determined. A new model for the BBPLL is also introduced that considers the non-ideality of the PD and its effect on the loop. To evaluate the performance, a time-amplifier is used to improve the resolution of the PD. Jitter and spurious tone of the BBPLL with TA assisted PD are then compared with those of a loop with a regular PD. The results show that the TAPD improves the performance by a factor of 3. The design and simulations have been done in a 32-nm CMOS technology.
CD4-positive T-helper cell responses to the PASD1 protein in patients with diffuse large B-cell lymphoma

Background Vaccine development targeting the novel immunogenic Per ARNT Sim Domain containing 1 (PASD1) cancer testis antigen represents an attractive therapeutic approach for the significant number of patients with diffuse large B-cell lymphoma who are refractory to conventional treatment. Since CD4-positive T helper cells have crucial roles in promoting and maintaining immune responses to tumor antigens, the presence of a CD4-positive T-helper immune response to the PASD1 antigen in patients with diffuse large B-cell lymphoma was investigated in the current study. Design and Methods Thirty-one patients with diffuse large B-cell lymphoma (25 with de novo, five with transformed and one with T-cell-rich B-cell lymphoma) were studied. Five immunogenic PASD1 peptides predicted to bind to several major histocompatibiliy complex, class II DR beta 1 alleles were identified using web-based algorithms. Peripheral blood mononuclear cells from patients were used to investigate the immunogenicity of these DR beta 1-restricted peptides in vitro using both gamma-interferon release enzyme-linked immunospot and cytolytic assays. Results Two of the five PASD1 peptides, PASD1(6) and PASD1(7), were shown to be immunogenic in 14 out of 32 patients studied in a gamma-interferon release assay. CD4-positive T-helper cell lines from two patients raised against PASD1 peptides were able to lyse cell lines derived from hematologic malignancies expressing endogenous PASD1 protein. Conclusions This is the first report of a CD4-positive T-helper response to the PASD1 protein in patients with lymphoma. The immunogenic peptides described here represent valuable additional candidates for inclusion in a vaccine to treat patients with PASD1-positive diffuse large B-cell lymphoma whose disease is refractory to conventional therapies.
Primary care supports for children with chronic health conditions: identifying and predicting unmet family needs.

OBJECTIVE To examine unmet needs among families of children with chronic health conditions treated in primary care settings and to identify predictors of these needs. METHOD Primary care physicians referred 83 caregivers of children with chronic health conditions. Mothers completed the Family Needs Survey, as well as other measures of child and family functioning. RESULTS Mothers reported a high prevalence and broad range of unmet family needs. The most frequent area of need was for information about services and ways to promote child health and development. Predictors of total number of family needs included demographic characteristics, ratings of social support, and appraisals of family burden. Predictors of specific types of family needs varied according to category of need. CONCLUSIONS Innovative psychosocial intervention programs are needed in primary care settings to reduce family needs and promote child health. More intensive family supports may be indicated for those with minority-group or low socioeconomic status, limited social support, or high perceived burden.
Background adaptive linearization of high-speed digital-to-analog Converters

This paper presents a digital background linearization technique for high-speed Nyquist-rate digital-to-analog Converters (DACs), based on the use of a least-mean-square (LMS) multipath adaptive filter that continuously measures and cancels non-linearity arising from static errors. In contrast to previously-published correlation-based techniques, the proposed method is not limited to the cancellation of component mismatches, but it performs the correction of the overall static characteristic regardless of the source of non-linearities. It requires only an additional low-speed accurate DAC and moderate digital hardware complexity, avoiding the need for a multibit analog-to-digital converter. The effectiveness of the proposed technique applied to a current-steering DAC suggests that it could be useful to overcome the typical high-speed DAC trade-off, allowing the elimination of static non-linearity errors without sacrificing dynamic performances.
A Euglena gracilis zinc endonuclease.

