Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-dimensional right-ventricular regional deformation and survival in pulmonary hypertension

Aims Survival in pulmonary hypertension (PH) relates to right ventricular (RV) function. However, the RV unique anatomy and structure limit 2D analysis and its regional 3D function has not been studied yet. The aim of this study was to assess the implications of global and regional 3D RV deformation on clinical condition and survival in adults with PH and healthy controls. Methods and results We collected a prospective longitudinal cohort of 104 consecutive PH patients and 34 healthy controls between September 2014 and December 2015. Acquired 3D transthoracic RV echocardiographic sequences were analysed by semi-automatic software (TomTec 4D RV-Function 2.0). Output meshes were post-processed to extract regional motion and deformation. Global and regional statistics provided deformation patterns for each subgroup of subjects. RV lateral and inferior regions showed the highest deformation. In PH patients, RV global and regional motion and deformation [both circumferential, longitudinal, and area strain (AS)] were affected in all segments (P < 0.001 against healthy controls). Deformation patterns gradually worsened with the clinical condition. Over 6.7 [5.8-7.2] months follow-up, 16 (15.4%) patients died from cardio-pulmonary causes. Right atrial pressure, global RV AS, tricuspid annular plane systolic excursion, 3D RV ejection fraction, and end-diastolic volume were independent predictors of survival. Global RV AS > -18% was the most powerful RV function parameter, identifying patients with a 48%-increased risk of death (AUC 0.83 [0.74-0.90], P < 0.001). Conclusion Right ventricular strain patterns gradually worsen in PH patients and provide independent prognostic information in this population.
Biomarkers in Acute Myocardial Infarction

Acute coronary syndrome (ACS) is a significant cause of morbidity and mortality worldwide. Patients can be stratified by symptoms, risk factors and electrocardiogram results but cardiac biomarkers also have a prime role both diagnostically and prognostically. The proper diagnosis of ACS requires reliable and accurate biomarker assays to detect evidence of myocardial necrosis. Currently, troponin is the gold standard biomarker for myocardial injury and is used commonly in conjunction with creatine kinase-MB (CK-MB) and myoglobin to enable a more rapid diagnosis of ACS. Other markers of myocardial necrosis, inflammation and neurohormonal activity have also been shown to have either diagnostic or prognostic utility, but none have been shown to be superior to troponin. The measurement of multiple biomarkers and the use of point of care markers may accelerate current diagnostic protocols for the assessment of such patients
The effect of Enterobius vermicularis infection (oxyuriasis) on eosinophil and IgE levels in allergic rhinitis

Objective: Elevated levels of serum IgE and eosinophilia are the indicators of atopy and intestinal parasitic infections. We evaluated the effect of Enterobius vermicularis infection (enterobiasis) on blood eosinophil count and IgE levels in allergic rhinitis. Methods: A total of 110 patients diagnosed with allergic rhinitis (with symptoms of rhinorrhea, itchy nose and nasal congestion) consisting of 41 (37.27%) males and 69 (62.73%) females were examined. Forty-one (37.27%) patients with enterobiasis were selected as the study group. The remaining 69 (62.73%) patients accepted as the control group. Results: In the study group the mean serum total IgE level and mean serum eosinophil count were 393.10 ± 159.83 IU/mL and 0.56 ± 0.04 10 3 /mL, respectively. In the control group the mean serum total IgE level and mean serum eosinophil count were 236.91 ± 63.55 IU/mL and 0.37 ± 0.12 10 3 /mL, respectively. The difference between the two groups was statistically significant for serum total IgE levels ( p 0.05). The correlation coefficients between serum total IgE level and eosinophil count were statistically insignificant ( p > 0.05). Conclusions : More comprehensive and long-term placebo-controlled studies should be performed in order to find the answer to the question of whether helminth infections play a role in allergic disease.
Robust Wide-Beam Analog Beamforming With Inaccurate Channel Angular Information

Hybrid precoding is widely used in millimeter wave massive multiple-input multiple-output system to reduce the hardware complexity. Previous works have shown that hybrid precoding by using angular information can acquire good performance. However, in practice, perfect angular information is hard to be obtained. In this work, a robust analog beamforming method based on chirp sequence is proposed to deal with the inaccurate angle estimations. Our method can adjust the beamwidth arbitrarily, and the optimal beamwidth is derived according to the SNR and angle estimation error variance. Simulation results show that the method can dramatically improve user fairness and cell-edge user rates.
Predictors of mortality in high-risk patients with QT prolongation in a community hospital.