A 26-kDa endonuclease has been purified to homogeneity from zinc-sufficient Euglena gracilis. The protein binds to single-stranded DNA with a higher affinity than to double-stranded DNA, but it exhibits nucleolytic activity toward both. Thus, it converts supercoiled plasmid pBR322 DNA into the linear form, a property characteristic of endonucleases, and it continues to act on the linearized DNA until it is completely degraded. It also hydrolyzes heat-denatured, single-stranded calf thymus DNA. Moreover, at amounts below 1 microgram, it enhances RNA synthesis by RNA polymerase II, a characteristic observed with other DNases. Its addition to an in vitro transcription assay increases RNA synthesis up to 3-fold. The nuclease requires two metal components to carry out its enzymatic activities. It hydrolyzes DNA only in the presence of millimolar amounts of magnesium or micromolar quantities of other activating metal ions, such as manganese, zinc, or cobalt. However, even when optimal concentrations of Mg2+ are present, micromolar amounts of the metal-chelating agents OP and HQSA completely inhibit pBR322 digestion. Transcription enhancement is also inhibited completely by both chelators at concentrations that do not affect the intrinsic polymerase II activity. By atomic absorption spectrometry, the enzyme contains 1 g-atom of Zn/mol, which is the likely target of chelator action. The nuclease protein can also be isolated from zinc-deficient E. gracilis, but remarkably it then contains 1 mol of Cu/g-atom and no zinc. (ABSTRACT TRUNCATED AT 250 WORDS)
A parallel quasi-Monte Carlo approach to pricing multidimensional American options

In this paper, we develop parallel algorithms for pricing American options on multiple assets. Our parallel methods are based on the Low Discrepancy (LD) mesh method which combines the quasi-Monte Carlo technique with the stochastic mesh method. We present two approaches to parallelise the backward recursion step, which is the most computational intensive part of the LD mesh method. We perform parallel run time analysis of the proposed methods and prove that both parallel approaches are scalable. The algorithms are implemented using MPI. The parallel efficiency of the methods are demonstrated by pricing several American options, and near optimal speedup results are presented.
A pre–post intervention study of pulmonary rehabilitation for adults with post-tuberculosis lung disease in Uganda

Setting The study was conducted at Mulago Hospital, Kampala, Uganda. Objective As chronic respiratory disease (CRD) is a huge, growing burden in Africa, with few available treatments, we aimed to design and evaluate a culturally appropriate pulmonary rehabilitation (PR) program in Uganda for people with post-tuberculosis lung disorder (p-TBLD). Design In a pre–post intervention study, a 6-week, twice-weekly PR program was designed for people with p-TBLD. Outcome measures included recruitment, retention, the Clinical COPD Questionnaire (CCQ), tests of exercise capacity, and biometrics. Given this was a developmental study, no formal statistical significance testing was undertaken. Results In all, 34 participants started PR and 29 (85%) completed all data collection. The mean age of the 29 participants was 45 years, and 52% were female. The mean (95% confidence interval) CCQ score at baseline was 1.8 (1.5, 2.0), at the end of PR was 1.0 (0.8, 1.2), and at 6 weeks after the end of PR was 0.8 (0.7, 1.0). The Incremental Shuttle Walking Test (ISWT) was 299 m (268.5, 329.4) at baseline, 377 (339.6, 413.8) at the end of PR, and 374 (334.2, 413.5) at 6 weeks after the end of PR. Improvements were seen in measures of chest pain; 13/29 (45%) participants reported chest pain at baseline but only 7/29 (24%) at the end of PR, and in those with persistent pain, the mean pain scores decreased. Mild hemoptysis was reported in 4/29 (17%) participants at baseline and in 2/29 (7%) at the end of PR. Conclusion PR for people with p-TBLD in Uganda was feasible and associated with clinically important improvements in quality of life, exercise capacity, and respiratory outcomes. PR uses local resources, requires little investment, and offers a new, sustainable therapy for p-TBLD in resource-limited settings. With the rising global burden of CRD, further studies are needed to assess the value of PR in p-TBLD and other prevalent forms of CRD.