Aims To determine predictors of mortality in patients with corrected QT interval (QTc) ≥ 500 ms in a community hospital. Methods and results In this retrospective observational study, we searched the electrocardiogram (ECG) database at Telemark Hospital Trust, Norway, from January 2004 to December 2014. Medication, electrolyte abnormalities, and medical conditions known to prolong the QT interval were recorded. From the medical records, we assessed whether the prolonged QTc was noted by the health care providers. We identified 1531 patients (age = 70 ± 15 years, 59% female) with an ECG with QTc ≥ 500 ms. All-cause mortality during 952 (range 0-4161) days of follow-up was 50% (n = 765/1531). Main predictors of mortality were aborted cardiac arrest [hazard ratio (HR) 2.40, 95% confidence interval (CI) 1.44-4.01; P = 0.001], cerebral stroke/head trauma (HR 2.28, 95% CI 1.70-3.05; P < 0.001), and heart failure (HR 1.74, 95% CI 1.43-2.12; P< 0.001). Females with prolonged QTc had better survival compared with males (P = 0.006). We constructed a risk-weighted QTc mortality score. QT prolongation was acknowledged in the medical records in 12% of the cases. Conclusions QTc ≥ 500 ms was associated with high all-cause mortality with increased mortality in males compared with females. A new QTc mortality score was constructed to predict mortality. Only a minority of cases with prolonged QTc ≥ 500 ms were acknowledged in the medical records.
The evolution of sex: A new hypothesis based on mitochondrial mutational erosion

The evolution of sex in eukaryotes represents a paradox, given the “twofold” fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favored the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high‐mutation rate across most eukaryote taxa, and several lines of evidence suggest that this high rate is an ancestral character. This seems inexplicable given that mtDNA‐encoded genes underlie the expression of life's most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA‐induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation.
Patterns of interstitial lung disease and mortality in rheumatoid arthritis

Objective. To characterize a cohort of patients with RA who have interstitial lung disease (ILD) and to assess the utility of previously developed mortality staging systems [gender, age, lung physiology (GAP) and ILD-GAP]. Methods. All patients with RA and ILD seen at the Mayo Clinic from 1998 to 2014 were identified and manually screened for study inclusion. RA disease characteristics and pulmonary findings including high-resolution CT and pulmonary function testing were evaluated. Survival was estimated using Kaplan–Meier methods. GAP and ILD-GAP models were evaluated using c-statistics and standardized incidence ratios. Results. The study included 181 patients with RA-associated ILD (96% Caucasian; 48% females; 37% never-smokers). The mean age at ILD diagnosis was 67.4 years (S.D. 9.9). The median time from RA diagnosis to ILD was 4.9 years (range −10.9–48.1). The median follow-up was 3.1 years (range 0.01–14.8). Age, RA disease duration and low initial diffusing capacity for carbon monoxide were predictive of premature mortality in multivariate modelling. Sex, smoking status, obstructive lung disease, seropositivity and erosive disease were not associated with mortality. The 5-year survival rate was 59.7% (95% CI 51.5, 69.2). Survival did not differ between usual interstitial pneumonia, non-specific interstitial pneumonia and organizing pneumonia (P = 0.42). The GAP model performed well in this cohort for both discrimination and calibration (c-statistic 0.71, standardized incidence ratio 0.97). Conclusion. In this large single-centre cohort of patients with RA-ILD, most patients were seropositive and had a history of smoking. ILD most commonly occurred after the RA diagnosis. Mortality was high and did not differ among the types. The GAP model may be useful in assessing mortality risk.
Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters

The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of ‘proximal promoter motifs’ (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.
Accent detection and social cognition: evidence of protracted learning.

How and when do children become aware that speakers have different accents? While adults readily make a variety of subtle social inferences based on speakers' accents, findings from children are more mixed: while one line of research suggests that even infants may be acutely sensitive to accent unfamiliarity, other studies suggest that 5-year-olds have difficulty identifying accents as different from their own. In an attempt to resolve this paradox, the current study assesses American children's sensitivity to American vs. Dutch accents in two situations. First, in an eye-tracked sentence processing paradigm where children have previously shown sensitivity to a salient social distinction (gender) from voice cues, 3-5-year-old children showed no sensitivity to accent differences. Second, in a social decision-making task where accent sensitivity has been found in 5-year-olds, an age gradient appeared, suggesting that familiar accent preferences emerge slowly between 3 and 7 years. Counter to claims that accent is an early, salient signal of social group, results are more consistent with a protracted learning hypothesis that children need extended exposure to native-language sound patterns in order to detect that an accent deviates from their own. A video abstract of this article can be viewed at: https://www.youtube. com/watch? v=BQAgy3IFYXA.
Code extraction algorithms which unify slicing and concept assignment

One approach to reverse engineering is to partially automate subcomponent extraction, improvement and subsequent recombination. Two previously proposed automated techniques for supporting this activity are slicing and concept assignment. However, neither is directly applicable in isolation; slicing criteria (sets of program variables) are simply too low level in many cases, while concept assignment typically fails to produce executable subcomponents. This paper introduces a unification of slicing and concept assignment which exploits their combined advantages, while overcoming their individual weaknesses. Our 'concept slices' are extracted using high level criteria, while producing executable subprograms. The paper introduces three ways of combining slicing, and concept assignment and algorithms for each. The application of the concept slicing algorithms is illustrated with a case study from a large financial organisation.
Prognosis of Masked and White Coat Uncontrolled Hypertension Detected by Ambulatory Blood Pressure Monitoring in Elderly Treated Hypertensive Patients

BACKGROUND Prognosis of masked and white coat uncontrolled hypertension (MUCH and WCUCH, respectively) detected by ambulatory blood pressure (BP) monitoring is incompletely clear in elderly treated hypertensive patients. We evaluated prognosis of MUCH and WCUCH identified by ambulatory BP monitoring in this setting. METHODS The occurrence of a composite endpoint was evaluated in 1,191 elderly treated hypertensive patients. Controlled hypertension (CH) was defined as clinic BP <140/90 mm Hg and 24-hour BP <130/80 mm Hg, MUCH as clinic BP <140/90 mm Hg and 24-hour BP ≥130 and/or ≥80 mm Hg, WCUCH as clinic BP ≥140 and/or ≥90 mm Hg and 24-hour BP <130/80 mm Hg and sustained uncontrolled hypertension (SUCH) as clinic BP ≥140 and/or ≥90 mm Hg and 24-hour BP ≥130 and/or ≥80 mm Hg. RESULTS MUCH was identified in 142 patients (12% of all the population, 34% of those with normal clinic BP) and WCUCH in 230 patients (19% of all the population, 30% of those with high clinic BP). During the follow-up (9.1 ± 4.9 years, range 0.4-20 years), 392 events occurred. After adjustment for various covariates, patients with MUCH (hazard ratio (HR) 1.60, 95% confidence interval (CI) 1.12-2.29, P = 0.01) and SUCH (HR 1.81, 95% CI, 1.35-2.42, P < 0.001) had significantly higher cardiovascular risk than those with CH, whereas those with WCUCH (HR 1.09, 95% CI, 0.74-1.60, P = 0.66) had not significantly higher risk. CONCLUSIONS In elderly treated hypertensive patients evaluated by ambulatory BP monitoring, compared to individuals with CH, those with MUCH have significantly higher risk and those with WCUCH have slightly and not significantly higher risk.
Youth Codesign of a Mobile Phone App to Facilitate Self-Monitoring and Management of Mood Symptoms in Young People With Major Depression, Suicidal Ideation, and Self-Harm

Background Effective treatment of depression in young people is critical, given its prevalence, impacts, and link to suicide. Clinical practice guidelines point to the need for regular monitoring of depression symptom severity and the emergence of suicidal ideation to track treatment progress and guide intervention delivery. Yet, this is seldom integrated in clinical practice. Objective The objective of this study was to address the gap between guidelines about monitoring and real-world practice by codesigning an app with young people that allows for self-monitoring of mood and communication of this monitoring with a clinician. Methods We engaged young people aged 18 to 25 years who had experienced depression, suicidal ideation including those who self-harm, as well as clinicians in a codesign process. We used a human-centered codesign design studio methodology where young people designed the features of the app first individually and then as a group. This resulted in a minimal viable product design, represented through low-fidelity hand-drawn wireframes. Clinicians were engaged throughout the process via focus groups. Results The app incorporated a mood monitoring feature with innovative design aspects that allowed customization, and was named a “well-being tracker” in response to the need for a positive approach to this function. Brief personalized interventions designed to support young people in the intervals between face-to-face appointments were embedded in the app and were immediately available via pop-ups generated by a back-end algorithm within the well-being tracker. Issues regarding the safe incorporation of alerts generated by the app into face-to-face clinical services were raised by clinicians (ie, responding in a timely manner) and will need to be addressed during the full implementation of the app into clinical services. Conclusions The potential to improve outcomes for young people via technology-based enhancement to interventions is enormous. Enhancing communication between young people and their clinicians about symptoms and treatment progress and increasing access to timely and evidence-based interventions are desirable outcomes. To achieve positive outcomes for young people using technology- (app) based interventions, it is critical to understand and incorporate, in a meaningful way, the expectations and motivations of both young people and clinicians.
Beyond Antigenic Match: Possible Agent-Host and Immuno-epidemiological Influences on Influenza Vaccine Effectiveness During the 2015–2016 Season in Canada

Vaccine effectiveness estimates for 2015–2016 seasonal influenza vaccine are reported from Canada. Findings suggest that agent-host and immuno-epidemiologic factors beyond antigenic match—including viral genomic variation, birth (immunological) cohort effects, repeat vaccination, and potential within-season waning immunity—may influence vaccine performance.
Change in End-Expiratory Lung Volume During Sleep in Patients at Risk for Obstructive Sleep Apnea.

STUDY OBJECTIVES As lung volume decreases radial traction on the upper airway is reduced, making it more collapsible. The purpose of this study was to measure change in end-expiratory lung volume (EELV) following sleep onset and to evaluate the relationship between change in EELV and sleep-disordered breathing. METHODS Twenty subjects underwent overnight polysomnography, of whom 14 (70%) had obstructive sleep apnea (OSA). Change in EELV was measured throughout the night using magnetometry. Sleep was staged and respiratory events scored using American Academy of Sleep Medicine criteria. An additional 10 subjects had change in EELV measured simultaneously by magnetometer and spirometer while awake. RESULTS In the subjects studied while awake, change in EELV calculated from magnetometer data correlated very strongly (r = 0.89, P < .001) with that obtained by spirometry. In the 20 subjects who underwent polysomnography, there was a decline in EELV for sleep stages N1, N2, N3, and R (REM sleep); 17.9 ± 121.0 mL (mean ± standard deviation), 228.5 ± 151.8 mL, 198.1 ± 122.1 mL, and 316.7 ± 131.9 mL, respectively. Mean EELV reduction during stage R sleep doubled that noted during non-stage R sleep (316.7 ± 131.9 mL versus 150.9 ± 89.7 mL, respectively) (P < .001). The difference in EELV between non-stage R and stage R sleep inversely correlated with mean oxygen saturation (r = -0.56, P = .06). EELV reduction in individuals with moderate and severe OSA was greater than in those with mild SDB but did not reach statistical significance. CONCLUSIONS Magnetometry provides a precise, unobtrusive, and continuous means to study lung volume changes during sleep. EELV declines from sleep onset, reaching its nadir during stage R sleep. The reduction in EELV in stage R sleep was associated with lower mean oxygen saturation but was not associated with greater sleep-disordered breathing.
HARE: Hardware accelerator for regular expressions

Rapidly processing text data is critical for many technical and business applications. Traditional software-based tools for processing large text corpora use memory bandwidth inefficiently due to software overheads and thus fall far short of peak scan rates possible on modern memory systems. Prior hardware designs generally target I/O rather than memory bandwidth. In this paper, we present HARE, a hardware accelerator for matching regular expressions against large in-memory logs. HARE comprises a stall-free hardware pipeline that scans input data at a fixed rate, examining multiple characters from a single input stream in parallel in a single accelerator clock cycle. We describe a 1GHz 32-character-wide HARE design targeting ASIC implementation that processes data at 32 GB/s - matching modern memory bandwidths. This ASIC design outperforms software solutions by as much as two orders of magnitude. We further demonstrate a scaled-down FPGA proof-of-concept that operates at 100MHz with 4-wide parallelism (400 MB/s). Even at this reduced rate, the prototype outperforms grep by 1.5-20x on commonly used regular expressions.
Combination epigenetic therapy in metastatic colorectal cancer (mCRC) with subcutaneous 5-azacitidine and entinostat: a phase 2 consortium/stand Up 2 cancer study

Purpose Therapy with demethylating agent 5-azacitidine and histone deacetylase inhibitor entinostat shows synergistic re-expression of tumor-suppressor genes and growth inhibition in colorectal (CRC) cell lines and in vivo studies. Experimental Design We conducted a phase II, multi-institutional study of the combination in metastatic CRC patients. Subcutaneous azacitidine was administered at 40 mg/m2 days 1-5 and 8-10 and entinostat was given 7 mg orally on days 3 and 10. An interim analysis indicated toxicity crossed the pre-specified safety boundary but was secondary to disease. A 2nd cohort with added eligibility restrictions was accrued: prior therapies were limited to no more than 2 or 3 (KRAS-mutated and KRAS-wildtype cancers, respectively) and <30% of liver involvement. The primary endpoint was RECIST response. Serial biopsies were performed at baseline and after 2 cycles of therapy. Results Forty-seven patients were enrolled (24:Cohort 1, 23:Cohort 2). Patients were heavily pre-treated (median prior therapies 4: Cohort 1 and 2.5: cohort 2). No responses were observed. Median progression-free survival was 1.9 months; overall survival was 5.6 and 8.3 months in Cohorts 1 and 2, respectively. Toxicity was tolerable and as expected. Unsupervised cluster analysis of serial tumor biopsies suggested greater DNA demethylation in patients with PFS above the median. Conclusion In this first trial of CRC patients with combination epigenetic therapy, we show tolerable therapy without significant clinical activity as determined by RECIST responses. Reversal of hypermethylation was seen in a subset of patients and correlated with improved PFS.